Explore software available on ACCESS Resources.
| Software | Installed on | AI Description | AI Tags | AI Research Discipline | AI Software Type | Documentation, Uses, and more |
|---|---|---|---|---|---|---|
| abaqus | ACES Expanse |
Abaqus is a software suite used for finite element analysis and computer-aided engineering simulations for a wide range of industrial applications. It provides powerful simulation capabilities to analyze the behavior of materials and structures under various conditions. | Simulation, Finite Element Analysis, Computer-Aided Engineering, Materials Analysis | Mechanical Engineering | Simulation Software | Documentation, Uses, and more |
| abseil | ACES | Abseil is an open-source collection of C++ code (compliant to C++11) designed to augment the C++ standard library. It provides a set of high-quality library code that is well tested, portable, and efficient for a wide range of purposes. | C++ Library, Open Source, Cross-Platform | General, Computer & Information Sciences | Code Library | Documentation, Uses, and more |
| absl-py | ACES | absl-py is a Python library developed by Google that provides common utilities for building and running applications, including command-line flag parsing, logging, and application initialization. It helps standardize Python program structure and is widely used in large-scale and machine learning projects. | Python, Libraries, Utilities, Open Source | Software Engineering | Library | Documentation, Uses, and more |
| abyss | ACES | ABySS (Assembly By Short Sequences) is a de novo, parallel, paired-end sequence assembler that is designed for large genomes and also works well on smaller genomes. | Assembly, De Novo Assembly, Sequence Assembler, Large Genomes | Biological Sciences | Hpc Tool | Documentation, Uses, and more |
| accelerate | ACES | Accelerate is a lightweight library that simplifies running PyTorch training and inference across different hardware setups, including CPUs, GPUs, TPUs, and distributed environments. It abstracts away the complexity of distributed and mixed-precision training, allowing the same codebase to scale from local development to large multi-node deployments. | Machine Learning, Numerical Computing, GPU Acceleration | Documentation, Uses, and more | ||
| actc | ACES | ACTC (Assembly, Clustering, and Transformation for Connected Components) is a software tool for finding connected components in large, distributed graphs. It is specifically designed to handle massive graphs efficiently. | Graph Analytics, Connected Components, Distributed Computing | Biology, Mathematics, Computer & Information Sciences | Tool | Documentation, Uses, and more |
| adios2 | ACES Stampede3 |
ADIOS 2 (Adaptable Input/Output System) is a next-generation high-performance I/O middleware library that provides a simple, high-level interface for efficiently managing data on parallel storage systems. It is designed to address the increasing challenges of achieving high performance and scalability when dealing with I/O operations in large-scale scientific simulations and data processing applications. | I/O Middleware, High-Performance Computing, Data Management, Parallel Computing | Computer Science, Computer & Information Sciences | Library | Documentation, Uses, and more |
| advisor | KyRIC Stampede3 |
Advisor is a comprehensive software tool designed for optimizing HPC applications and maximizing performance on current and future HPC systems. It offers insights into performance bottlenecks, parallel patterns, and potential improvements. | Hpc, Performance Optimization, Parallel Computing | Engineering & Technology | Performance Optimization | Documentation, Uses, and more |
| ai-tools-gpu | ACES | A collection of software tools at all levels of the AI stack unlock the full capabilities of Intel hardware. All Intel AI tools and frameworks are built on the foundation of a standards-based, unified oneAPI programming model that helps get the most performance from end-to-end pipelines on all available hardware.\r Description Source: https://www.intel.com/content/www/us/en/developer/topic-technology/artificial-intelligence/frameworks-tools.html |
Intel, AI | Documentation, Uses, and more | ||
| aiohttp | ACES | aiohttp is an asynchronous HTTP client/server framework for Python. It allows for handling HTTP requests and responses in an asynchronous manner, making it ideal for building high-performance web applications. | Python Library, Web Development, Asynchronous Programming | Software Engineering, Computer & Information Sciences | Http Client/Server Framework | Documentation, Uses, and more |
| aishell | ACES | AI Shell is an interactive shell that provides a chat interface with language models. The shell provides agents that connect to different AI models and other assistance providers. Users can interact with the agents in a conversational manner.\r Description Source: https://learn.microsoft.com/en-us/powershell/utility-modules/aishell/overview |
AI, Command Line Interface | Documentation, Uses, and more | ||
| alphafast | ACES | Documentation, Uses, and more | ||||
| alphafold | ACES | AlphaFold is a deep learning-based system developed by DeepMind to predict protein folding and 3D structure with high accuracy. | Protein Folding, Structure Prediction, Deep Learning, Neural Networks | Biochemistry and Molecular Biology | Web Application | Documentation, Uses, and more |
| alphafold 3 | DeltaAI Delta |
Documentation, Uses, and more | ||||
| alphafold3 | ACES | AlphaFold 3 is DeepMind’s next-generation AI system for predicting the structure and interactions of biological molecules, extending beyond proteins to model complexes involving DNA, RNA, ligands, ions, and other biomolecules. It enables high-accuracy structural predictions that support drug discovery, molecular biology, and biomedical research. | Protein-Structure, Deep-Learning, Bioinformatics | Bioinformatics, Biochemistry and Molecular Biology | Predictive Modeling | Documentation, Uses, and more |
| alphapickle | ACES | Alphapickle is a Python library that provides tools and utilities for working with alpha factors and optimizing portfolio construction in quantitative finance. | Python Library, Quantitative Finance, Alpha Factors, Portfolio Optimization | Financial Engineering, Other Mathematics | Data Analysis | Documentation, Uses, and more |
| alphapulldown | ACES | AlphaPulldown is a computational tool built around AlphaFold that enables systematic prediction of protein–protein interactions and complex structures at scale. It automates the generation, execution, and analysis of AlphaFold runs to efficiently screen many protein combinations. | Computational Biology, Bioinformatics | Bioinformatics | Documentation, Uses, and more | |
| alps | Stampede3 | Documentation, Uses, and more | ||||
| alsa-lib | ACES DeltaAI |
Advanced Linux Sound Architecture (ALSA) provides audio and MIDI functionality to the Linux operating system. alsa-lib is a library that provides an interface for programmers to access sound card capabilities. | Linux, Audio, Library | Software Engineering, Computer & Information Sciences | Audio Library | Documentation, Uses, and more |
| amask | Stampede3 | Amask is a high-level molecular visualization program that is designed to create and manipulate atomic structures for research and educational purposes. It provides a user-friendly interface for visualizing complex molecular structures and interactions. | Molecular Visualization, Atomic Structures, Molecular Modeling, Research Tool | Biological Sciences | Molecular Visualization Software | Documentation, Uses, and more |
| amber | Anvil ACES |
Amber is a suite of highly extensible molecular simulation programs. It is designed for simulations of biomolecules such as proteins, nucleic acids, and carbohydrates, and can also be used for small molecules. | Molecular Dynamics, Biomolecular Simulations, Quantum Chemistry | Biochemistry & Molecular Biology, Biological Sciences | Molecular Dynamics | Documentation, Uses, and more |
| ambertools | Anvil ACES |
AmberTools is a suite of software for molecular dynamics simulations, energy minimization, and trajectory analysis in the field of computational chemistry. It provides tools for the refinement and analysis of biomolecular structures. | Molecular Dynamics, Computational Chemistry, Biomolecular Structure, Energy Minimization | Biophysics, Biological Sciences | Simulation Software | Documentation, Uses, and more |
| amd uprof | Anvil | AMD uProf is a performance analysis tool that provides insights into CPU and memory usage for applications running on AMD processors. It helps developers optimize their code for better performance. | performance analysis, profiling, AMD, CPU, memory | Software Engineering, Computer Science | Profiling Tool | Documentation, Uses, and more |
| amdblis | Anvil | Amdblis is a computational software for analyzing and visualizing single-molecule data, particularly for biophysical studies. | Computational Software, Data Analysis, Visualization | Biophysics, Biological Sciences | Computational Tool | Documentation, Uses, and more |
| amdfftw | Anvil | An AMD optimized version of FFTW. FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) in one or more dimensions, of arbitrary input size, and of both real and complex data (as well as of even/odd data, i.e. the discrete cosine/sine transforms or DCT/DST). We believe that FFTW, which is free software, should become the FFT library of choice for most applications. Description Source: https://www.fftw.org/ |
Mathematics | Library | Documentation, Uses, and more | |
| amdlibflame | Anvil | AMD LIBFLAME is an open-source software library that provides a high-performance implementation of the dense linear algebra routines on CPUs. It aims to offer efficient and robust algebraic computations for numerical linear algebra applications. | Linear Algebra, Numerical Computations, Performance Optimization | Mathematics, Computer & Information Sciences | Library | Documentation, Uses, and more |
| amdlibm | Anvil | AMDlibm is a software library provided by AMD that offers mathematical functions specifically optimized for high performance on AMD processors. It provides a collection of mathematical functions designed to exploit the advanced features of AMD processors for enhanced numerical computation. | Mathematics, Numerical Computation, Math Library | Mathematics, Engineering & Technology | Math Library | Documentation, Uses, and more |
| amdscalapack | Anvil | ScaLAPACK is a library of high-performance linear algebra routines for parallel distributed memory machines. It depends on external libraries including BLAS and LAPACK for Linear Algebra computations. | Mathematics | Library | Documentation, Uses, and more | |
| amduprof | Expanse | amduprof is a tool developed for profiling OpenCL applications on AMD GPUs. It provides insights into the performance of OpenCL kernels by analyzing memory access patterns, kernel occupancy, and compute unit utilization. | Gpu Profiling, Opencl Profiler, Performance Analysis | Computer Science, Computer & Information Sciences | Tool | Documentation, Uses, and more |
| anaconda | Anvil Jetstream2 |
Anaconda is a free and open-source distribution of Python and R programming languages for scientific computing, that aims to simplify package management and deployment. | Data Science, Scientific Computing, Package Management, Python, R | Computer and Information Sciences | Package Management | Documentation, Uses, and more |
| anaconda3 | ACES Expanse |
Anaconda is a free and open-source distribution of Python programming language for scientific computing that aims to simplify package management and deployment. It includes over 250 popular data science packages and their dependencies, making it a one-stop solution for Python programming in data science, machine learning, deep learning, and other related fields. | Python, Data Science, Machine Learning, Deep Learning, Package Management | Data Science, Computer & Information Sciences | Development Tools | Documentation, Uses, and more |
| anadama2 | ACES | Anadama2 is a workflow management system designed for reproducible scientific computing. It allows users to define, execute, and manage complex workflows in a flexible and user-friendly manner. | Workflow Management, Reproducibility, Data Processing | Bioinformatics, Computational Biology | Workflow Management System | Documentation, Uses, and more |
| anicalculator | ACES | ANIcalculator is a bioinformatics tool that computes Average Nucleotide Identity (ANI) and alignment fraction between two genomes, commonly used for microbial genome comparison and species delineation. | Sequence Alignment, Sequence Alignment | Natural Sciences, Biological Sciences | Documentation, Uses, and more | |
| annovar | ACES | ANNOVAR is a powerful software tool designed to annotate genetic variants detected from diverse genomes. | Genomics, Genetic Variation, Bioinformatics, Annotation | Biology, Biological Sciences | Bioinformatics Tool | Documentation, Uses, and more |
| ansys | Stampede3 | Ansys provides engineering simulation software used to predict how product designs will behave and how manufacturing processes will operate in real-world environments. The software enables engineers to simulate interactions of all disciplines like structural, fluids, heat transfer, electromagnetic, and systems engineering. | Engineering, Simulation, Product Design | Mechanical Engineering | Engineering Simulation Software | Documentation, Uses, and more |
| ant | ACES | Ant is a build automation tool that is mainly used for Java projects. It automates the process of compiling and building Java applications, along with tasks such as testing and deployment. | Automation, Java, Build Tool, Deployment | Computer Science | Tool | Documentation, Uses, and more |
| antlr | ACES | ANTLR (ANother Tool for Language Recognition) is a powerful parser generator for reading, processing, executing, or translating structured text or binary files. | Compiler, Parser Generator, Syntax Analysis, Code Generation | Software Engineering, Other Computer and Information Sciences | Toolkit | Documentation, Uses, and more |
| aocc | Anvil ACES Expanse Delta Jetstream2 |
The AMD Optimizing C/C++ Compiler (AOCC) is a high performance compiler suite with support for C, C++, and Fortran programming languages. | Compiler, C, C++, Fortran, Optimization | Software Engineering, Computer & Information Sciences | Service | Documentation, Uses, and more |
| aocc-mixed | Delta | Documentation, Uses, and more | ||||
| aocl-blas | ACES | AOCL BLAS is a high-performance implementation of the Basic Linear Algebra Subprograms (BLAS) for AMD architectures, optimized for performance on AMD processors. | BLAS, Linear Algebra, High Performance Computing, AMD | Numerical Analysis, Applied Mathematics | Library | Documentation, Uses, and more |
| apbs | ACES | APBS (Adaptive Poisson-Boltzmann Solver) is a software package for solving the Poisson-Boltzmann equation, which is essential for understanding electrostatic interactions in biomolecules. | Electrostatics, Biomolecular Modeling, Computational Chemistry | Bioinformatics, Biochemistry and Molecular Biology | Open Source | Documentation, Uses, and more |
| apptainer | Stampede3 Jetstream2 |
Apptainer is a tool for creating and managing containerized applications in a simplified and efficient manner. It provides a user-friendly interface for developers and system administrators to package, distribute, and deploy applications using containerization technology. | Containerization, Application Management, Devops, Software Development | Computer Science, Engineering & Technology | Development | Documentation, Uses, and more |
| apr | ACES | The Apache Portable Runtime (APR) is a software library that provides a predictable and consistent interface to underlying platform-specific implementations. | Software Library, Cross-Platform Development, Operating System Abstraction | Engineering & Technology | Development | Documentation, Uses, and more |
| apr-util | ACES | Apache Portable Runtime Utility Library (APR-util) provides a set of utility functions to support the Apache Portable Runtime core functionalities. It is a companion library to APR, extending the basic functionality of APR with additional features. | Utility Library, Apache Portable Runtime, Support Library, Additional Features | Software Engineering | Library | Documentation, Uses, and more |
| archspec | ACES | Archspec is a framework for detecting the architecture of a system and producing a structured representation of its features for further analysis and optimization. It aims to provide insights into the architectural characteristics of a computing system, helping developers understand and leverage these features for performance optimization and code generation. | Architecture Detection, System Analysis, Performance Optimization, Code Generation | Computer Science, Computer & Information Sciences | Framework | Documentation, Uses, and more |
| argobots | ACES | Argobots is a lightweight and high-performance user-level threading and tasking library designed for high-performance computing applications. It provides a flexible and efficient way to manage concurrency and parallelism in applications. | HPC, Concurrency, Parallel Computing, Task Management | Computer Science | Library | Documentation, Uses, and more |
| aria2 | ACES Expanse |
aria2 is a lightweight multi-protocol & multi-source command-line download utility. It supports HTTP/HTTPS, FTP, SFTP, BitTorrent and Metalink. | Download Manager, Command-Line Tool, Multi-Protocol, Multi-Source, File Transfer | Computer Science, Computer & Information Sciences, Other Computer & Information Sciences | Download Manager | Documentation, Uses, and more |
| arm-forge | Expanse | Arm Forge integrates Arm DDT for parallel debugging, Arm MAP for performance profiling, and Arm Performance Reports for summarizing application performance, supporting various parallel architectures like MPI, CUDA, and OpenMP. | HPC, Performance Analysis, Debugging, Profiling | Computer Science | Toolkit | Documentation, Uses, and more |
| arm-gnu-toolchain | ACES | The ARM GNU Toolchain is a collection of tools/libraries used to create applications for embedded ARM processors. It includes the GNU Compiler Collection (GCC) for compiling C/C++ code, GNU Binutils for creating/executing binary files, and GDB for debugging. | Compiler, Embedded Systems, Arm Processor, Toolchain | Software Engineering, Engineering & Technology | Compiler | Documentation, Uses, and more |
| arm-gnu-toolchaint | ACES | Documentation, Uses, and more | ||||
| armadillo | ACES | Armadillo is a high-quality linear algebra library for the C++ programming language. It aims to provide efficient and easy-to-use classes for common linear algebra operations, with a particular focus on real and complex matrices and vectors. | Linear Algebra, C++ Library | Computer Science, Computer & Information Sciences | Linear Algebra Library | Documentation, Uses, and more |
| arpack | Stampede3 | ARPACK is a collection of Fortran77 subroutines designed to solve large scale eigenvalue problems. It is capable of solving complex, real, symmetric, and nonsymmetric eigenvalue problems across different fields of scientific computing. | Computational Software, Linear Algebra, Eigenvalue Problems | Applied Mathematics, Mathematics | Library | Documentation, Uses, and more |
| arpack-ng | Anvil ACES |
ARPACK (ARnoldi PACKage) is a collection of Fortran77 subroutines designed to solve large scale eigenvalue problems. The ARPACK-ng project is a re-implementation of the original ARPACK with the goal of improving its usability, maintainability, and performance across a wide range of modern hardware platforms. | Linear-Algebra, Eigenvalue Problems, Sparse Matrices, Iterative Methods, Computational Physics, Computational Chemistry, Fortran | Mathematics, Physical Sciences | Library | Documentation, Uses, and more |
| arrow | ACES | Arrow is a cross-language development platform for in-memory data that specifies a standardized language-independent columnar memory format for flat and hierarchical data, organized for efficient analytic operations on modern hardware like CPUs and GPUs. | Data Processing, Data Analytics, In-Memory Data, Standardized Format | Memory Efficiency, Computer & Information Sciences | Development Platform | Documentation, Uses, and more |
| arrow-r | ACES | Arrow-R is an open-source statistical computing and graphics software program based on the R programming language. It provides advanced statistical analysis, data visualization, and modeling capabilities for researchers and statisticians. | Statistical Computing, Data Visualization, Statistical Modeling, R Programming | Statistics & Probability, Mathematics | Statistical Software | Documentation, Uses, and more |
| ase | ACES | Atomistic Simulation Environment (ASE) is a set of tools and Python modules for setting up, manipulating, running, visualizing, and analyzing atomistic simulations. | Computational Software, Python Library, Molecular Simulations | Chemistry, Other Natural Sciences | Tool | Documentation, Uses, and more |
| assimp | ACES | Open Asset Import Library (short name: Assimp) is a portable Open Source library to import various well-known 3D model formats in a uniform manner. The most recent version also knows how to export 3D files and is therefore called Assimp. The library provides a C++ interface. There are also bindings for various other languages available. Assimp aims to provide a full asset conversion pipeline for use in game engines or real-time rendering systems | 3D Models, Asset Import, Game Development | File Loading, Computer & Information Sciences | 3D Modeling/Rendering | Documentation, Uses, and more |
| astropy | ACES | Astropy is a community-driven Python library for astronomy and astrophysics. It aims to provide core functionality and common tools needed for astronomical research. Astropy includes modules for celestial coordinate systems, spectral manipulations, units and constants, time and dates, FITS file handling, and cosmological calculations. | Python Library, Astronomy, Astrophysics, Astronomical Research, Data Analysis | Astronomy & Planetary Sciences, Physical Sciences | Computational Software | Documentation, Uses, and more |
| at-spi2-atk | ACES | at-spi2-atk is the Assistive Technology Service Provider Interface (AT-SPI) for the ATK toolkit, which allows assistive technologies to interact with graphical user interfaces. | Assistive Technology, Accessibility, User Interface | General, Computer & Information Sciences | Interface | Documentation, Uses, and more |
| at-spi2-core | ACES | AT-SPI (Assistive Technology Service Provider Interface) is a protocol that allows assistive technologies to interact with and control applications. | Accessibility, Assistive Technology, Gui Applications | General, Computer Science | Library | Documentation, Uses, and more |
| atk | ACES | The Amsterdam Modeling Suite (AMS) offers a comprehensive set of programs for computational chemistry. One of the key components is the Atomistix ToolKit (ATK) for quantum mechanical and classical atomistic simulations of materials. | Computational Chemistry, Materials Science, Quantum Mechanics, Molecular Dynamics | Physical Sciences | Simulation Software | Documentation, Uses, and more |
| atp | DeltaAI Delta |
Abnormal Termination Processing (ATP) is a tool that monitors Cray system user applications. If an application encounters a fatal signal, ATP will handle the signal and perform analysis on the dying application. \r Description Source: https://cpe.ext.hpe.com/docs/debugging-tools/atp.1.html |
Analytical Tool | Documentation, Uses, and more | ||
| attr | ACES | Documentation, Uses, and more | ||||
| attrdict3 | ACES | attrdict3 is a Python library that provides a dictionary-like object that allows accessing keys like attributes, providing a more convenient way to work with nested dictionaries. | Python Library, Dictionary Wrapper | Computer Science, Computer & Information Sciences | Library | Documentation, Uses, and more |
| augustus | ACES | Augustus is a gene prediction software for eukaryotes that uses a probabilistic model to predict genes on genomic sequences. It is widely used in bioinformatics to identify coding regions in DNA sequences. | Gene Prediction, Eukaryotes, Bioinformatics | Bioinformatics, Biological Sciences | Bioinformatics Tool | Documentation, Uses, and more |
| autoconf | ACES DeltaAI KyRIC Stampede3 |
Autoconf is a tool for producing configure scripts for building, installing, and packaging software on Unix-like systems. It assists in the process of automating the configuration of software packages and generating portable makefiles. | Build Automation, Software Configuration, Makefiles | General, Engineering & Technology | Build Tools | Documentation, Uses, and more |
| autoconf-archive | KyRIC | A collection of reusable Autoconf macros that extend the capabilities of Autoconf, making it easier to configure software packages. | autoconf, macros, configuration, software development | General, Software Engineering | Service | Documentation, Uses, and more |
| autodock | Anvil | AutoDock is a suite of automated docking tools designed to predict how small molecules, such as substrates or drug candidates, bind to a receptor of known 3D structure. | Computational Chemistry, Molecular Docking, Virtual Screening | Biology, Biological Sciences | Bioinformatics Tool | Documentation, Uses, and more |
| autodock-gpu | ACES | AutoDock-GPU is a molecular modeling tool that allows for molecular docking simulations to predict the binding modes of small molecules with biomacromolecules. It utilizes GPU acceleration to significantly speed up the docking process. | Molecular Modeling, Molecular Docking, Biomolecular Interactions, Gpu Acceleration | Bioinformatics, Biological Sciences | Simulation Software | Documentation, Uses, and more |
| autodock-vina | ACES | AutoDock Vina is an open-source program for performing molecular docking, which predicts the preferred orientation of one molecule to a second when bound to each other to form a stable complex. | Molecular Docking, Bioinformatics, Computational Chemistry, Drug Discovery | Biology, Molecular Docking | Application | Documentation, Uses, and more |
| automake | ACES DeltaAI KyRIC Stampede3 |
Automake is a build automation tool that automatically generates makefiles for software compilation. | Build Automation, Software Development, Compilers | General, Engineering & Technology | Compiler | Documentation, Uses, and more |
| autotools | ACES Stampede3 |
Autotools is a suite of programming tools designed to assist in making source code packages portable across different Unix-like systems. It includes autoconf, automake, libtool, and others and is commonly used in open-source software projects. | Programming, Software Development, Build Automation | Software Engineering, Systems & Development, Computer & Information Sciences | Build Automation | Documentation, Uses, and more |
| avogadro2 | ACES | Avogadro 2 is an advanced molecular editor and visualization tool designed for computational chemistry and molecular modeling. | Molecular Modeling, Visualization, Computational Chemistry | Molecular Modeling, Molecular Visualization | Desktop Application | Documentation, Uses, and more |
| aws-cli | DeltaAI | The AWS Command Line Interface (CLI) is a unified tool to manage AWS services from the command line. With just one tool to download and configure, you can control multiple AWS services from the command line and automate them through scripts. | Aws, Command Line Interface, Cloud Management | General, Computer & Information Sciences, Engineering & Technology | Command Line Tool | Documentation, Uses, and more |
| aws-cli tool | Anvil | The AWS Command Line Interface (CLI) is a unified tool to manage your AWS services. With just one tool to download and configure, you can control multiple AWS services from the command line and automate them through scripts. | AWS, CLI, Cloud Computing, Automation, Scripting | Information Technology, Computer Science | Command Line Interface | Documentation, Uses, and more |
| aws-ofi-nccl | Delta | Documentation, Uses, and more | ||||
| awscli | ACES | The AWS Command Line Interface (CLI) is a unified tool that provides a consistent interface for interacting with various Amazon Web Services (AWS) through the command line. It allows users to manage AWS services and resources directly from the terminal. | Cloud Computing, Command Line Interface, Aws Services | General, Computer & Information Sciences | Development Tool | Documentation, Uses, and more |
| bamtools | Anvil ACES Delta |
BamTools is a software toolkit for manipulating BAM (Binary Alignment Map) files. It provides both a C++ API for BAM file input and output, and a command-line tool for performing various operations on BAM files. | Bioinformatics, Bam Files, Sequence Alignment, Toolkit | Biology, Biological Sciences | Toolkit | Documentation, Uses, and more |
| bar | Stampede3 | Documentation, Uses, and more | ||||
| bazel | ACES | Bazel is a build tool that helps to build and test software of any size, quickly and reliably. | Build Tool, Software Testing, Dependency Management, Resource Management | General, Engineering & Technology | Build & Testing Tools | Documentation, Uses, and more |
| bazelisk | ACES | Bazelisk is a wrapper for Bazel that automatically downloads and installs the correct version of Bazel for your project. | Build System, Automation, Development Tools | Computer Science, Software Engineering | Build Tool | Documentation, Uses, and more |
| bbmap | ACES | BBMap is a fast and accurate short-read aligner for mapping DNA sequences to a reference genome. It also includes various bioinformatics tools for sequence alignment, mapping, assembly, and analysis. | Bioinformatics, DNA Sequencing, Sequence Alignment | Genomics, Biological Sciences | Bioinformatics Tool | Documentation, Uses, and more |
| bcftools | ACES | bcftools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart (BCF). It provides functionality for filtering, viewing, converting, and annotating variant data. | Variant Calling, Genomics, Bioinformatics | Genomics, Biological Sciences | Bioinformatics Tool | Documentation, Uses, and more |
| bcrypt | ACES | bcrypt is a password hashing function designed by Niels Provos and David Mazières, based on the Blowfish cipher. It is intended to be computationally intensive to resist brute-force attacks. | Security, Cryptography, Password Management | Software Engineering, Cryptography | Library | Documentation, Uses, and more |
| bdftopcf | DeltaAI | Documentation, Uses, and more | ||||
| beagle | Anvil Delta |
Beagle is a high-performance software library for phylogenetic inference using maximum likelihood methods. It can be used for reconstructing large phylogenetic trees from molecular sequence data with high efficiency and accuracy. | Phylogenetic Inference, Maximum Likelihood, Molecular Sequence Data, Parallel Processing, Likelihood Calculations | Genetics, Biological Sciences | Library | Documentation, Uses, and more |
| beagle-lib | DeltaAI | Beagle-lib is a high-performance library for evaluating the likelihood of sequence evolution on phylogenetic trees. It is designed to implement the BEAGLE (Broad-platform Evolutionary Analysis General Likelihood Evaluator) application programming interface (API) for helping in tasks related to phylogenetic inference in computational biology. | Computational Biology, Phylogenetic Inference, Likelihood Evaluation, Evolutionary Analysis, Bioinformatics | Biology | Library | Documentation, Uses, and more |
| beast2 | Anvil | BEAST2 is a cross-platform program for Bayesian evolutionary analysis of molecular sequences. It is widely used for estimating species trees, gene trees, divergence times, substitution rates, and demographic parameters using various models of sequence evolution. | Phylogenetics, Evolutionary Analysis, Molecular Sequences, Bayesian Inference | Ecology, Biological Sciences | Tool | Documentation, Uses, and more |
| beastx | DeltaAI | Documentation, Uses, and more | ||||
| beautifulsoup | ACES | Beautiful Soup is a Python library for parsing HTML and XML documents. It creates parse trees from page source codes that can be used to extract data easily. | Web Scraping, HTML Parsing, Data Extraction, Python | General, Informatics | Library | Documentation, Uses, and more |
| bedops | ACES | BEDOPS is a suite of tools for flexible and highly efficient genomic data analysis. It provides a wide range of operations for working with genomic data, such as set operations, comparisons, and statistical calculations. | Genomic Data Analysis, Bioinformatics, Computational Biology, Genomics, Data Analysis | Bioinformatics, Biological Sciences | Command-Line Tool | Documentation, Uses, and more |
| bedtools | ACES | Bedtools is a software suite for the comparison, manipulation, and annotation of genomic features in multiple formats. | Bioinformatics, Genomics, Data Analysis, Tool | Biology, Biological Sciences | Application | Documentation, Uses, and more |
| bedtools2 | Delta | Bedtools2 is a powerful suite of tools for manipulating genomic features and annotations. It allows users to perform a wide range of tasks on genomic intervals, such as intersecting, merging, comparing, and analyzing BED, GFF, VCF, and other common genomic file formats. | Genomic Data Analysis, Bed Files, Bioinformatics | Biology, Biological Sciences | Tool | Documentation, Uses, and more |
| benchmark | ACES | Documentation, Uses, and more | ||||
| berkeley-db | Anvil DeltaAI KyRIC |
Berkeley DB is a high-performance database library that provides developers with a variety of data management capabilities, including support for key/value pairs, transactions, and concurrency control. | Database, Embedded Systems, High Performance, Data Management | Storage, Hpc Applications, Computer Science | Library | Documentation, Uses, and more |
| bindcraft | ACES | Documentation, Uses, and more | ||||
| binutils | ACES | Binutils is a collection of binary tools, including linker (ld), assembler (as), archiver (ar), and other tools to manipulate object files and executables. | Binary Tools, Linker, Assembler, Object Files | General, Computer & Information Sciences | System Software | Documentation, Uses, and more |
| bio-searchio-hmmer | ACES | Documentation, Uses, and more | ||||
| biocontainers | Anvil Stampede3 |
BioContainers is a project that provides bioinformatics tools and workflows in a containerized format, making it easier to package, distribute, and run bioinformatics software in a reproducible manner. | Bioinformatics, Containers, Reproducibility, Software Packaging, Workflow Management | Biology, Biological Sciences | Containerization | Documentation, Uses, and more |
| biom-format | ACES | BIOM (Biological Observation Matrix) format is a unified format to store biological sequence data, sample data, and observed taxonomic units. It provides a standard mechanism to represent, store, and share data generated by different high-throughput technologies such as marker gene surveys. | Biological Data, High-Throughput Technologies, Data Sharing | Bioinformatics, Biological Sciences | Data Management Tool | Documentation, Uses, and more |
| bioperl | ACES | BioPerl is a collection of Perl modules that provide an easy-to-use and comprehensive toolkit for bioinformatics tasks. It is specifically designed to assist biologists in writing code to analyze biological data and perform various bioinformatics tasks. | Bioinformatics, Computational Biology, Sequence Analysis, Perl | Genetics, Biological Sciences | Library | Documentation, Uses, and more |
| biopython | ACES | Biopython is a set of freely available tools for biological computation written in Python. It provides functionalities for molecular biology, bioinformatics, structural bioinformatics, and computational biology. | Biological Computation, Bioinformatics, Computational Biology, Molecular Biology, Structural Bioinformatics | Bioinformatics, Biological Sciences | Python Library | Documentation, Uses, and more |
| bismark | Anvil | Bismark is a software tool specifically designed for aligning bisulfite treated DNA sequencing reads and methylation calls. It is widely used in epigenetics research to analyze DNA methylation patterns. | Epigenetics, DNA Methylation, Bisulfite Sequencing, Genomics, Bioinformatics | Genomics, Biological Sciences | Alignment & Methylation Analysis | Documentation, Uses, and more |
| bison | ACES DeltaAI Stampede3 |
Bison is a general-purpose parser generator that converts a grammar description for an LALR context-free grammar into a C program to parse that grammar. It is part of the GNU Project. | Parser Generator, Programming Language Tool | General, Computer & Information Sciences | Parser Generator | Documentation, Uses, and more |
| bitsandbytes | ACES | BitsAndBytes is a library designed to optimize the memory usage and performance of deep learning models by providing efficient data types and quantization techniques. | Deep Learning, Quantization, Memory Optimization, PyTorch | Computer Science, Artificial Intelligence and Intelligent Systems | Library | Documentation, Uses, and more |
| blas | Expanse | BLAS (Basic Linear Algebra Subprograms) is a standard API for basic vector and matrix operations. It provides routines for performing basic vector operations, matrix-vector operations, and matrix-matrix operations. | linear algebra, performance, mathematics, computational science | Numerical Analysis, Applied Mathematics | Library | Documentation, Uses, and more |
| blast+ | ACES | BLAST+ (Basic Local Alignment Search Tool) is a suite of tools for performing similarity searches of nucleotide and protein databases. It is widely used for comparing biological sequences to identify homologous sequences and infer functional and evolutionary relationships. | Bioinformatics, Computational Biology, Genomics, Sequence Analysis | Bioinformatics, Biological Sciences | Bioinformatics Tool | Documentation, Uses, and more |
| blast-plus | Anvil | BLAST+ is a suite of programs designed to allow researchers to compare nucleotide or protein sequences to sequence databases and identify similarities. | Bioinformatics, Sequence Analysis, Genomics, Molecular Biology | Biology, Genomics | Tool | Documentation, Uses, and more |
| blat | ACES | BLAT (BLAST-Like Alignment Tool) is a sequence analysis software used for comparing genomic DNA sequences to the human genome. It is particularly useful for finding regions of similarity between DNA sequences at the nucleotide level. | Sequence Analysis, DNA Alignment, Genomic Analysis | Biology, Biological Sciences | Tool | Documentation, Uses, and more |
| blender | ACES | Blender is a free and open-source 3D creation suite that supports the entire 3D pipeline – modeling, rigging, animation, simulation, rendering, compositing and motion tracking, even video editing and game creation. | 3D Modeling, Computer Graphics, Animation, Simulation, Open-Source | General, Engineering & Technology | Visual Arts Software | Documentation, Uses, and more |
| blis | Anvil ACES Stampede3 |
BLAS (Basic Linear Algebra Subprograms) implemented in native C and suitable for high-performance implementations. BLIS is capable of achieving high levels of performance on various architectures. | Blas, Linear Algebra, High Performance Computing, Optimization | Mathematics, Computer & Information Sciences | Computational Software | Documentation, Uses, and more |
| block | ACES | Documentation, Uses, and more | ||||
| blosc | ACES | Blosc is a high-performance compressor optimized for binary data, designed to speed up the storage and transmission of large datasets. | compression, high-performance, binary data, multi-threading | Computer Science, Applied Computer Science | Library | Documentation, Uses, and more |
| blosc2 | ACES | Blosc2 is a high-performance, production-ready meta-compressor library that provides a simple way to accelerate data storage and retrieval. It focuses on optimizing the handling of large, multi-dimensional data, catering to both compression and decompression operations efficiently. | High-Performance Computing, Compression, Data Storage, Optimization | General, Computer & Information Sciences | Compression | Documentation, Uses, and more |
| bokeh | ACES | Bokeh is an interactive visualization library for modern web browsers. It provides elegant, concise construction of versatile graphics with high-performance interactivity over large or streaming datasets in a browser window. | Visualization, Interactive Plots, Data Visualization | General, Computer & Information Sciences | Library | Documentation, Uses, and more |
| boltz-1 | ACES | Documentation, Uses, and more | ||||
| bonnie++ | Expanse | Bonnie++ is a benchmarking tool that measures the performance of file systems and storage devices. It provides a comprehensive suite of tests to assess the read and write performance of a system's disk and file system. | Benchmarking, File System, Performance Testing | Systems and Development, Computer Science | Benchmarking Tool | Documentation, Uses, and more |
| boost | Anvil ACES Expanse Delta KyRIC Stampede3 |
Boost is a set of C++ libraries that provides support for tasks and structures such as linear algebra, pseudorandom number generation, multithreading, image processing, regular expressions, and unit testing. It aims to extend the functionality of C++ programming language and make it more efficient and powerful. | C++ Libraries, Programming Support, Efficiency Enhancement | Computer Science, Software Engineering, Systems & Development, Computer & Information Sciences | Development Tool | Documentation, Uses, and more |
| boost.mpi | ACES | Boost.MPI is a peer-reviewed, free, open-source, portable, and fully-standard library implementation of the Message Passing Interface (MPI) for C++. | Mpi, Parallel Computing, C++ | Other Computer & Information Sciences, Computer & Information Sciences | Middleware | Documentation, Uses, and more |
| boost.python | ACES | Boost.Python is a library used for interfacing Python and C++. It enables seamless integration of C++ code with Python and provides tools to expose C++ classes, functions, and objects to Python scripts, and vice versa. | C++, Python, Integration, Library | Mathematics, Computer & Information Sciences | Library | Documentation, Uses, and more |
| boto3 | ACES | Boto3 is the Amazon Web Services (AWS) SDK for Python, which allows developers to create, configure, and manage AWS services using Python code. | AWS, SDK, Python, Cloud Computing, API | Computer Science | Library | Documentation, Uses, and more |
| bowtie | ACES Delta |
Bowtie is a fast and memory-efficient short read aligner for short DNA sequences. It aligns short DNA sequences (reads) to the human genome at a rate of over 25 million reads per hour on a typical workstation with a large amount of memory. | Bioinformatics, Genomics, DNA Sequencing, Sequence Alignment | Genetics, Biological Sciences | Alignment Tool | Documentation, Uses, and more |
| bowtie2 | Anvil ACES Delta |
Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. It is particularly well-suited for aligning sequencing reads of DNA sequences, such as those generated by high-throughput sequencing technologies. | Alignment, Sequencing Reads, DNA Sequences, High-Throughput Sequencing, Bioinformatics, Genomics | Bioinformatics, Biological Sciences | Sequence Alignment | Documentation, Uses, and more |
| brotli | ACES | Brotli is a generic-purpose lossless compression algorithm that compresses data using a combination of a modern variant of the LZ77 algorithm, Huffman coding, and 2nd order context modelling. It is developed by Google and designed to replace the zlib compression. | Compression Algorithm, Lossless Compression, Data Compression | General, Computer Science | Tool | Documentation, Uses, and more |
| brotli-python | ACES | brotli-python is a Python binding for the Brotli compression library. It allows users to compress and decompress data using the Brotli algorithm within Python applications. | Compression, Data Compression, Brotli, Python Library | Computer Science, Computer & Information Sciences | Compression Library | Documentation, Uses, and more |
| brunsli | ACES | Brunsli is an advanced lossless image compressor that focuses on high-speed encoding. It aims to achieve significant compression ratios while maintaining fast encoding and decoding speeds. | Image Compression, Lossless Compression, High-Speed Encoding | General, Computer & Information Sciences | Image Compressor | Documentation, Uses, and more |
| bsbolt | ACES | BSBolt is a bioinformatics software toolkit for efficient alignment, methylation calling, and variant analysis of bisulfite sequencing data. It provides a fast, integrated pipeline for whole-genome and targeted bisulfite sequencing, optimized for accuracy and scalability. | bisulfite sequencing, DNA methylation, read alignment, variant calling, epigenomics, bioinformatics | Epigenomics, Bioinformatics | Analysis software | Documentation, Uses, and more |
| btllib | ACES | Documentation, Uses, and more | ||||
| btop | DeltaAI Delta |
btop is a resource monitor that provides a visually appealing and interactive interface for monitoring system resources such as CPU, memory, and network usage. | System Monitoring, Resource Management, Performance Analysis | Systems, Computer Science | Monitoring Tool | Documentation, Uses, and more |
| bucky | ACES | Documentation, Uses, and more | ||||
| build | ACES | Build is a task automation tool that allows users to define tasks in a buildfile. It is commonly used for compiling source code, running tests, creating distributions, and other repetitive tasks in software development projects. | Task Automation, Build Tool, Software Development | General, Engineering & Technology | Task Automation | Documentation, Uses, and more |
| busco | ACES | BUSCO (Benchmarking Universal Single-Copy Orthologs) is a software package that assesses genome assembly, gene set, and transcriptome completeness based on evolutionarily informed expectations of gene content. | Genomics, Genome Assembly, Gene Set, Transcriptome, Orthologs | Bioinformatics, Biological Sciences | Tools | Documentation, Uses, and more |
| bwa | Anvil ACES |
Burrows-Wheeler Aligner (BWA) is a software package for mapping low-divergent sequences against a large reference genome, such as the human genome. It consists of three algorithms: BWA-backtrack, BWA-SW, and BWA-MEM. The BWA-backtrack algorithm is designed for Illumina sequence reads up to 100bp, while BWA-SW and BWA-MEM are for longer Illumina reads, including 100bp reads produced by the HiSeq 2000 platform. | Sequence Alignment, Bioinformatics, Genomics, Next-Generation Sequencing (Ngs) | Biology, Biological Sciences | Bioinformatics Tool | Documentation, Uses, and more |
| bwa-mem2 | ACES | bwa-mem2 is a fast and accurate alignment tool for mapping DNA sequences against a reference genome, designed to handle large datasets efficiently. | bioinformatics, genomics, alignment, DNA sequencing | Bioinformatics, Genomics | Command-line tool | Documentation, Uses, and more |
| bwa-meth | ACES | BWA-Meth is a software tool for aligning bisulfite-treated sequencing reads to a reference genome, enabling the analysis of DNA methylation. | bioinformatics, DNA methylation, genome alignment, sequencing | Bioinformatics, Biological Sciences | Alignment Tool | Documentation, Uses, and more |
| bwidget | ACES | Bwidget is a collection of useful widgets for the Tcl/Tk GUI toolkit, providing enhanced functionality and improved aesthetics for applications. | Tcl, Tk, GUI, Widgets | Software Engineering, Other Computer and Information Sciences | Library | Documentation, Uses, and more |
| bx-python | ACES | bx-python is a Python library for bioinformatics that provides tools for manipulating and analyzing biological data, particularly in the context of genomic data. | bioinformatics, genomics, data analysis, Python | Genomics | Library | Documentation, Uses, and more |
| byacc | Expanse | byacc is a public domain LALR parser generator which is often used as a replacement for yacc. LALR parsers are used in the generation of efficient parsers for modern programming languages. | Parser Generator, Lalr, Context-Free Grammar | General, Computer & Information Sciences | Development Tool | Documentation, Uses, and more |
| bzip2 | Anvil ACES DeltaAI Expanse KyRIC |
bzip2 is a free and open-source file compression program that uses the Burrows-Wheeler algorithm for compression and Huffman coding for decompression. It is designed to be fast and efficient in compressing large files while retaining a high compression ratio. | File Compression, Data Compression, Utility Software | General, Computer & Information Sciences | Compression Tool | Documentation, Uses, and more |
| c-ares | ACES | c-ares is a C library that performs DNS requests and name resolutions asynchronously. It is designed to be lightweight and efficient, providing asynchronous DNS capabilities to applications. | Dns, Asynchronous, Networking, Library, C | General, Computer & Information Sciences | Networking | Documentation, Uses, and more |
| cairo | Anvil ACES DeltaAI |
Cairo is a 2D graphics library with support for multiple output devices. It provides a vector-based rendering engine for high-quality graphics with full support for transparency and anti-aliasing. | Graphics Library, 2D Graphics, Rendering Engine | Graphics, Computer & Information Sciences | Library | Documentation, Uses, and more |
| camus | ACES | Documentation, Uses, and more | ||||
| cantera | Stampede3 | Cantera is an open-source suite of tools for chemical kinetics, thermodynamics, and transport processes. | chemistry, thermodynamics, kinetics, transport phenomena, open-source | Thermodynamics and Kinetics, Chemical Engineering | Library | Documentation, Uses, and more |
| capnproto | ACES | Cap'n Proto is an open-source data interchange format that is designed for high performance. It is used for serialization and deserialization of data structures, allowing for efficient data exchange between different systems. | Serialization, Data Interchange, Performance, Cross-platform | Software Engineering, Other Computer and Information Sciences | Library | Documentation, Uses, and more |
| capstone | ACES | Capstone is a disassembly framework with the target of becoming the ultimate disasm engine for binary analysis and reversing in the security community. Created by Nguyen Anh Quynh, it is open-source software distributed under the Simplified BSD License. | Disassembly, Binary Analysis, Reverse Engineering | Computer Science, Computer & Information Sciences | Tool | Documentation, Uses, and more |
| captum | ACES | Captum is an extensible library for model interpretation in PyTorch. It provides a flexible and unified API for different interpretability methods and allows users to easily interpret deep learning models. | Interpretability, Model Interpretation, Deep Learning, Pytorch | Artificial Intelligence, Machine Learning, Computer & Information Sciences | Model Interpretation | Documentation, Uses, and more |
| cartopy | ACES | Cartopy is a Python package designed for geospatial data processing to produce high-quality visualizations of maps using matplotlib. It aims to simplify and enhance the mapping capabilities in Python, providing rich, interactive, and customized maps for various scientific disciplines. | Geospatial Data Processing, Data Visualization, Python Library, Mapping, Scientific Visualization | Earth & Environmental Sciences, Physical Sciences | Python Library | Documentation, Uses, and more |
| catch | ACES | Documentation, Uses, and more | ||||
| catch2 | ACES Stampede3 |
Catch2 is a C++ testing framework that is easy to use, yet powerful. It supports test-driven development, behavior-driven development, and specification by example. | Testing Framework, C++, Unit Testing | Computer Science, Engineering & Technology | Testing Framework | Documentation, Uses, and more |
| cbc | ACES | CBC (Coin-or branch and cut) is an open-source mixed integer programming solver that is part of the COIN-OR (Computational Infrastructure for Operations Research) project. It is designed to handle large-scale optimization problems efficiently. | Optimization, Operations Research, Mathematics | Optimization, Mathematics | Solver | Documentation, Uses, and more |
| ccache | ACES | ccache is a compiler cache tool designed to speed up C and C++ compilation by caching previous compilations. It acts as a caching proxy for compilers, storing compiled object files in a cache directory, which can be reused when the same compilation is done again. This reduces compilation times significantly, especially during iterative development processes. | Compiler Cache, C/C++ Compilation, Build Optimization | General, Engineering & Technology | Compiler Utility | Documentation, Uses, and more |
| ccdb | DeltaAI Delta |
CCDB (Cell Cycle Database) is a freely accessible, comprehensive resource for the cell cycle community. It provides information and tools to study cell cycle regulation and its role in cancer and other diseases. | Cell Cycle, Cell Biology, Database | Cell Biology, Biological Sciences | Curated Data Resource | Documentation, Uses, and more |
| cce | DeltaAI Delta |
Compiler Construction Engine (CCE) is a software tool used for building compilers and interpreters. It provides a set of tools and libraries to assist in the creation of programming language implementations. | Compiler, Interpreter, Programming Language, Compiler Construction | Computer Science, Computer & Information Sciences | Compiler/Interpreter | Documentation, Uses, and more |
| cce-mixed | DeltaAI Delta |
cce-mixed is a software package designed for performing calculations in the framework of many-body perturbation theory for the electronic structure of solids. It focuses on the GW approximation, self-energy calculations, and the solution of the Bethe-Salpeter equation for optical excitations. | Computational Chemistry, Quantum Mechanics, Electronic Structure Calculations | Condensed Matter Physics, Physical Sciences | Electronic Structure Calculation | Documentation, Uses, and more |
| ccl | KyRIC | CCL (Cpp Command Line Library) is a C++ library targeting Unix platform that makes it easy to define and parse command line arguments. It provides a simple and intuitive way to define and parse command-line arguments for C++ programs. | Command Line Interface, C++ Library | Documentation, Uses, and more | ||
| cd-hit | ACES | cd-hit is a widely used program for clustering and comparing protein or nucleotide sequences. It clusters a large set of sequences to reduce redundancy and generate a non-redundant representative set. This tool is beneficial for sequence analysis, especially in bioinformatics studies. | Sequence Analysis, Clustering, Bioinformatics | Bioinformatics, Biological Sciences | Bioinformatics Software | Documentation, Uses, and more |
| cdo | Anvil ACES Stampede3 |
Climate Data Operators (CDO) is a collection of command-line operators for manipulating and analyzing climate and numerical weather prediction (NWP) model data. | Climate Data, Data Manipulation, Command Line, Data Analysis | Environmental Science, Earth & Environmental Sciences | Command Line Tool | Documentation, Uses, and more |
| cdsapi | ACES | cdsapi is a Python client library for Climate Data Store (CDS) API, which allows users to access climate and weather data provided by the European Centre for Medium-Range Weather Forecasts (ECMWF). | Python Library, Climate Data, Weather Data | Environmental Science, Earth & Environmental Sciences | Api | Documentation, Uses, and more |
| cdtools | Stampede3 | Documentation, Uses, and more | ||||
| cereal | ACES | Cereal is a C++11 library for serialization. It is designed to be fast, compact, and have an easy-to-use API. | Serialization, C++, Library | Software Engineering, Computer & Information Sciences | Data Serialization | Documentation, Uses, and more |
| ceres-solver | ACES | Ceres Solver is an open-source C++ library for modeling and solving large, complicated optimization problems. | Optimization, Mathematics, C++, Non-linear problems | Optimization, Applied Mathematics | Library | Documentation, Uses, and more |
| cesm-deps | ACES | CESM-DEPS is a set of dependencies and tools for supporting the Community Earth System Model (CESM) software. It includes various libraries, compilers, and software packages necessary for running CESM simulations. | Dependencies, Cesm, Earth System Model, Simulation, Software Package | Earth & Environmental Sciences | Libraries & Dependencies | Documentation, Uses, and more |
| cffi | ACES | CFFI is a Foreign Function Interface between Python and C. It allows calling C code from Python and using Python code from C. It provides a way to interact with foreign functions and call them from Python without having to write any C code. | Foreign Function Interface, C Library Integration, Python | Computer Science, Computer & Information Sciences | Interfacing | Documentation, Uses, and more |
| cfitsio | ACES Stampede3 |
CFITSIO is a library of C and Fortran subroutines for reading and writing data files in FITS (Flexible Image Transport System) data format. | Astronomy, Data Processing, File Format, Fits | Astronomy & Planetary Sciences, Physical Sciences | Data Processing | Documentation, Uses, and more |
| cgal | ACES | CGAL (Computational Geometry Algorithms Library) is a software library that provides a wide range of efficient and reliable geometric algorithms for use in various applications in computational geometry, such as mesh generation, geometric processing, visualization, and more. It is designed to be versatile, easy to use, and highly efficient. | Computational Geometry, Geometric Algorithms, Software Library | Computer Science, Computer & Information Sciences | Algorithm Library | Documentation, Uses, and more |
| cgl | ACES | Documentation, Uses, and more | ||||
| cgns | ACES | The CFD General Notation System (CGNS) provides a standard for recording and recovering computer data associated with the numerical solution of the equations of fluid dynamics. It is designed to facilitate the exchange of data between sites and applications, as well as to help stabilize the archiving of fluid dynamics data. | Computational Software | Fluid & Plasma Physics, Physical Sciences | File Format | Documentation, Uses, and more |
| chameleon | ACES | Chameleon is a Python library for creating customizable color palettes for data visualization purposes. It provides a user-friendly interface to easily generate aesthetically pleasing color schemes for various types of visualizations. | Python Library, Data Visualization, Color Palette, Visualization, Python | Other Computer & Information Sciences | Library | Documentation, Uses, and more |
| charliecloud | Stampede3 | Charliecloud is a software tool that provides user-defined software stacks in userspace with no privileged operations or daemons. It uses containers for software isolation and runs in user space, making it lightweight and secure. | Containerization, Software Development, Research Tools | High-Performance Computing, Computer & Information Sciences | Tool | Documentation, Uses, and more |
| charmpp | KyRIC | Charm++ is a parallel programming model and system that provides an object-oriented approach to parallel programming. It is designed to facilitate the development of parallel applications by allowing developers to focus on the structure of their applications rather than the underlying details of parallel execution. | Parallel Computing, Object-oriented Programming, Load Balancing, Adaptive Applications | Computer Science | Library | Documentation, Uses, and more |
| check | ACES | Check is a unit testing framework for C. It features a simple interface for defining unit tests, putting little in the way of the developer. Tests are run in a separate address space, so both assertion failures and code errors that cause segmentation faults or other signals can be caught. Description Source: https://libcheck.github.io/check/ |
Documentation, Uses, and more | |||
| checklist | Stampede3 | Documentation, Uses, and more | ||||
| checkm | ACES | CheckM is a software tool for assessing the quality of microbial genomes recovered from isolates, single cells, or metagenomes. It provides robust statistical evaluation of genome completeness and contamination, as well as identification of marker genes for phylogenetic placement. | Microbial Genomics, Genome Quality Assessment, Phylogenetic Analysis, Bioinformatics | Ecology, Biological Sciences | Bioinformatics Tool | Documentation, Uses, and more |
| checkm-database | ACES | Documentation, Uses, and more | ||||
| chemprop | ACES | Chemprop is a deep learning-based tool for molecular property prediction. It allows users to train models to predict chemical properties and enables transfer learning to easily apply pre-trained models to new datasets. | Chemoinformatics, Molecular Property Prediction, Deep Learning | Chemoinformatics, Chemical Sciences | Bioinformatics | Documentation, Uses, and more |
| chemps2 | ACES | Documentation, Uses, and more | ||||
| chimerax | ACES | ChimeraX is a software tool for the visualization and analysis of molecular structures, density maps, and related data. It is widely used in the field of structural biology and computational chemistry for studying complex biomolecular systems. | Molecular Visualization, Structural Biology, Computational Chemistry | Bioinformatics, Biological Sciences | Analysis & Visualization Tool | Documentation, Uses, and more |
| cimfomfa | ACES | This library supports both MCL, a cluster algorithm for graphs, and zoem, a macro/DSL language. It supplies abstractions for memory management, I/O, associative arrays, strings, heaps, and a few other things. The string library has had heavy testing as part of zoem. | Documentation, Uses, and more | |||
| cistem | ACES | CISTEM is a computational framework designed for the prediction of dual phase RNA secondary structures. | Computational Framework, RNA Secondary Structures Prediction | Bioinformatics, Biological Sciences | Bioinformatics Tool | Documentation, Uses, and more |
| ckdmip | ACES | CKDmip is a software for computing cosmic microwave background (CMB) radiation temperature anisotropies and polarization spectra using the Cosmic Microwave Background (CMB) perturbation code. | Cosmic Microwave Background, Cmb Radiation, Temperature Anisotropies, Polarization Spectra | Astronomy & Planetary Sciences, Physical Sciences | Hpc Tool | Documentation, Uses, and more |
| clang | ACES | Clang is a compiler front end for the C, C++, and Objective-C programming languages. It uses LLVM as its back end, providing highly optimized code generation. Clang is designed to provide fast compiles, expressive diagnostics, and a modular architecture for easy integration with other tools and libraries. | Compiler, Software Development, Programming Languages | Software Engineering, Systems & Development, Computer & Information Sciences | Development Tool | Documentation, Uses, and more |
| clck | KyRIC | Documentation, Uses, and more | ||||
| clhep | ACES | CLHEP (Class Library for High Energy Physics) is a library of C++ classes specifically designed for high energy physics (HEP) applications. It provides a set of utility classes for HEP-specific tasks, such as vectors, matrices, random number generation, and units of measurement. | C++ Library, High Energy Physics, Hep Applications | Physics, Physical Sciences | Computational Tool | Documentation, Uses, and more |
| climetlab | ACES | climetlab is a Python library designed for easy access, manipulation, and visualization of climate data. It aims to simplify the process of working with climate datasets by providing a unified interface and tools for data exploration. | Python Library, Climate Data, Data Visualization | Earth & Environmental Sciences | Library | Documentation, Uses, and more |
| clip | ACES | CLIP (Contrastive Language-Image Pretraining) is a framework for learning joint representations of images and text. It is designed to pretrain on large scale image-text datasets to learn a powerful visual-linguistic understanding. | Machine Learning, Deep Learning, Image-Text Representation, Pretraining | Artificial Intelligence & Intelligent Systems, Computer & Information Sciences | Deep Learning | Documentation, Uses, and more |
| clp | ACES | CLP (Cbc, Lapack, and ParallelCbc) is an open-source linear programming solver that provides both a standalone solver and a framework for building custom optimization algorithms. It is designed to solve large-scale linear programming problems efficiently and offers a range of features for linear optimization. | Linear Programming, Optimization, Large-Scale Problems, Open-Source | Operations Research, Industrial Engineering, Engineering & Technology | Solver | Documentation, Uses, and more |
| clusterbot | Anvil | Documentation, Uses, and more | ||||
| cm-image | Expanse | Documentation, Uses, and more | ||||
| cm-pmix3 | Expanse | cm-pmix3 is a lightweight, high-performance library that provides process management and control functions for large-scale computing environments. | Process Management, High-Performance Computing, Job Scheduling | Other Computer & Information Sciences, Engineering & Technology | System & Process Management | Documentation, Uses, and more |
| cm-scale | Expanse | Documentation, Uses, and more | ||||
| cm-setup | Expanse | Documentation, Uses, and more | ||||
| cmake | Anvil ACES DeltaAI Expanse Delta KyRIC Stampede3 |
CMake is an open-source, cross-platform family of tools designed to build, test, and package software. It is used to control the software compilation process using simple platform and compiler-independent configuration files. | Build System, Cross-Platform, Software Development | Software Engineering, Systems & Development, Engineering & Technology | Developer Tools | Documentation, Uses, and more |
| cmd | Expanse | The cmd module in Python provides a framework for building interactive command line applications. It allows developers to easily create command-line interfaces by defining a set of commands and their associated functions. | Command Line, Python Module | Computer & Information Sciences | Framework | Documentation, Uses, and more |
| cmjob | Expanse | cmjob is a Python-based tool for computational materials science that aids in automating the submission of multiple jobs on high-performance computing clusters. It simplifies the process of handling multiple job submissions, tracking job statuses, and organizing job outputs. | Hpc, Computational Materials Science, Python Library | Documentation, Uses, and more | ||
| cmsh | Expanse | Documentation, Uses, and more | ||||
| coco | ACES | Documentation, Uses, and more | ||||
| coinutils | ACES | CoinUtils is an open-source C++ library that provides utilities and tools for optimization problems. It is part of the COIN-OR project, a collection of operations research software tools. | Optimization, Operations Research, Mathematical Programming | Applied Mathematics, Mathematics | Optimization Software | Documentation, Uses, and more |
| colabfold | ACES Delta |
ColabFold is a collaborative project that aims to bring together deep learning and biophysical modeling for protein structure prediction. It provides an easy-to-use interface for researchers to perform protein folding predictions using state-of-the-art techniques. | Protein Structure Prediction, Deep Learning, Biophysical Modeling | Bioinformatics, Biological Sciences | Protein Structure Prediction Tool | Documentation, Uses, and more |
| colmap | ACES | COLMAP is a general-purpose, open-source Structure-from-Motion (SfM) and Multi-View Stereo (MVS) pipeline with a focus on ease of use and extensibility. | 3D Reconstruction, Computer Vision, Structure-from-Motion, Multi-View Stereo | Computer Science | Open-source | Documentation, Uses, and more |
| colorize | ACES | Documentation, Uses, and more | ||||
| colossalai | ACES | ColossalAI is an open-source deep learning framework that focuses on large-scale distributed training and efficient model serving. It provides a unified platform for researchers and practitioners to build, train, and deploy deep learning models at scale. | Deep Learning Framework, Large-Scale Training, Model Serving | Artificial Intelligence & Intelligent Systems, Computer & Information Sciences | Open Source | Documentation, Uses, and more |
| compiler | KyRIC | A compiler is a special program that processes statements written in a particular programming language and turns them into machine language or "code" that a computer's processor uses. It typically acts as a translator that converts high-level programming languages into machine language. | Compiler, Software Development, Programming | Software Engineering, Computer & Information Sciences | Compiler | Documentation, Uses, and more |
| compiler-rt | KyRIC | compiler-rt stands for Compiler Runtime Library. It is a collection of runtime libraries that provide low-level support for compiler-generated code. It is designed to be used with the LLVM compiler infrastructure and is commonly used in conjunction with Clang. The compiler-rt libraries implement runtime parts of the language features that are not supported directly by the compiler. | Runtime Library, Compiler Support, Low-Level Support, Language Features | Computer Science, Computer & Information Sciences | Library | Documentation, Uses, and more |
| compiler-rt32 | KyRIC | The compiler-rt32 project is a runtime library that provides functionality for compilers in the 32-bit architecture. It includes various runtime components such as sanitizers, builtins, and support libraries for handling memory operations and error detection. | Compiler, Runtime Library, 32-Bit Architecture | Computer Science, Computer & Information Sciences | Runtime Library | Documentation, Uses, and more |
| compiler32 | KyRIC | compiler32 is a lightweight and efficient compiler software designed for compiling source code into executable programs. It supports various programming languages and optimization techniques to enhance the performance of the compiled code. | Compiler, Software Development, Programming | Computer & Information Sciences | Development Tools | Documentation, Uses, and more |
| conceptual captions 3 million (cc3m) | ACES | Documentation, Uses, and more | ||||
| conda | Anvil | Conda is an open-source package management system and environment management system that runs on Windows, macOS, and Linux. It is designed to quickly install, run, and update packages and their dependencies. | package management, environment management, cross-platform, open-source | Software Engineering, Computer Science | Package Manager | Documentation, Uses, and more |
| configurable-http-proxy | ACES | A proxy server that allows for configurable routing of HTTP requests, often used in conjunction with JupyterHub and other web applications. | proxy, HTTP, web, JupyterHub, routing | Software Engineering, Other Computer and Information Sciences | Web Application | Documentation, Uses, and more |
| coordgenlibs | ACES | CoordGenLibs is a set of computational chemistry libraries and tools for generating 3D coordinates for small molecules. It provides functions for assigning coordinates to atoms based on connectivity information and geometric constraints. | Computational Chemistry, 3D Coordinate Generation, Small Molecules | Chemical Sciences | Chemical Informatics | Documentation, Uses, and more |
| cp2k | Anvil ACES Stampede3 |
CP2K is an open-source quantum chemistry and solid state physics software package designed to perform atomistic simulations of solid-state, liquid, molecular, and biological systems. It can be used to study a wide range of properties, including electronic structures, molecular dynamics, and vibrational spectra. | Computational Chemistry, Quantum Mechanics, Molecular Dynamics | Physical Sciences | Molecular Simulation | Documentation, Uses, and more |
| cpe | DeltaAI Delta |
CPE (Common Platform Enumeration) is a standardized method to describe and identify classes of applications, operating systems, and hardware devices in a consistent format. It provides unique identifiers for these entities to facilitate accurate and efficient information exchange between different security tools and databases. | Software Identification, Cybersecurity, Information Exchange | Computer Science, Computer & Information Sciences | Tool | Documentation, Uses, and more |
| cpio | ACES | cpio is a general file archiver and compression utility that is used to manage archives of files. It can create, extract, and list the contents of archives in various formats. | file management, archiving, compression, Unix, Linux | Computer Science | Command-line utility | Documentation, Uses, and more |
| cppe | ACES | Documentation, Uses, and more | ||||
| cppunit | ACES | CppUnit is a C++ unit testing framework designed to assist in writing and running automated test suites for C++ code. It is based on the xUnit architecture and is similar in functionality to JUnit for Java. | Unit Testing, C++ | Software Development, Computer & Information Sciences | Library | Documentation, Uses, and more |
| cppy | ACES | C++ embedded Python library to seamlessly interact with C++ and Python code within the same application. | C++, Python, Embedded Python, Interoperability | Computer & Information Sciences | Integration Tool | Documentation, Uses, and more |
| cpu | Expanse | CPU (Central Processing Unit) is a hardware component of a computer that executes instructions and performs calculations. It is considered the brain of the computer and is responsible for carrying out tasks and running applications. | Hardware, Computing, Technology | Computer & Information Sciences | Component | Documentation, Uses, and more |
| craype | DeltaAI Delta |
Cray Programming Environment (CrayPE) is a suite of tools and libraries designed for high-performance computing on Cray supercomputers. | HPC, Supercomputing, Compilers, Performance Libraries | Computer Science | Development Tools | Documentation, Uses, and more |
| craype-accel | DeltaAI Delta |
Documentation, Uses, and more | ||||
| craype-x86 | DeltaAI Delta |
Documentation, Uses, and more | ||||
| craypkg-gen | DeltaAI Delta |
Documentation, Uses, and more | ||||
| crb-blast | ACES | Documentation, Uses, and more | ||||
| cryosparc | ACES | CryoSPARC is a comprehensive software platform for cryo-EM data processing that enables high-resolution structure determination of biological macromolecules. | Cryo-Em, Biological Macromolecules, Structural Biology, Data Processing | Biophysics, Biological Sciences | Cryo-Em Software | Documentation, Uses, and more |
| cryptography | ACES | Cryptography is the practice and study of techniques for secure communication in the presence of third parties. It involves creating and analyzing protocols that prevent third parties or the public from reading private messages. | Security, Privacy, Encryption, Decryption | Applied Computer Science, Computer & Information Sciences | Software | Documentation, Uses, and more |
| cryptsetup | KyRIC | cryptsetup is a utility used to conveniently set up disk encryption based on the Dm-crypt kernel module. It allows users to easily configure encrypted block devices using LUKS (Linux Unified Key Setup), manage cryptographic volumes, and interact with encrypted volumes. | Disk Encryption, Data Security, Cryptography, Linux | Cryptography, Computer & Information Sciences | System Software | Documentation, Uses, and more |
| ctffind | ACES | Documentation, Uses, and more | ||||
| cti | DeltaAI Delta |
CTI (Common Threat Intelligence) is an open source library designed to parse and manipulate structured threat intelligence information. It provides a set of APIs to work with different threat intelligence data formats and supports the serialization of data into various formats. | Threat Intelligence, Data Parsing, Open Source | Threat Intelligence | Documentation, Uses, and more | |
| cubegui | ACES | Cubegui is a graphical user interface (GUI) software designed for visualizing and analyzing volumetric data in computational chemistry and materials science. | Gui Software, Volumetric Data Visualization, Computational Chemistry, Materials Science | Chemical Sciences, Natural Sciences | Graphical User Interface (Gui) | Documentation, Uses, and more |
| cubelib | ACES | cubelib is a C++ library for parallel reduction operations on multi-dimensional arrays using CUDA. | Software Library, C++, Cuda, Parallel Computing, Multi-Dimensional Arrays | Computer Science, Computer & Information Sciences | Computational Software | Documentation, Uses, and more |
| cubewriter | ACES | Cubewriter is a software tool that enables researchers to organize, write, and format scientific papers efficiently. | Scientific Writing, Document Formatting, Research Collaboration, References Management | Other Natural Sciences | Productivity Tool | Documentation, Uses, and more |
| cuda | ACES DeltaAI Anvil Delta |
CUDA is a parallel computing platform and application programming interface model created by NVIDIA. It allows software developers to use a CUDA-enabled graphics processing unit for general-purpose processing. | Parallel Computing, Gpu Programming, High Performance Computing, Software Development | Computer Science, Computer & Information Sciences | Compiler | Documentation, Uses, and more |
| cuda (deprecated shim) | DeltaAI | Documentation, Uses, and more | ||||
| cuda-compat | DeltaAI Delta |
Documentation, Uses, and more | ||||
| cuda-compat (deprecated shim) | DeltaAI | Documentation, Uses, and more | ||||
| cuda-python | ACES | cuda-python is a Python package that provides bindings to the CUDA API, allowing developers to write Python code that can leverage the power of NVIDIA GPUs for high-performance computing tasks. | CUDA, Python, GPU Computing, High-Performance Computing | High-Performance Computing, Computer Science | Library | Documentation, Uses, and more |
| cuda-quantum | Anvil | cuda-quantum is a CUDA-accelerated quantum computing simulator designed to efficiently simulate quantum circuits on NVIDIA GPUs. It provides a high-performance platform for simulating large-scale quantum computations with a focus on speed and scalability. | Quantum Computing, Cuda-Accelerated, Quantum Simulator, Nvidia Gpu, High-Performance Computing | Computer Science | Quantum Computing Simulator | Documentation, Uses, and more |
| cuda-samples | ACES | cuda-samples is a collection of CUDA code samples and examples provided by NVIDIA. These samples cover a wide range of CUDA programming concepts and techniques, serving as useful resources for developers to learn and practice GPU programming using CUDA. | Cuda, Gpu Programming, Code Samples, Nvidia | Computer Science, Computer & Information Sciences | Code Sample Repository | Documentation, Uses, and more |
| cuda10.2/profiler | Expanse | Documentation, Uses, and more | ||||
| cuda10.2/toolkit | Expanse | Documentation, Uses, and more | ||||
| cuda11.7/profiler | Expanse | Documentation, Uses, and more | ||||
| cuda11.7/toolkit | Expanse | Documentation, Uses, and more | ||||
| cuda12.2/profiler | Expanse | Documentation, Uses, and more | ||||
| cuda12.2/toolkit | Expanse | Documentation, Uses, and more | ||||
| cuda_python | ACES | Documentation, Uses, and more | ||||
| cudacore | ACES | cudacore is a high-performance computational software that leverages GPU (Graphics Processing Unit) computing through CUDA (Compute Unified Device Architecture) for accelerated processing of scientific and engineering applications. | Computational Software, Cuda, Gpu Computing, Scientific Computing, Engineering Applications | Other Engineering & Technologies, Engineering & Technology | High-Performance Computing Tool | Documentation, Uses, and more |
| cudatoolkit | DeltaAI Delta |
The CUDA Toolkit is a development environment for creating high-performance GPU-accelerated applications. It includes libraries, debugging and optimization tools, a compiler, and a runtime environment. | GPU Computing, Parallel Computing, High-Performance Computing | Computer Science, Artificial Intelligence and Intelligent Systems | Development Toolkit | Documentation, Uses, and more |
| cudf | ACES | CUDF is part of the RAPIDS suite of open-source software libraries and APIs built on CUDA. It provides a DataFrame manipulation library leveraging GPU acceleration for loading, joining, aggregating, filtering, and otherwise manipulating tabular data. | Dataframe, Gpu Acceleration, Data Manipulation | Computational Data Analysis, Computer & Information Sciences, Artificial Intelligence & Intelligent Systems | Library | Documentation, Uses, and more |
| cudnn | ACES DeltaAI Anvil |
The NVIDIA CUDA Deep Neural Network library (cuDNN) is a GPU-accelerated library for deep neural networks. It provides highly optimized implementations of common deep learning operations. | Deep Learning, Artificial Intelligence, Machine Learning, Gpu Acceleration, Neural Networks | Computer Science | Deep Learning Accelerator | Documentation, Uses, and more |
| cue-login-env | Anvil Expanse Delta |
Cue-login-env is a Python library that provides an easy way to configure user-specific environments within shared servers or computing clusters. It helps users manage their environment variables, aliases, and paths without interfering with the system-wide configurations. | Python Library, User-Specific Environment, Shared Servers, Computing Clusters | Computer & Information Sciences | Python Library | Documentation, Uses, and more |
| cufflinks | Anvil | Cufflinks assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples. | RNA-Seq, Transcriptomics, Bioinformatics | Biology, Biological Sciences | Tool | Documentation, Uses, and more |
| cunit | ACES | CUnit is a lightweight C unit testing framework for automated testing of C code. It provides an easy-to-use framework for writing test cases and test suites to verify the correct functioning of C programs. | Unit Testing, C Programming, Development Tools | Computer Science, Computer & Information Sciences | Testing Framework | Documentation, Uses, and more |
| cupy | ACES | CuPy is an open-source library that provides GPU-accelerated computing with Python. It is built as a drop-in replacement for NumPy and works seamlessly with other libraries in the Python ecosystem. | Python Library, Gpu Computing, Numpy Replacement | Computer Science, Computer & Information Sciences | Gpu Computing | Documentation, Uses, and more |
| cuquantum-appliance | Anvil | Documentation, Uses, and more | ||||
| curl | Anvil ACES DeltaAI Expanse KyRIC |
curl is a command-line tool and library for transferring data with URLs. It supports various protocols including HTTP, HTTPS, FTP, FTPS, SCP, SFTP, and more. It is widely used in scripting and automation tasks, as well as for debugging network issues. | Networking, Data Transfer, Command-Line, Scripting | Computer Science, Computer & Information Sciences, Other Computer & Information Sciences | Networking Tool | Documentation, Uses, and more |
| cusparselt | ACES | CusparseLT library is a lightweight version of NVIDIA's cuSPARSE library designed for sparse matrix operations on NVIDIA GPUs. It offers high-performance accelerated computation for sparse matrix manipulation in GPU-accelerated applications. | Sparse Matrix Operations, Gpu Acceleration, Linear Algebra, Cuda Programming | Computer Science, Computer & Information Sciences | Computational Software | Documentation, Uses, and more |
| cutadapt | ACES | cutadapt removes adapter sequences from high-throughput sequencing reads. It finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads. | Bioinformatics, Ngs, Sequence Analysis, Genomics | Computational Biology, Biological Sciences | Sequence Analysis Tool | Documentation, Uses, and more |
| cutensor | ACES | cuTensor is a CUDA-accelerated library for tensor operations in NVIDIA GPUs. It provides optimized implementations for tensor contractions and element-wise operations, allowing for efficient computation of large-scale tensor operations in parallel. | Cuda, Gpu Acceleration, Tensor Operations, Parallel Computing | Applied Computer Science, Computer & Information Sciences | Computational Software | Documentation, Uses, and more |
| cutlass | ACES | CUTLASS (CUDA Templates for Linear Algebra Subroutines and Solvers) is a collection of CUDA C++ templates that facilitate high-performance matrix-multiplication (GEMM) and other linear algebra operations. | CUDA, Linear Algebra, Matrix Multiplication, High Performance Computing | Numerical Analysis, Computer Science | Library | Documentation, Uses, and more |
| cxxopts | Stampede3 | A lightweight C++ library for parsing command line arguments, inspired by Python's argparse library. | C++, Command Line Arguments, Parsing, Library | Software Engineering, Computer & Information Sciences | Library | Documentation, Uses, and more |
| cython | ACES | Cython is a programming language that makes it easy to write C extensions for Python. It provides a superset of the Python language that allows for calling C functions and declaring C types on variables and class attributes. | Programming Language, C Extensions, Python, Cython | Computer Science, Computer & Information Sciences | Language Compiler | Documentation, Uses, and more |
| cython-blis | ACES | Cython wrapper around BLIS linear algebra library for Python. | Cython, Blis, Linear Algebra, Python | Applied Mathematics, Computer & Information Sciences | Library | Documentation, Uses, and more |
| dace | ACES | dace (Data Assimilation for Categorical and High-Dimensional Data) is a Python toolkit for data assimilation, specifically designed for high-dimensional and categorical data. It provides a range of data assimilation algorithms and tools to effectively integrate observational data and models to improve predictions and understanding of complex systems. | Data Assimilation, Python Toolkit, Observational Data Integration | Computer Science, Computer & Information Sciences | Framework | Documentation, Uses, and more |
| dal | KyRIC | DAL is a library for collision avoidance in robotics applications. | Robotics, Collision Avoidance | Engineering & Technology | Collision Avoidance Software | Documentation, Uses, and more |
| dask | ACES | Dask is a flexible parallel computing library for analytic computing, designed to scale from single machines to large clusters. It provides advanced parallelism for analytics, enabling performance at scale for the tools you love. | Parallel Computing, Scalable Computing, Analytics, Data Science | Data Analytics, Computer & Information Sciences | Library | Documentation, Uses, and more |
| dask-labextension | ACES | Dask Labextension is a JupyterLab extension that provides a graphical interface for Dask, enabling users to manage and visualize Dask clusters and tasks directly from JupyterLab. | Dask, JupyterLab, Data Science, Parallel Computing | Data Analysis, Computer Science | Extension | Documentation, Uses, and more |
| datamash | ACES | Datamash is a command-line program that performs basic numeric, textual, and statistical operations on input data, typically in tabular format. | Data Analysis, Command Line, Statistics, Text Processing | Statistics, Data Analysis | Command-line tool | Documentation, Uses, and more |
| dataspaces | ACES | Documentation, Uses, and more | ||||
| dataversioncontrol/dvc | ACES | Documentation, Uses, and more | ||||
| db | ACES | db is a simple and minimalistic database library for Python, designed to provide a lightweight interface for basic database operations. | Database, Python Library | Computer & Information Sciences, Computer Science | Library | Documentation, Uses, and more |
| db_file | ACES | db_file is a software tool designed for managing and manipulating database files. It provides functionalities for creating, modifying, querying, and extracting data from database files. | Database Management, Data Manipulation, Querying, Data Extraction | Computer & Information Sciences | Tool | Documentation, Uses, and more |
| dbcsr | ACES | dbcsr (distributed block compressed sparse row) is a library for creating distributed block-sparse matrix data structures and performing operations on them efficiently. It is designed for high-performance computing (HPC) applications that involve large, sparse matrices. | Hpc, Sparse Matrices, Parallel Computing | Quantum Chemistry, Other Natural Sciences | Library | Documentation, Uses, and more |
| dbus | ACES | D-Bus is a message bus system, a simple way for applications to talk to one another. In addition to interprocess communication, D-Bus helps coordinate process lifecycle management. | Message Bus System, Interprocess Communication, Process Lifecycle Management | Software Engineering, Computer & Information Sciences | Middleware | Documentation, Uses, and more |
| dbus-glib | ACES | D-Bus is a message bus system for inter-application communication and coordination. dbus-glib is a library for GLib based applications to communicate with D-Bus. | D-Bus, Inter-Process Communication, Glib | Software Engineering, Computer & Information Sciences | Api | Documentation, Uses, and more |
| dcmtk | ACES | DCMTK is a collection of libraries and applications implementing large parts the DICOM standard. It includes software for examining, constructing and converting DICOM image files, handling offline media, sending and receiving images over a network connection, as well as demonstrative image processing, and pattern recognition techniques. | Dicom, Medical Imaging, Healthcare, Image Processing | Medical & Health Sciences | Data Processing & Analysis | Documentation, Uses, and more |
| ddt | Stampede3 | DDT is a powerful, flexible, scalable, and easy-to-use debugging and performance analysis tool for parallel and serial codes. | Debugging Tool, Performance Analysis, Parallel Computing, Serial Computing | Computer & Information Sciences | Debugger | Documentation, Uses, and more |
| debugger | KyRIC | A debugger is a software tool that allows programmers to track down and fix bugs (errors) in their programs. It enables users to step through code, inspect variables, set breakpoints, and analyze the program's execution flow. | Debugging, Software Development | Engineering & Technology | Debugger | Documentation, Uses, and more |
| deepdiff | ACES | DeepDiff is a Python library for deep (nested) comparisons of objects. | Python Library, Data Comparison, Object Comparison | Software Engineering, Computer & Information Sciences | Python Library | Documentation, Uses, and more |
| default-orig | DeltaAI | Documentation, Uses, and more | ||||
| default-rh9test | Delta | Documentation, Uses, and more | ||||
| default-sp5 | DeltaAI | Documentation, Uses, and more | ||||
| default-update | DeltaAI | Documentation, Uses, and more | ||||
| default_svc | DeltaAI | Documentation, Uses, and more | ||||
| defaultmodules | Expanse | Documentation, Uses, and more | ||||
| deltalake | ACES | Documentation, Uses, and more | ||||
| dendropy | ACES | DendroPy is a flexible and modular phylogenetic computing library in Python, offering reading, writing, simulation, and manipulation of phylogenetic trees and associated data. | Phylogenetics, Computational Biology, Python Library, Bioinformatics, Phylogenetic Trees | Biological Sciences | Computational | Documentation, Uses, and more |
| desmond | ACES | Desmond is a molecular dynamics simulation software designed for studying biological systems at the atomic level. It is widely used for drug discovery, protein folding, and molecular interactions. | Molecular Dynamics, Biological Systems, Drug Discovery, Protein Folding | Biochemistry & Molecular Biology, Biological Sciences | Molecular Dynamics Software | Documentation, Uses, and more |
| dev-utilities | KyRIC | Dev-utilities is a collection of various development utilities that assist software developers in various aspects of the development process. These utilities can range from code editors and version control systems to build automation tools and testing frameworks. | Development, Utilities | Computer & Information Sciences, Other Computer & Information Sciences | Tools | Documentation, Uses, and more |
| diamond | ACES | Diamond is a sequence aligner for protein and translated DNA searches, designed for high performance analysis of protein sequence data utilizing the Diamond heuristic aligner. It is particularly optimized for aligning sequencing reads produced by next-generation sequencing (NGS) machines. | Sequence Alignment, Ngs Analysis, Bioinformatics | Bioinformatics, Biological Sciences | Bioinformatics Tool | Documentation, Uses, and more |
| dice | ACES | Documentation, Uses, and more | ||||
| diffutils | KyRIC | Diffutils is a collection of utilities for comparing and finding differences between text files. It includes programs like `diff` for showing the differences between two files, `cmp` for comparing two files byte by byte, and `diff3` for comparing three files. | Text Comparison, File Difference, Text Analysis, Version Control | Software Engineering, Engineering & Technology | Text Processing | Documentation, Uses, and more |
| dill | ACES | Dill is a serialization library for Python datastructures. It provides the ability to serialize all standard Python data types without needing to be pre-informed about their existence, offering extended functionality beyond what is available in the standard `pickle` library. | Serialization, Python, Datastructures, Library | Computer Science, Computer & Information Sciences | Library | Documentation, Uses, and more |
| dimemas | KyRIC | DIMemas is a software tool for the automatic performance prediction of parallel applications. It utilizes simulation techniques to estimate the performance of parallel applications on large-scale systems. | Performance Prediction, Parallel Applications, Simulation, Large-Scale Systems | Computer Science, Engineering & Technology | Performance Prediction Tool | Documentation, Uses, and more |
| dm-haiku | ACES | Documentation, Uses, and more | ||||
| dm-tree | ACES | dm-tree is a Python library for manipulating nested tree-like data structures with ease and efficiency. It provides a comprehensive set of tools for working with hierarchical data in a user-friendly manner. | Python Library, Hierarchical Data, Tree Structures, Data Manipulation | Computer & Information Sciences | Library | Documentation, Uses, and more |
| dnnl | KyRIC | Deep Neural Network Library (DNNL) is an open-source, performance-oriented library for deep learning applications. Formerly known as Intel Math Kernel Library for Deep Neural Networks (MKL-DNN), it provides optimized building blocks for implementation of deep learning neural network layers on various hardware platforms. | Deep Learning, Neural Networks, Machine Learning, Performance Optimization | Artificial Intelligence & Intelligent Systems, Computer & Information Sciences | Deep Learning Library | Documentation, Uses, and more |
| dnnl-cpu-gomp | KyRIC | The dnnl-cpu-gomp is an open-source deep neural network library developed for CPU-based computations employing OpenMP (Open Multi-Processing) as a thread-processing technology. | Deep Learning, Neural Networks, Openmp, Cpu Computing | Machine Learning, Computer & Information Sciences | Computational Software | Documentation, Uses, and more |
| dnnl-cpu-iomp | KyRIC | dnnl-cpu-iomp is an optimization library for deep neural network computations on CPU using Intel OpenMP (iomp) for improved performance. | Deep Learning, Optimization, Cpu Acceleration | Computer & Information Sciences | Documentation, Uses, and more | |
| dnnl-cpu-tbb | KyRIC | DNNL (Deep Neural Network Library) with TBB (Threading Building Blocks) support for optimized performance on CPU architectures. | Deep Learning, High-Performance Computing, Multi-threading, CPU Optimization | Artificial Intelligence, Artificial Intelligence and Intelligent Systems | Library | Documentation, Uses, and more |
| docker | Expanse | Docker is a platform that enables users to develop, ship, and run applications within containers. Containers allow developers to package up an application with all parts it needs, such as libraries and other dependencies, and ship it all out as one package. | Containerization, Deployment, Scalability, Isolation | Computer Science, Computer & Information Sciences | Virtualization | Documentation, Uses, and more |
| dorado | ACES | Dorado is a software tool used for performance evaluation and benchmarking in HPC (High-Performance Computing) environments. It allows users to assess the performance of parallel applications and optimize their running times on supercomputers and clusters. | Performance Evaluation, Benchmarking, Hpc, Supercomputing | Biology, Engineering & Technology | Tool | Documentation, Uses, and more |
| dos2unix | Delta | dos2unix is a command-line utility that converts text files with DOS or Windows line endings (CRLF) to Unix line endings (LF) format. | Text Conversion, Line Endings, Command-Line Utility | Software Engineering, Computer & Information Sciences | Utility | Documentation, Uses, and more |
| dot | Expanse | Graphviz is open source graph visualization software. It has several main graph layout programs. It also has web and interactive graphical interfaces, and auxiliary tools, libraries, and language bindings. | Graph Visualization, Open Source, Graph Layout | Graph Theory, Computer & Information Sciences | Graph Visualization Software | Documentation, Uses, and more |
| double-conversion | ACES | double-conversion is a performant library for converting double-precision floating-point values to and from decimal strings, designed for high-performance and precision in conversions. | Conversion, Performance, Precision | Numerical Analysis, Computer & Information Sciences | Library | Documentation, Uses, and more |
| doxygen | ACES Expanse |
Doxygen is a documentation generator tool that is used to generate software reference documentation from annotated source code. It supports multiple programming languages and produces output in various formats, including HTML, LaTeX, RTF, and more. | Documentation Generator, Software Development, Programming | Software Development, Software Engineering, Systems & Development | Tool | Documentation, Uses, and more |
| dpct | KyRIC | Data Parallel C++ for CUDA is a C++ programming model for accelerators based on the NVIDIA CUDA architecture. It allows users to write C++ code that can be compiled to target NVIDIA GPUs using CUDA for parallel execution. | Cuda Programming, Gpu Computing, Parallel Programming | Computer Science, Computer & Information Sciences | Development Compiler | Documentation, Uses, and more |
| dpl | KyRIC | dpl is a software for performing direct programming language analysis. | Programming Language Analysis, Syntax Analysis, Language Structure Analysis | Documentation, Uses, and more | ||
| draco | ACES | Draco is a software library for compressing and decompressing 3D geometric meshes and point clouds. It is designed to improve the storage and transmission of 3D graphics data by offering high compression ratios while maintaining the geometric integrity of the data. | Compression, 3D Graphics, Geometric Data, Mesh, Point Cloud | Computer & Information Sciences | Library | Documentation, Uses, and more |
| drep | ACES | drep (Dereplicator) is a tool for fast and accurate dereplication of genomes in microbial datasets. It helps to identify and remove duplicate sequences to ensure that downstream analyses are not biased by redundant data. | Microbiome, Genome Analysis, Bioinformatics | Bioinformatics, Biological Sciences | Bioinformatics | Documentation, Uses, and more |
| dsmml | DeltaAI Delta |
dsmml is a deep learning library specifically designed for molecular machine learning applications. It offers a range of tools and techniques tailored for computational chemistry and drug discovery tasks. | Deep Learning, Molecular Machine Learning, Computational Chemistry, Drug Discovery | Chemical Sciences, Other Chemical Sciences | Deep Learning Library | Documentation, Uses, and more |
| dtcmp | ACES | Documentation, Uses, and more | ||||
| duckdb | Anvil | DuckDB is an in-process SQL OLAP database management system designed for analytical query workloads. It is optimized for fast query execution and supports a wide variety of data formats. | Database, SQL, OLAP, Analytics, Data Science | Computer Science | Database Management System | Documentation, Uses, and more |
| dyninst | DeltaAI Delta |
Dyninst is a versatile and powerful binary instrumentation and analysis tool that provides capabilities for runtime code analysis, modification, and monitoring in C, C++, and Fortran applications. | Binary Instrumentation, Code Analysis, Runtime Monitoring | Software Engineering, Computer & Information Sciences | Tool | Documentation, Uses, and more |
| easybuild | ACES KyRIC |
EasyBuild is an open-source framework for building and installing software packages on High-Performance Computing (HPC) systems. It aims to make building software easier for system administrators and users on HPC systems by automating the build process. | Software Building, High-Performance Computing, Automation | Computer Science, Engineering & Technology | Build Automation | Documentation, Uses, and more |
| easybuild-aces | ACES | EasyBuild-ACES is a collection of EasyBuild framework recipes for building commonly used software packages within the Army Combat Capabilities Development Command Army Research Laboratory (CCDC-ARL) Computational and Information Sciences Directorate (CISD) Advanced Computing, Engineering and Software (ACES) research group. | Software Development, Tools, Packages | Computer & Information Sciences | Tools | Documentation, Uses, and more |
| easybuild-aces-myeb | ACES | User EasyBuild environment for aces.hprc.tamu.edu in $SCRATCH/eb. Description Source: https://hprc.tamu.edu/software/aces/# |
Documentation, Uses, and more | |||
| easybuild-aces-scratch | ACES | User EasyBuild environment for aces.hprc.tamu.edu in $SCRATCH/eb. Description Source: https://hprc.tamu.edu/software/aces/# |
Documentation, Uses, and more | |||
| easybuild-aces-tmp | ACES | EasyBuild is a software build and installation framework for high-performance computing (HPC) systems. The aces-tmp tool is a temporary directory management tool that is part of the EasyBuild framework. | Software Build, Installation Framework, Hpc Systems, Temporary Directory Management | Infrastructure & Instrumentation, Engineering & Technology | Tool | Documentation, Uses, and more |
| ecbuild | ACES | ecBuild is a CMake-based build system generator for Earth system model (ESM) projects. It focuses on enabling easy configuration and management of complex ESM projects by automating the generation of build systems. | Build System Generator, Earth System Model, Cmake-Based, Esm Project, Model Coupling, Parallel Execution | Meteorology, Earth & Environmental Sciences | Build System Generator | Documentation, Uses, and more |
| eccodes | ACES | eccodes is a software package for encoding/decoding and manipualting meteorological data in GRIB format. It provides a large number of functionalities to work with data in meteorology, oceanography, and climatology. | Grib Data, Meteorology, Oceanography, Climatology | Atmospheric Sciences, Earth & Environmental Sciences | Data Encoding/Decoding | Documentation, Uses, and more |
| eggnog-mapper | ACES | EggNOG-mapper is a tool that allows functional annotation of non-model species using orthology-based methods. It leverages precomputed clusters of orthologous genes from multiple species to predict gene function through orthology transfer. | Functional Annotation, Orthology, Gene Function Prediction | Bioinformatics, Biological Sciences | Bioinformatics Tool | Documentation, Uses, and more |
| eigen | Anvil ACES Stampede3 |
Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms. | Linear Algebra, Numerical Computation, C++ Library | Applied Mathematics, Computer & Information Sciences | Linear Algebra Library | Documentation, Uses, and more |
| einops | ACES | einops is a Python library for tensor operations and reshaping with a focus on readability and flexibility. It provides a more intuitive and concise way of manipulating tensor dimensions in deep learning frameworks. | Python Library, Tensor Manipulation, Deep Learning Frameworks | Computer Science, Computer & Information Sciences | Python Library | Documentation, Uses, and more |
| elfutils | ACES DeltaAI |
elfutils is a collection of various binary tools for working with ELF files. It includes utilities for analyzing, manipulating, and creating programs and object files in the Executable and Linkable Format (ELF). These tools are commonly used by programmers, debuggers, and system administrators to inspect and modify ELF binaries. | Binary Tool, Elf Files, Debugging, Programming | Software Engineering, Other Computer and Information Sciences | Utility | Documentation, Uses, and more |
| elpa | ACES | ELPA (Eigenvalue SoLvers for Petaflop Applications) is a library for solving the standard and generalized eigenvalue problems for dense Hermitian matrices. It is designed for high-performance computing systems and utilizes highly scalable algorithms to achieve high efficiency. | Linear Algebra, Eigenvalue Problems, High-Performance Computing, Scalable Algorithms | Numerical Linear Algebra, Computer & Information Sciences | Library | Documentation, Uses, and more |
| elsi | ACES | ELSI (Electron-Lattice Solvation Interface) is a software package designed for simulating the interaction of electrons with lattice structures in materials science. | Materials Science, Quantum Mechanics, Simulation | Computational Materials Science, Quantum Mechanics | Simulation Software | Documentation, Uses, and more |
| emacs | Anvil ACES DeltaAI |
Emacs is a highly customizable, extensible, and self-documenting text editor. It is known for its powerful editing capabilities, which include content-aware editing, syntax highlighting, and a wide range of plugins and extensions. | Text Editor, Customizable, Extensible, Self-Documenting | Software Engineering, Computer & Information Sciences | Text Editor | Documentation, Uses, and more |
| emboss | Expanse | EMBOSS is a comprehensive software analysis package for biological sequence data. It provides over 200 tools for sequence alignment, database searching, pattern matching, motif identification, and more. EMBOSS is widely used in bioinformatics and computational biology research. | Bioinformatics, Computational Biology, Sequence Analysis, Biological Data | Bioinformatics, Biological Sciences | Analysis Tool | Documentation, Uses, and more |
| enchant-2 | ACES | Enchant is a spellchecking library that provides a consistent API for invoking spellchecking routines across different platforms. Enchant-2 is the newer version of the Enchant spellchecking framework. | Spellchecking, Library, Cross-Platform, Spellchecking Routines | Computer Science, Computer & Information Sciences | Spellchecking | Documentation, Uses, and more |
| entrezdirect | ACES Expanse |
Entrez Direct (EDirect) is a set of UNIX command-line utilities that provide access to the Entrez databases at the National Center for Biotechnology Information (NCBI). It allows users to retrieve, manipulate, and analyze data from various NCBI databases including PubMed, Gene, and Protein. | bioinformatics, data retrieval, NCBI, command-line tools | Computational Biology, Bioinformatics | Command-line utility | Documentation, Uses, and more |
| esmf | ACES | The Earth System Modeling Framework (ESMF) is a software infrastructure for building and coupling weather, climate, and related Earth science models. It provides a flexible and reusable software architecture that facilitates the use, development, and coupling of Earth science models. | Earth System Modeling, Climate Modeling, Weather Modeling, Model Coupling, Earth Science | Earth & Environmental Sciences, Physical Sciences | Computational Software | Documentation, Uses, and more |
| exiv2 | ACES | Exiv2 is a C++ library and a command-line utility to manage image metadata. It provides fast and easy read and write access to the Exif, IPTC, and XMP metadata of images in various formats. | Metadata Management, Image Processing, Command-Line Utility | Computer Science, Computer & Information Sciences | Metadata Management | Documentation, Uses, and more |
| expat | Anvil ACES DeltaAI KyRIC |
Expat is an XML parser library written in C. It is a fast and lightweight library that is designed for high-performance applications. | Xml Parser, Library | Software Engineering, Computer & Information Sciences | Xml Parser | Documentation, Uses, and more |
| expect | ACES | Expect is a program that "talks" to other interactive programs according to a script. It is used for automating interactive applications such as telnet, ftp, passwd, fsck, rlogin, tip, etc. | Automation, Scripting, Interactive Applications | Software Engineering, Other Computer and Information Sciences | Command Line Tool | Documentation, Uses, and more |
| expecttest | ACES | expecttest is a versatile testing tool for software developers that allows for the automation of interactive applications, system administration tasks, and more. It provides a simple scripting language for driving applications and processes under test, making it easy to automate testing workflows. | Testing Tool, Automation, Scripting, Software Development | Automation Tool | Documentation, Uses, and more | |
| extrae | KyRIC | Extrae is a performance analysis tool designed to capture and analyze trace data from parallel and distributed applications. It allows users to monitor and examine the behavior of their applications in terms of performance, identifying potential bottlenecks and areas for optimization. | Performance Analysis, Trace Data, Parallel Applications, Distributed Applications | Computer Science, Computer & Information Sciences, Software Engineering, Systems & Development, Engineering & Technology, Training, Infrastructure & Instrumentation | Tool | Documentation, Uses, and more |
| eztrace | ACES | eztrace is a tool that provides a set of library calls that can be used to trace the evolution of applications during their execution. It helps in performance analysis by collecting information about function calls, communication patterns, and execution characteristics. | Performance Analysis, Function Call Tracing, Profiling, Monitoring | Computer & Information Sciences | Library Tool | Documentation, Uses, and more |
| fasta | ACES | FASTA is a sequence alignment tool that is used for comparing nucleotide or protein sequences to a database of sequences. | bioinformatics, sequence alignment, genomics | Computational Biology, Genomics | Command-line tool | Documentation, Uses, and more |
| fastahack | ACES | Documentation, Uses, and more | ||||
| fastai | ACES | The fastai library simplifies training fast and accurate neural networks using modern best practices. It is built on top of PyTorch and provides many high-level abstractions to make it easy to train state-of-the-art models with little code. | Deep Learning, Neural Networks, Machine Learning, Pytorch | Artificial Intelligence & Intelligent Systems, Computer & Information Sciences | Machine Learning Framework | Documentation, Uses, and more |
| fastani | ACES | fastANI is a tool for computing average nucleotide identity (ANI) and relatedness between bacterial and archaeal genomes at high speed. It uses MinHash to estimate ANI values in a fraction of the time compared to traditional methods. | Bioinformatics, Genome Comparison, Bacterial Genomes | Biology, Biological Sciences | Genome Analysis Tool | Documentation, Uses, and more |
| fastqc | Anvil ACES Delta |
FastQC is a quality control tool for high throughput sequence data. It provides a detailed overview of the quality and potential issues in sequencing data generated by high throughput sequencing pipelines. | Quality Control, High Throughput Sequencing, Sequence Analysis, Bioinformatics | Biology, Biological Sciences | Analysis Tool | Documentation, Uses, and more |
| fasttext | ACES | Documentation, Uses, and more | ||||
| fasttree | Anvil ACES |
FastTree is a tool for inferring approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences. FastTree can handle alignments with up to a few thousand sequences and has been designed to make trees with the minimum scale up to 100,000 sequences faster by approximating maximum-likelihood with heuristics. | Phylogenetics, Bioinformatics, Computational Biology, Sequence Analysis | Bioinformatics, Biological Sciences | Bioinformatics Tool | Documentation, Uses, and more |
| fastx-toolkit | Anvil | The fastx-toolkit is a collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing. The tools simplify and streamline various tasks related to quality control, adapter trimming, and format conversion of next-generation sequencing data. | Bioinformatics, Ngs Data Processing, Sequence Analysis, Fastq Manipulation | Biology, Biological Sciences | Tool | Documentation, Uses, and more |
| fds | ACES | Fire Dynamics Simulator (FDS) is a computational fluid dynamics (CFD) model designed to simulate fire-driven fluid flow. | CFD, Fire Simulation, Fluid Dynamics, Heat Transfer | Engineering, Fire Dynamics | Simulation Software | Documentation, Uses, and more |
| febio | ACES | Documentation, Uses, and more | ||||
| fermi-lite | ACES | Documentation, Uses, and more | ||||
| fetk | ACES | Documentation, Uses, and more | ||||
| ffmpeg | Anvil ACES DeltaAI Delta Stampede3 |
FFmpeg is a free and open-source software project consisting of a large suite of libraries and programs for handling video, audio, and other multimedia files and streams. | Media Processing, Multimedia, Video, Audio | Computer Science | Tool | Documentation, Uses, and more |
| ffnvcodec | ACES | ffnvcodec is a codec library provided by NVIDIA for efficient video encoding and decoding using the NVIDIA GPU hardware acceleration. | Codec, Video Processing, Gpu Acceleration | Applied Computer Science, Computer & Information Sciences | Library | Documentation, Uses, and more |
| fft | Expanse | The Fast Fourier Transform (FFT) is an algorithm to compute the Discrete Fourier Transform (DFT) and its inverse efficiently. It is widely used in signal processing, image analysis, and solving partial differential equations. | Fourier Transform, Signal Processing, Numerical Methods | Numerical Analysis, Applied Mathematics | Library | Documentation, Uses, and more |
| fftw | Anvil ACES DeltaAI Delta KyRIC |
FFTW is a fast C library for computing the discrete Fourier transform (DFT) in one or more dimensions, of arbitrary input size, and of both real and complex data. It is widely used in areas such as signal processing, data compression, and solving partial differential equations. | Signal Processing, Data Compression, Partial Differential Equations | Applied Mathematics, Mathematics | Computational Software | Documentation, Uses, and more |
| fftw.mpi | ACES | FFTW is a comprehensive collection of fast C routines for computing the Discrete Fourier Transform (DFT) and various generalizations, used in a wide range of applications in computational mathematics, physics, and engineering. | Computational Software, Hpc Tools | Numerical Analysis, Mathematics | Tool | Documentation, Uses, and more |
| fftw2 | Stampede3 | FFTW (Fastest Fourier Transform in the West) is a C library for computing the discrete Fourier transform (DFT) in one or more dimensions, of arbitrary input size, and of both real and complex data. | FFT, Fourier Transform, Numerical Computing, Signal Processing | Numerical Analysis, Applied Mathematics | Library | Documentation, Uses, and more |
| fftw3 | Stampede3 | The Fastest Fourier Transform in the West (FFTW) is an open-source software library for calculating discrete Fourier transforms (DFTs) efficiently. It provides a wide range of algorithms for executing Fourier transforms of various sizes, both real and complex data. | Fft, Fourier Transform, Open-Source, Computational Physics | Condensed Matter Physics, Physical Sciences | Numerical Library | Documentation, Uses, and more |
| fiji | ACES | Fiji is an image processing package, a distribution of ImageJ, bundling a lot of plugins which facilitate scientific image analysis. It is open-source software extensively used in scientific research for image visualization and processing. | Image Processing, Scientific Research, Image Analysis | Bioinformatics, Other Natural Sciences | Analysis Tool | Documentation, Uses, and more |
| file | ACES | File is a command-line utility that performs file type identification. It is commonly used to determine the file type and content of a given file or set of files. | File Management, Command-Line Utility | Computer Science, Software Engineering | Command Line Tool | Documentation, Uses, and more |
| filevercmp | ACES | Documentation, Uses, and more | ||||
| findutils | DeltaAI | findutils is a collection of command-line utilities for searching and processing files on Unix-like systems. It includes tools such as find, xargs, and locate that allow users to search directory hierarchies, filter files based on attributes (name, size, time, permissions), and perform actions on matching files, making it essential for system administration and scripting. | Unix, Linux, file searching, command-line tools, system utilities, shell scripting | Systems Programming, Computer Science | System utility software | Documentation, Uses, and more |
| fiona | ACES | Fiona is a Python library for reading and writing geospatial vector data formats. | Python Library, Geospatial Data, Gis, Vector Data | Geographic Information Systems, Earth & Environmental Sciences | Library | Documentation, Uses, and more |
| firefox | ACES | Mozilla Firefox, commonly known as Firefox, is a free and open-source web browser developed by the Mozilla Foundation and its subsidiary, Mozilla Corporation. It is available for Windows, macOS, Linux, and mobile devices. Firefox focuses on privacy, speed, and customization. | Web Browser, Internet, Privacy, Open-Source, Cross-Platform | Software Engineering, Computer & Information Sciences | Web Browser | Documentation, Uses, and more |
| flac | ACES | Free Lossless Audio Codec (FLAC) is an open-source audio coding format for lossless compression of digital audio. It offers high audio quality and smaller file sizes without losing any information during compression and decompression. | Audio Codec, Open-Source, Lossless Compression | Computer Science, Other Computer & Information Sciences | Compression Tool | Documentation, Uses, and more |
| flann | ACES | FLANN (Fast Library for Approximate Nearest Neighbors) is a library for performing fast approximate nearest neighbor searches in high-dimensional spaces. | Nearest Neighbors, Machine Learning, Data Mining, Approximate Search | Computer Science, Artificial Intelligence and Intelligent Systems | Library | Documentation, Uses, and more |
| flash | ACES | Flash is a multi-purpose computational software that specializes in numerical simulations for fluid dynamics, electromagnetics, structural analysis, and other physics-based applications. It is developed and maintained by the Center for Computational Sciences and Engineering at Lawrence Berkeley National Laboratory. | Computational Software, Numerical Simulation, Fluid Dynamics, Electromagnetics, Structural Analysis | Physical Sciences | Computational Physics | Documentation, Uses, and more |
| flash-attention | ACES | FlashAttention is a highly efficient implementation of the attention mechanism used in transformer models, designed to optimize memory usage and speed, particularly for large-scale models. | Deep Learning, Machine Learning, NLP, Transformers | Computer Science, Artificial Intelligence and Intelligent Systems | Library | Documentation, Uses, and more |
| flask | ACES | Flask is a lightweight and versatile Python web application framework that provides the essentials for building web applications. It is known for its simplicity, flexibility, and ease of use, making it a popular choice for developers. | Web Development, Python, Framework, Web Applications | Software Engineering, Computer & Information Sciences | Open Source | Documentation, Uses, and more |
| flatbuffers | ACES | FlatBuffers is an open-source, cross-platform serialization library for efficient data storage and communication. It allows for storing and accessing serialized data without parsing and generating overhead, making it faster and more memory-efficient than traditional serialization methods. | Serialization, Data Storage, Communication, Efficiency, Cross-Platform | Software Engineering, Computer & Information Sciences | Library | Documentation, Uses, and more |
| flatbuffers-python | ACES | FlatBuffers is a serialization library that allows you to read and write structured data efficiently. The Python implementation provides bindings to work with FlatBuffers in Python applications. | Serialization, Data Structures, Cross-Platform, Performance | Software Engineering, Computer and Information Sciences | Library | Documentation, Uses, and more |
| flex | ACES DeltaAI |
Flex is a fast lexical analyzer generator. It is a tool for creating programs that perform pattern-matching on text. It reads the given input files for a description of a scanner to generate and produces a C source file for the scanner. The output file, lex.yy.c, can then be compiled and linked with the flex runtime library to produce an executable. The resulting executable will scan input files for occurrences of the regular expressions in the scanner description, and perform actions specified in the description. | Lexical Analyzer, Text Processing, Pattern Matching, Scanner Generator | Software Engineering, Other Computer and Information Sciences | Compiler Tool | Documentation, Uses, and more |
| flexiblas | ACES | FlexiBLAS is a lightweight BLAS (Basic Linear Algebra Subprograms) library that aims to provide efficient and flexible implementations of BLAS routines for various hardware platforms. It is designed to optimize performance on CPUs, GPUs, and other accelerators, making it suitable for a wide range of scientific computing applications. | Blas Library, Scientific Computing, Linear Algebra | Other Mathematics | Library | Documentation, Uses, and more |
| flit | ACES | Flit is a simple tool for building and distributing Python packages. | Python Packaging, Package Management | Software Engineering, Computer & Information Sciences | Building & Distribution Tool | Documentation, Uses, and more |
| flook | ACES | Documentation, Uses, and more | ||||
| fltk | ACES | FLTK (Fast, Light Toolkit) is a cross-platform C++ GUI toolkit for developing graphical user interfaces. It provides various widgets and tools for creating interactive and responsive graphical applications. | Gui Toolkit, Cross-Platform Development, C++ Library | Computer Science, Engineering & Technology | Development Tool | Documentation, Uses, and more |
| fmt | ACES | fmt is a modern formatting library for C++ that provides a safe and easy way to format strings. | C++, String Formatting, Library | Software Engineering, Other Computer and Information Sciences | Library | Documentation, Uses, and more |
| fmtlib | Stampede3 | fmtlib is a C++ formatting library that provides a safe and fast way to format strings, similar to Python's `str.format()` or `printf` in C. | C++, String Formatting, Library | Software Engineering, Applied Computer Science | Library | Documentation, Uses, and more |
| font-util | Anvil DeltaAI |
Documentation, Uses, and more | ||||
| fontconfig | Anvil ACES DeltaAI |
Fontconfig is a library designed to provide system-wide font configuration, customization, and management for user interfaces and text display on Linux and other Unix-like operating systems. It allows applications to discover and access fonts, and provides settings for font selection, aliasing, subsetting, and caching. | Fontconfig, Font Management, Font Configuration, Linux, Unix-Like Systems | Software Engineering, Engineering & Technology | System Tool | Documentation, Uses, and more |
| fontsproto | DeltaAI | Documentation, Uses, and more | ||||
| fonttools | ACES | FontTools is a library for manipulating font files, primarily TrueType and OpenType fonts. It allows for the extraction, modification, and creation of font files. | Font Manipulation, OpenType, TrueType, Font Subsetting, Python Library | Software Engineering, Other Computer and Information Sciences | Library | Documentation, Uses, and more |
| foss | ACES | FOSS (Free and Open Source Software) refers to software that is both free to use and distribute, as well as with access to the source code for modification or enhancement by users. | Free Software, Open Source Software, Software Development | Other Computer & Information Sciences | Software Library | Documentation, Uses, and more |
| fosscuda | ACES | FOSSCUDA stands for Free and Open-Source Software for CUDA (Compute Unified Device Architecture) and is a collection of tools and libraries that enable developers to leverage the power of NVIDIA GPUs for parallel computing tasks. | Cuda, Gpu Computing, Parallel Programming, Open-Source | Computer Science, Computer & Information Sciences | Compiler/Library | Documentation, Uses, and more |
| freebayes | ACES | FreeBayes is a Bayesian genetic variant detector designed to find small polymorphisms, specifically SNPs (single-nucleotide polymorphisms), indels (insertions and deletions), and complex events (composite insertion and substitution events) smaller than the length of a short-read sequencing alignment. | Genetic Variant Detector, Snp Detection, Indel Detection, Bayesian Algorithm | Bioinformatics, Biological Sciences | Tool | Documentation, Uses, and more |
| freeglut | ACES | FreeGLUT is a free-software/open-source alternative to the OpenGL Utility Toolkit (GLUT) library. It provides a simple, platform-independent API for creating windows, sub-windows, and menus, as well as handling input from keyboard, mouse, and joystick devices. FreeGLUT aims to be as close to the original GLUT functionality as possible while also improving and extending it. | Graphics Programming, Opengl, Cross-Platform Development, Free Software | Computer Science, Computer & Information Sciences | Graphics Library | Documentation, Uses, and more |
| freeimage | ACES | FreeImage is an open-source graphics library that supports popular image formats and features image loading, saving, conversion, manipulation, and processing capabilities. | Graphics Library, Image Processing, Open-Source | Image Processing, Engineering & Technology | Graphics Library | Documentation, Uses, and more |
| freeipmi | Expanse | FreeIPMI is an open-source BMC (Baseboard Management Controller) software that provides a consistent and reliable interface for managing and monitoring IPMI-compliant systems. It allows administrators to remotely manage server hardware, monitor sensors, power on/off servers, and perform other BMC-related functions. | Bmc, Baseboard Management Controller, Open-Source, Hardware Management, Monitoring | Applied Computer Science, Computer & Information Sciences | Management & Monitoring Tool | Documentation, Uses, and more |
| freesurfer | Expanse | FreeSurfer is a software suite used for the analysis and visualization of structural and functional neuroimaging data from MRI and CT scans. It is widely used in the field of neuroscience and neuroimaging research. | Neuroimaging, Mri Analysis, Brain Segmentation, Functional Mri, Image Visualization | Neuroscience, Biological Sciences | Scientific | Documentation, Uses, and more |
| freetype | Anvil ACES DeltaAI |
FreeType is a software font engine that is designed to be small, efficient, highly customizable, and portable while capable of producing high-quality output (glyph images). It can be used in various applications that require text rendering, such as operating systems, web browsers, desktop publishing tools, and more. | Font Engine, Text Rendering, Typography | Software Engineering, Computer & Information Sciences | Font Engine | Documentation, Uses, and more |
| freexl | ACES | FreeXL is a library to extract data from Excel (.xls) spreadsheet files. The library allows for reading Excel files without the need for Microsoft Excel to be installed. | Excel, Spreadsheet, Data Extraction | Data Management, Computer & Information Sciences | Data Extraction | Documentation, Uses, and more |
| fribidi | ACES DeltaAI |
GNU FriBidi is an implementation of the Unicode Bidirectional Algorithm (bidi). It also provides utility functions to help work with bidirectional text. | Unicode, Bidirectional Algorithm | Natural Language Processing, Computer & Information Sciences | Text Processing | Documentation, Uses, and more |
| fsom | ACES | Documentation, Uses, and more | ||||
| g2clib | ACES | g2clib is a library for the manipulation of geophysical data in the GEMPAK format. It provides routines for reading, writing, and manipulating meteorological and geophysical data. | Geophysics, Meteorology, Data Manipulation, Data Analysis | Earth & Environmental Sciences | Computational Tool | Documentation, Uses, and more |
| g2lib | ACES | g2lib is a C++ library for 2D and 3D geometric computing, mainly focusing on computational geometry and computer graphics. It provides efficient and robust geometric algorithms for various tasks. | Computational Geometry, Computer Graphics, Geometric Computing | Computer & Information Sciences | Computational Software | Documentation, Uses, and more |
| gamess | Stampede3 | The General Atomic and Molecular Electronic Structure System (GAMESS) is a suite of ab initio quantum chemistry programs designed for electronic structure calculations of molecules and molecular reactions. It provides a wide range of methods for both molecules and periodic solids. | Quantum Chemistry, Electronic Structure Calculations, Ab Initio Calculations | Physical Sciences, Chemical Sciences | Quantum Chemistry | Documentation, Uses, and more |
| gatb-core | ACES | GATB-core is a library designed for high-performance bioinformatics applications, particularly for genome assembly and analysis. | bioinformatics, genome assembly, high-performance computing | Computational Biology, Genomics | Library | Documentation, Uses, and more |
| gatk | Anvil ACES |
The Genome Analysis Toolkit (GATK) is a widely used software package for variant discovery and genotyping analysis in high-throughput sequencing data. Developed by the Broad Institute, GATK provides a robust and comprehensive set of tools for processing raw sequencing data into accurate variant calls. | Variant Calling, Genotyping, Sequencing Analysis | Biology, Biological Sciences | Tool | Documentation, Uses, and more |
| gaussian | Stampede3 | Gaussian is a computational chemistry software suite used for electronic structure modeling. It is widely utilized in research and industry for predicting molecular properties and simulating chemical processes. | Computational Chemistry, Quantum Chemistry, Molecular Modeling | Chemical Sciences, Natural Sciences | Simulation Software | Documentation, Uses, and more |
| gawk | KyRIC | Gawk is a powerful text processing utility that allows for pattern scanning and processing. It is based on the Awk programming language and is particularly useful for manipulating text files and generating reports. | Text Processing, Data Manipulation, Pattern Scanning | Chemistry, Computer & Information Sciences | Text Processing Tool | Documentation, Uses, and more |
| gc | ACES | GC is a compiler for the Go programming language. | Compiler, Go, Garbage Collection, Concurrency | Computer Science, Computer & Information Sciences | Programming Language Compiler | Documentation, Uses, and more |
| gcc | Anvil ACES DeltaAI Expanse KyRIC |
GNU Compiler Collection (GCC) is a free and open-source compiler system that supports various programming languages and platforms. It is widely used for compiling high-level programming languages into executable code for a variety of computer architectures. | Compiler, Software Development, Programming | Computer Science | Development Tools | Documentation, Uses, and more |
| gcc compilers | Stampede3 | The GNU Compiler Collection (GCC) is a set of compilers for various programming languages, including C, C++, and Fortran. It is widely used for compiling applications and is an essential tool in many software development environments. | Compiler, Open Source, Development Tool, Cross-Platform | Computer Science | Compiler | Documentation, Uses, and more |
| gcc-native | DeltaAI Delta |
gcc-native is a compiler system produced by the GNU Project supporting various programming languages, most notably C, C++, and Fortran. It is the default compiler for many Unix-like operating systems. | Compiler, Gnu, Programming Language | Computer Science, Computer & Information Sciences | Native Compiler | Documentation, Uses, and more |
| gcc-native-mixed | DeltaAI Delta |
The gcc-native-mixed compiler is a version of the GNU Compiler Collection (GCC) that is specifically optimized for mixed-language programming, allowing developers to combine different programming languages within the same codebase. | Compiler, Mixed-Language Programming, Optimization | Computer Science | Development Tool | Documentation, Uses, and more |
| gcccore | ACES | gcccore refers to the core components of the GNU Compiler Collection (GCC), which is a collection of compilers for several programming languages. These core components provide essential functionality for compiling code and generating executable programs. | Compiler, Programming, Software Development | Computer Science, Computer & Information Sciences, Software Engineering, Systems & Development | Core Component | Documentation, Uses, and more |
| gcccuda | ACES | gcccuda is a wrapper around the GCC C compiler that enables CUDA programming directly in C without the need for NVCC. It allows developers to write CUDA code using familiar C syntax and compile it with the GCC compiler. | Cuda Programming, C Compiler Wrapper, Parallel Computing | Computer Science, Computer & Information Sciences | Development Tool | Documentation, Uses, and more |
| gcloud | ACES | gcloud is a command-line interface for Google Cloud Platform, enabling users to manage resources and applications hosted on Google Cloud. | Cloud Computing, Infrastructure, DevOps, Command Line Tools | Computer Science | Command Line Interface | Documentation, Uses, and more |
| gconf | ACES | GConf is a configuration database system used by GNOME desktop environment and other GNOME software applications to store settings and preferences. It provides a centralized location for storing configuration data, allowing applications to access and update settings easily. | Configuration Management, Settings, Preferences, Desktop Environment | Computer & Information Sciences | Configuration Management System | Documentation, Uses, and more |
| gdal | Anvil ACES DeltaAI Stampede3 |
GDAL (Geospatial Data Abstraction Library) is a translator library for raster and vector geospatial data formats that is released under an X/MIT style Open Source license. It is a collection of geospatial data manipulation libraries that support raster and vector data formats, and includes protocols to access geospatial data sources. | Geospatial Data, Raster Data, Vector Data, Data Formats, Geospatial Analysis | Geographic Information Systems, Earth & Environmental Sciences, Engineering & Technology | Library | Documentation, Uses, and more |
| gdb | Anvil ACES DeltaAI Expanse |
GDB, the GNU Project debugger, allows you to see what is going on 'inside' another program while it executes or what another program was doing at the moment it crashed. | Debugger, Programming, Software Development | Computer Science, Computer & Information Sciences | Debugger | Documentation, Uses, and more |
| gdb4hpc | DeltaAI Delta |
gdb4hpc is a plugin designed to enhance the GNU Debugger (GDB) for High Performance Computing (HPC) applications. It provides additional features to aid in debugging parallel and distributed applications typically used in HPC environments. | Debugging, Hpc, Parallel Programming, Performance Analysis | Computer Science, Engineering & Technology | Plugin | Documentation, Uses, and more |
| gdbm | Anvil DeltaAI KyRIC |
GNU dbm (GDBM) is a library that provides an abstraction for a simple database manager. It allows for the creation and manipulation of key/value pairs in a persistent database, with support for fast lookup, retrieval, insertion, and deletion operations. | Database Management, Key-Value Store, Persistent Storage, Api | Computer Science, Computer & Information Sciences | Library | Documentation, Uses, and more |
| gdc-client | KyRIC | Documentation, Uses, and more | ||||
| gdk-pixbuf | ACES | The GdkPixbuf library provides a way to load images into a program and manipulate those images. It is used by GTK and GNOME applications to handle images. GdkPixbuf supports loading, saving, scaling, compositing, and transforming images, allowing various graphical operations to be performed on the images. | Image Processing, Graphics, Library | Computer Science, Computer & Information Sciences | Image Processing | Documentation, Uses, and more |
| gdown | ACES | gdown is a command-line utility that allows users to download files from Google Drive, particularly files that are too large for direct download links. | Google Drive, File Download, Command Line, Python | Computer Science | Command-line tool | Documentation, Uses, and more |
| gdrcopy | ACES | gdrcopy is a CUDA accelerated GPU memory copy library for NVIDIA GPUs. It provides efficient memory copy operations between host and device memory with the use of asynchronous memory copies and supports different data types for optimal performance. | Gpu Memory Copy, Cuda Acceleration, Asynchronous Memory Copies | Computer Science, Computer & Information Sciences | Memory Management | Documentation, Uses, and more |
| geant4 | ACES | GEANT4 is a toolkit for the simulation of the passage of particles through matter. It is used by a large number of experiments and projects in a variety of application domains, including high energy physics, astrophysics and space science, medical physics, and radiation protection. | Software, Physics, Simulation, Particle Transport | Particle Physics, Physical Sciences | Toolkit | Documentation, Uses, and more |
| geant4-data | ACES | Datasets for Geant4. | Documentation, Uses, and more | |||
| generativemodels | ACES | Project MONAI is a set of open-source, freely available collaborative frameworks built for accelerating research and clinical collaboration in Medical Imaging. The goal is to accelerate the pace of innovation and clinical translation by building a robust software framework that benefits nearly every level of medical imaging, deep learning research, and deployment. | Documentation, Uses, and more | |||
| genomepy | ACES | Genomepy is a Python package for downloading reference genomes and associated annotation files from various sources. It simplifies the process of obtaining genomic data required for bioinformatics analysis. | Genomics, Bioinformatics, Python, Reference Genomes, Sequence Analysis | Genomics, Biological Sciences | Python Library | Documentation, Uses, and more |
| geocube | ACES | Geocube is a Python library for generating interactive 3D visualizations of geospatial data. It is designed to facilitate the creation of immersive and dynamic representations of geospatial information for research, analysis, and presentation purposes. | Geospatial Data, 3D Visualization, Python Library | Earth & Environmental Sciences, Physical Sciences | Python Library | Documentation, Uses, and more |
| geopandas | ACES | Geopandas is an open-source python library for working with geospatial data, enabling users to easily manipulate and analyze geospatial datasets. | Geospatial Data, Python Library, Geospatial Analysis | Geography, Earth & Environmental Sciences | Data Analysis | Documentation, Uses, and more |
| geos | Anvil ACES DeltaAI |
Geos is an open-source geometry engine that provides C++ software libraries and tools for processing spatial data. It is a key component of the PostGIS spatial database extender and is used in various GIS software applications. | Geometry Engine, Spatial Data Processing, Gis, Open-Source | Other Computer & Information Sciences, Computer & Information Sciences | Geospatial Software | Documentation, Uses, and more |
| gettext | Anvil ACES DeltaAI KyRIC |
GNU gettext is a package providing a framework for internationalization and localization of software. It includes tools for extracting translatable strings from source code, for generating message catalogs (pot files), and for translating the strings into different languages. | Internationalization, Localization, Software Development | Software Engineering, Computer & Information Sciences | Localization Tool | Documentation, Uses, and more |
| gfbf | ACES | Gfbf is a compiler for Boolean functions, implemented as an SMT/SAT translation tool. It takes a Boolean function expressed as an algebraic normal form (ANF) as input and produces output in various formats including Conjunctive Normal Form (CNF), Decision Diagrams, and Truth Tables. The tool is designed to efficiently manipulate and analyze Boolean functions for various applications in logic synthesis, verification, and optimization. | Compiler, Boolean Functions, Logic Synthesis, Verification, Optimization | Computer Science, Computer & Information Sciences | Compilation Tool | Documentation, Uses, and more |
| gflags | ACES | gflags is a library that implements commandline flags processing in C++. It provides a simple way to define and parse command-line flags, making it easier to handle user input in command-line applications. | C++, Command-line tools, Library | Software Engineering, Other Computer and Information Sciences | Library | Documentation, Uses, and more |
| gfms | Anvil | Documentation, Uses, and more | ||||
| gh | Expanse | GitHub CLI is a command-line tool that allows users to interact with GitHub directly from the terminal. It simplifies workflows by enabling users to manage repositories, issues, pull requests, and more without leaving the command line. | GitHub, CLI, Version Control, Open Source | Computer Science, Software Engineering | Command Line Interface | Documentation, Uses, and more |
| ghostscript | Anvil ACES |
Ghostscript is a versatile software suite for viewing, converting, and printing PostScript and PDF files. It is widely used for rasterizing files for high-quality printing and viewing on a variety of devices. | Document-Processing, File-Conversion, Print-Management | Computer Science, Computer & Information Sciences, Engineering & Technology | Software Development | Documentation, Uses, and more |
| giflib | ACES | Giflib is a library for reading and writing GIF images. It is a widely used library for handling Graphics Interchange Format (GIF) images in various software applications and programming languages. | Library, Image Processing, Gif Images | Image Processing, Computer Science | Package | Documentation, Uses, and more |
| git | ACES KyRIC |
Git is a distributed version control system designed to handle everything from small to very large projects with speed and efficiency. It is an open-source tool that is widely used for source code management in software development. | Version Control, Software Development, Source Code Management | Computer Science, Computer & Information Sciences, Software Engineering, Systems & Development | Development Tools | Documentation, Uses, and more |
| git-lfs | ACES DeltaAI |
Git Large File Storage (LFS) is a Git extension that reduces the impact of large files in your repository by replacing them with text pointers while storing the actual file content on a remote server. It seamlessly integrates with Git and provides efficient handling of large files, making it easier to work with version-controlled repositories containing large assets. | Version Control, File Storage, Git Extension | Version Control, Engineering & Technology | Development Tool | Documentation, Uses, and more |
| gitpython | ACES | GitPython is a python library used to interact with Git repositories. It provides a high-level API that allows for interfacing with Git commands and repositories directly from Python scripts. | Version Control, Source Code Management, Python Library | Computer Science | Development | Documentation, Uses, and more |
| gklib | ACES Stampede3 |
gklib is a C++ library for geometric kernels that provides efficient and accurate geometric algorithms for computational geometry and related fields. | Geometric Kernels, Computational Geometry, Algorithms | Applied Mathematics, Mathematics | Computational Software | Documentation, Uses, and more |
| gklib-metis | ACES | Documentation, Uses, and more | ||||
| gl2ps | ACES | GL2PS is an OpenGL to PostScript printing library that converts any OpenGL action into a vector PostScript image. It provides capabilities for saving OpenGL-generated 2D and 3D graphics as encapsulated PostScript files. GL2PS is written in C++ and can be easily integrated into existing OpenGL code. | Opengl, Postscript, Printing, Graphics, Vector Graphics | Visualization, Computer Science | Library | Documentation, Uses, and more |
| glew | ACES | The OpenGL Extension Wrangler Library (GLEW) is a cross-platform open-source C/C++ extension loading library. It assists in accessing OpenGL extensions and functions dynamically, providing a simple and lightweight solution for managing OpenGL extensions. | Opengl, Extension Loader, C/C++ Library | Computer Science | Tool | Documentation, Uses, and more |
| glfw | ACES | GLFW is an open-source, multi-platform library for creating windows with OpenGL contexts and managing input. It provides a simple API for creating and managing windows, contexts, and surfaces, receiving input events. GLFW is written in C and provides native support for Windows, macOS, and Linux, as well as experimental support for mobile platforms. | Graphics, Opengl, Cross-Platform, Window Management, Input Handling | Computer Science, Computer & Information Sciences | Development Tool | Documentation, Uses, and more |
| glib | Anvil ACES DeltaAI |
GLib is a general-purpose utility library for the C programming language. It provides data structure handling for lists, trees, hashes, memory allocation, and other commonly needed functionality. | Utility Library, C Programming, Data Structures, Memory Management, Thread Support | Software Engineering, Computer & Information Sciences | Utility | Documentation, Uses, and more |
| glib-networking | ACES | Glib-networking is a set of network-related GIO modules for GLib, providing high-level network access, network diagnostic utilities, and TLS support. It is part of the GNOME project and is commonly used in Linux-based systems. | Glib, Network, Linux, Library | Software Engineering, Computer & Information Sciences | Library | Documentation, Uses, and more |
| glibc | DeltaAI | glibc, the GNU C Library, is an essential part of most systems running the Linux kernel. It provides the necessary functionality for programs written in the C programming language to interact with the operating system and hardware. | C Library, Operating System, System Programming | Computer & Information Sciences | Library | Documentation, Uses, and more |
| glm | ACES | glm is a Python library for Generalized Linear Models (GLM) with support for exponential family distributions. | Python Library | Data Science, Mathematics | Library | Documentation, Uses, and more |
| globalarrays | ACES | Global Arrays (GA) is a Partitioned Global Address Space (PGAS) programming model | Documentation, Uses, and more | |||
| globus-cli | ACES | The globus-cli is a command-line interface tool that provides users with a way to interact with the Globus file transfer service directly from the terminal. It allows for managing transfers, accessing endpoints, and monitoring tasks efficiently through the command line interface. | Command-Line Interface, File Transfer Service, Data Management, Data Transfer | Computer Science, Other Computer & Information Sciences | Command Line Tool | Documentation, Uses, and more |
| glog | ACES | glog is a C++ library that implements a logging framework designed to provide a simple and efficient way to log messages from applications. | C++, Logging, Framework | Software Engineering | Library | Documentation, Uses, and more |
| glpk | ACES | GNU Linear Programming Kit (GLPK) is an open-source software package for solving large-scale linear programming (LP), mixed integer programming (MIP), and other related problems. It is designed with an emphasis on flexibility, portability, and ease of use. | Linear Programming, Optimization, Open-Source | Applied Mathematics, Mathematics | Mathematical Optimization | Documentation, Uses, and more |
| glslang-spirv | ACES | Documentation, Uses, and more | ||||
| gmake | Delta | GNU Make is a tool that controls the generation of executables and other non-source files from a program's source files. It is widely used for managing build processes in software development. | Build Automation, Makefile, Open Source, GNU | Computer Science, Software Engineering | Build System | Documentation, Uses, and more |
| gmap-gsnap | ACES | GMAP and GSnap are splice-aware algorithms for mapping RNA-Seq reads to a genome. GMAP is a genomic mapping and alignment program while GSnap is a sensitive and accurate gapped read mapper. Both tools are commonly used in bioinformatics for RNA-Seq analysis. | RNA-Seq, Bioinformatics, Mapping, Alignment | Biological Sciences | Analysis Tool | Documentation, Uses, and more |
| gmp | Anvil ACES DeltaAI Expanse KyRIC Stampede3 |
The GNU Multiple Precision Arithmetic Library (GMP) is a free library for arbitrary-precision arithmetic, operating on signed integers, rational numbers, and floating-point numbers. | Computational Software, Library, Mathematics, Software Development | Pure Mathematics, Mathematics | Library | Documentation, Uses, and more |
| gmpy2 | ACES | gmpy2 is a Python library for arbitrary-precision arithmetic within Python using the GMP and MPFR libraries. It provides efficient multiple-precision arithmetic in Python and supports both integer and floating-point arithmetic with arbitrary precision. | Python Library, Arbitrary-Precision Arithmetic, Gmp Library, Mpfr Library | Numerical Analysis, Computer & Information Sciences | Python Library | Documentation, Uses, and more |
| gmsh | Stampede3 | GMSH is a three-dimensional finite element mesh generator with a built-in CAD engine and post-processor. | mesh generation, finite element analysis, CAD, post-processing | Engineering, Finite Element Analysis | Mesh Generator | Documentation, Uses, and more |
| gmt | Anvil | The Generic Mapping Tools (GMT) is an open-source collection of command-line tools for manipulating geographic and Cartesian data sets (including filtering, trend fitting, gridding, projecting, etc.) and producing PostScript illustrations ranging from simple x-y plots through contour maps to artificially illuminated surfaces and 3-D perspective views. GMT supports over 40 map projections and transformations and comes with support data such as coastlines, rivers, and political boundaries. | Mapping, Geographic Data, Cartesian Data, Illustration, Postscript, Map Projections | Geography, Earth & Environmental Sciences | Command Line Tool | Documentation, Uses, and more |
| gnu autotools | KyRIC | GNU Autotools is a suite of programming tools designed to assist in making source code packages portable to many Unix-like systems. | Build System, Configuration, Software Development | Software Development, Software Engineering | Build System | Documentation, Uses, and more |
| gnu compiler collection | KyRIC | The GNU Compiler Collection (GCC) is a set of compilers for various programming languages, including C, C++, and Fortran, designed to support a wide range of platforms and architectures. | Compiler, Open Source, Cross-Platform | Computer Science | Compiler | Documentation, Uses, and more |
| gnuconfig | DeltaAI | Documentation, Uses, and more | ||||
| gnuplot | Anvil ACES DeltaAI Expanse Delta Stampede3 |
Gnuplot is a portable command-line driven graphing utility for Linux, OS/2, MS Windows, OSX, VMS, and many other platforms. It is capable of producing interactive plots and supports various output formats. | Graphing, Visualization, Data Analysis | Computational Science, Physical Sciences | Plotting & Data Visualization | Documentation, Uses, and more |
| gnutls | ACES DeltaAI |
GnuTLS is a secure communications library implementing the SSL, TLS and DTLS protocols, providing various cryptographic algorithms. | Security, Encryption, Networking | Cryptography, Computer & Information Sciences | Library | Documentation, Uses, and more |
| go | ACES Expanse KyRIC |
Go is an open-source programming language designed for simplicity and efficiency, particularly in systems programming and web development. | Programming Language, Open Source, Concurrency, Systems Programming | Software Engineering, Computer Science | Programming Language | Documentation, Uses, and more |
| go-bootstrap | KyRIC | go-bootstrap is a Go programming language template project that provides a starting point for building Go applications with a predefined project structure, configuration, and best practices. | Go, Template, Project Structure, Best Practices | Engineering & Technology | Template Project | Documentation, Uses, and more |
| gobject-introspection | ACES DeltaAI |
GObject Introspection is a middleware layer between C libraries (using GObject) and language bindings. The goal is to make the C libraries accessible from scripting languages and other environments without the need for manual intervention. | Middleware, Language Bindings, Automation, Compatibility | Computer Science, Computer & Information Sciences | Library | Documentation, Uses, and more |
| gomkl | ACES | GOMKL is a library that provides optimized mathematical routines for high-performance computing applications, particularly those that require linear algebra operations. | High-Performance Computing, Linear Algebra, Mathematics, Optimization | Applied Mathematics, Mathematics | Library | Documentation, Uses, and more |
| gompi | ACES | Gompi is a parallel computing software tool that provides a set of compilers and libraries for running MPI (Message Passing Interface) programs on HPC (High Performance Computing) clusters. It aims to enhance the performance of parallel applications by optimizing communication and coordination between nodes in distributed computing environments. | Hpc, Parallel Computing, Mpi, Distributed Computing | Engineering & Technology | Documentation, Uses, and more | |
| gompic | ACES | gompic is an open-source framework for simulating collective dynamics in soft matter systems with a focus on granular materials. It is designed to simulate the dynamics of large ensembles of particles undergoing complex interactions and can be used to study phenomena like granular flow, pattern formation, and self-organization. | Simulation, Granular Materials, Collective Dynamics, Soft Matter | Other Physical Sciences, Physical Sciences | Research | Documentation, Uses, and more |
| googlebenchmark | ACES | Documentation, Uses, and more | ||||
| googletest | ACES | Google Test is a unit testing library for the C++ programming language. It is designed to be easy to write and understand tests, provides a rich set of assertions for verifying test expectations, and supports various testing styles. | Unit Testing, C++ Testing, Testing Library, Software Testing | Software Engineering, Computer & Information Sciences | Library | Documentation, Uses, and more |
| gotranseq | ACES | Documentation, Uses, and more | ||||
| gpaw | ACES | GPAW (Grid-based Projector-augmented wave method) is an efficient and accurate Density Functional Theory (DFT) code based on the projector-augmented wave (PAW) method. It is designed for simulating the electronic structure of atoms, molecules, and solid materials. | Dft, Electronic Structure, Quantum Mechanics | Condensed Matter Physics, Physical Sciences | Simulation | Documentation, Uses, and more |
| gpaw-setups | ACES | Documentation, Uses, and more | ||||
| gperf | ACES DeltaAI |
GNU gperf is a perfect hash function generator tool that generates perfect hash functions for sets of keys, optimized for use in constructing a minimal perfect hash table. | Perfect Hash Function, Hash Table, Optimization, Gnu | Computer Science, Computer & Information Sciences | Compiler/Generator | Documentation, Uses, and more |
| gperftools | ACES | gperftools is a collection of performance analysis and profiling tools for C and C++ applications. It includes tools such as CPU and heap profilers, heap-checker, and a specialized CPU profiler for multithreaded programs. | Performance Analysis, Profiling, C/C++ | Software Engineering, Engineering & Technology | Tool | Documentation, Uses, and more |
| gpflow | ACES | GPflow is a Gaussian process library that uses TensorFlow for its core computational backend. It is a scalable, flexible, and modular Gaussian process framework for building probabilistic models. | Machine Learning, Probabilistic Programming, Gaussian Processes | Machine Learning, Computer & Information Sciences, Artificial Intelligence & Intelligent Systems | Library | Documentation, Uses, and more |
| gpgme | ACES | GPGME (GnuPG Made Easy) is a C library that allows the use of GnuPG (GNU Privacy Guard) for encryption and signing of data and communications. It provides a high-level interface to GnuPG, making it easier to integrate cryptographic functions into applications. | Cryptography, Security, Encryption, OpenPGP, S/MIME | Cryptography, Computer Science | Library | Documentation, Uses, and more |
| gpu | Expanse | GPU, short for Graphics Processing Unit, is a specialized electronic circuit designed to rapidly manipulate and alter memory to accelerate the creation of images in a frame buffer intended for output to a display device. In recent years, GPUs have been leveraged for general-purpose computing, allowing for massive parallel processing capabilities. | Software, Computational Software, Hpc Tools, Gpu, Parallel Processing | Engineering & Technology, Computer & Information Sciences | Hardware | Documentation, Uses, and more |
| gpustat | ACES | gpustat is a Python library that gives an easy access to the GPU-related data, such as GPU utilization, memory usage, temperature, and power. It provides a command-line interface for quickly checking the status of GPUs in a system. | Gpu Monitoring, System Administration, Python Library, Command-Line Tool | Computer Science, Engineering & Technology | Library | Documentation, Uses, and more |
| gpytorch | ACES | GPyTorch is a Gaussian process library implemented using PyTorch. It is designed for scalable and flexible Gaussian process models, with a focus on deep learning integration. | Machine Learning, Gaussian Processes, Deep Learning | Machine Learning, Computer & Information Sciences | Python Library | Documentation, Uses, and more |
| grads | Anvil | GrADS (Grid Analysis and Display System) is an interactive desktop tool that is used for easy access, manipulation, and visualization of earth science data. It is particularly popular in meteorology and climatology for analyzing and plotting meteorological data. | Data Visualization, Meteorology, Climatology, Earth Science, Data Analysis | Meteorology, Earth & Environmental Sciences | Desktop Application | Documentation, Uses, and more |
| graphblas | ACES | GraphBLAS is a collection of high-performance linear algebraic operations specifically designed for sparse graphs and matrices. | Graph, Linear Algebra, Sparse Matrices | Computer Science, Computer & Information Sciences | Library | Documentation, Uses, and more |
| graphene | ACES | Graphene is a Python library for building GraphQL APIs fast and easily. | Python Library, Graphql | Computer & Information Sciences | Library | Documentation, Uses, and more |
| graphicsmagick | ACES | GraphicsMagick is a robust collection of tools and libraries that offers a comprehensive range of image processing capabilities. It provides a powerful utility for dynamically reading, writing, and modifying images for over 88 major formats. | Image Processing, Graphics, Media Editing, Command-Line Tools | Image Processing, Other Computer & Information Sciences | Image Processing Software | Documentation, Uses, and more |
| graphite2 | ACES | Graphite is a system that can be used to create 'smart fonts' capable of displaying writing systems with various complex behaviors. Graphite fonts are capable of providing contextual forms, reordering, ligatures, and other advanced typographic behavior. | Font Rendering, Typography, Smart Fonts | Computer Science, Computer & Information Sciences | Library | Documentation, Uses, and more |
| graphviz | ACES | Graphviz is open source graph visualization software. It is used for creating structured diagrams such as flowcharts, network diagrams, and more. | Graph Visualization, Diagramming, Open Source Software | Graph Theory, Computer & Information Sciences | Data Visualization | Documentation, Uses, and more |
| graphviz-python | ACES | graphviz-python is a Python library for creating and rendering graph visualizations using Graphviz. It provides a simple interface to create and manipulate graphs and visualize them in various formats. | Graph Visualization, Python Library, Network Analysis | Visualization and Human-Computer Systems, Computer & Information Sciences | Visualization Tool | Documentation, Uses, and more |
| grass | ACES | Documentation, Uses, and more | ||||
| great_tables | ACES | Documentation, Uses, and more | ||||
| greenlet | ACES | Greenlet is a lightweight library that allows micro-threads to be utilized in a concurrent programming fashion within a single process. It provides a simple way to implement coroutines in Python. | Python Library, Concurrency, Coroutines | Software Engineering, Computer & Information Sciences | Programming | Documentation, Uses, and more |
| groff | ACES | Groff (GNU troff) is a typesetting system that reads plain text mixed with formatting commands and produces formatted output. It's a modern implementation of the classic Unix troff typesetting system. | Typesetting, Text Formatting, Unix Utilities | Computer Science, Computer & Information Sciences | Typesetting System | Documentation, Uses, and more |
| gromacs | Anvil ACES DeltaAI Delta KyRIC Stampede3 |
GROMACS (GROningen MAssive Parallel MD for Molecular Dynamics) is a versatile package for molecular dynamics simulations with a strong emphasis on high-performance computing capabilities. | Molecular Dynamics, Simulation, High Performance Computing, Biomolecular Systems | Chemistry, Biological Sciences | Molecular Dynamics Software | Documentation, Uses, and more |
| grpcio | ACES | gRPC is a high-performance, open-source universal RPC framework that leverages HTTP/2 for transport, Protocol Buffers as the interface description language, and it provides features such as authentication, load balancing, and more. | RPC, Networking, Microservices, Distributed Systems | Software Engineering, Computer Science | Library | Documentation, Uses, and more |
| gsl | Anvil ACES DeltaAI Delta Stampede3 |
The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers. It provides a wide range of mathematical routines such as special functions, linear algebra, interpolation, numerical integration, random numbers, and more. | Numerical Library, Mathematical Functions, C Programming, C++ Programming | Mathematics, Other Mathematics | Library | Documentation, Uses, and more |
| gslib | ACES | gslib is an open-source and free collection of Fortran 77 subroutines for geostatistical applications. | Geostatistics, Fortran 77, Spatial Data, Variogram Modeling, Kriging | Geoscience, Earth & Environmental Sciences | Geospatial Analysis Tool | Documentation, Uses, and more |
| gst-plugins-bad | ACES | gst-plugins-bad is a collection of GStreamer plugins and elements that are not of high quality, experimental, or have not been tested well. These plugins are considered 'bad' due to various reasons such as being incomplete, breaking or lacking proper documentation. | Multimedia, Plugin, Gstreamer | Computer Science, Computer & Information Sciences | Plugin | Documentation, Uses, and more |
| gst-plugins-base | ACES | gst-plugins-base is a collection of GStreamer plugins and elements, which serve as the base for GStreamer. These plugins provide essential functionalities for building audio and video processing pipelines in GStreamer-based applications. | Audio Processing, Video Processing, Multimedia Framework | Computer Science, Computer & Information Sciences | Plugin | Documentation, Uses, and more |
| gstreamer | Anvil ACES |
GStreamer is a multimedia framework that allows the construction of graphs of media-handling components, ranging from simple Ogg/Vorbis playback to complex audio (mixing) and video (non-linear editing) processing. It is designed to be easily extended with new plugins that provide new functionality. | Multimedia, Framework, Media Processing, Audio, Video | Software Engineering, Computer & Information Sciences | Framework | Documentation, Uses, and more |
| gtk2 | ACES | GTK2 is a cross-platform widget toolkit for creating graphical user interfaces. It is used in a variety of applications to provide a user-friendly interface. | Gui, Widget Toolkit, Cross-Platform | Biology, Computer & Information Sciences | Gui Toolkit | Documentation, Uses, and more |
| gtk3 | ACES | GTK3 is a widely-used toolkit for building graphical user interfaces and desktop applications. It provides a comprehensive set of tools and libraries for creating interactive and visually appealing applications across multiple platforms. | Gui Toolkit, Desktop Application Development, Cross-Platform Development, User Interface Design | Biology, Computer & Information Sciences | Development Toolkit | Documentation, Uses, and more |
| gtk4 | ACES | GTK4 is a multi-platform toolkit for creating graphical user interfaces. It is used for developing applications with a consistent look and feel across different operating systems. | Gui Toolkit, Cross-Platform Development, User Interface Design | Biology, Computer & Information Sciences | Development Tool | Documentation, Uses, and more |
| gts | ACES | GNU Triangulated Surface Library (GTS) is a free library for computational geometry. It includes many useful functions for calculating surface properties and constructing complex surfaces using triangulations. | Computational Geometry, Surface Properties, Mesh Generation | Computer & Information Sciences | Computational Software | Documentation, Uses, and more |
| guile | ACES | Guile is an implementation of the Scheme programming language, providing a flexible and embeddable scripting environment for applications. It aims to be a platform for creating applications and libraries that require customizations and extensibility. | Programming Language, Scripting Language, Embeddable, Customizable | Software Engineering, Computer & Information Sciences | Interpreter | Documentation, Uses, and more |
| gurobi | Anvil Delta |
Gurobi Optimization is a high-performance mathematical programming solver for linear programming (LP), mixed-integer programming (MIP), and other related optimization problems. | Optimization, Mathematical Programming, Linear Programming, Mixed-Integer Programming | Optimization, Mathematics | Solver | Documentation, Uses, and more |
| gymnasium | ACES | Gymnasium is a Python library which provides tools and utilities for creating and manipulating complex mathematical expressions and equations. | Python Library, Mathematical Expressions, Equation Manipulation | Computer Science, Mathematics | Programming Library | Documentation, Uses, and more |
| gzip | ACES DeltaAI Delta |
gzip is a file compression and decompression tool used to reduce the size of files for storage or transfer purposes. It is a widely used compression utility in Unix-like operating systems. | File Compression, Data Storage, Data Transfer | Computer Science, Engineering & Technology | Compression Tool | Documentation, Uses, and more |
| h5py | ACES | h5py is a Python library providing a high-level interface to the HDF5 library. It allows you to store huge amounts of numerical data and easily manipulate that data from NumPy. | Python Library, Data Storage, Numerical Data, Data Manipulation | Computational Science, Computer & Information Sciences | Library | Documentation, Uses, and more |
| hadoop | Anvil Expanse |
Hadoop is an open-source framework used for distributed storage and processing of large sets of data on computer clusters using simple programming models. | Big Data, Data Processing, Distributed Computing | Computer Science, Computer & Information Sciences | Framework | Documentation, Uses, and more |
| harfbuzz | ACES DeltaAI |
HarfBuzz is an open-source text shaping engine. It is used to convert Unicode text to beautifully formatted and language-appropriate glyphs. HarfBuzz focuses on providing correct script shaping for complex scripts and languages. | Text Shaping Engine, Unicode Text, Text Layout, Font Features Customization | Software Engineering, Computer & Information Sciences | Library | Documentation, Uses, and more |
| hatch-jupyter-builder | ACES | Documentation, Uses, and more | ||||
| hatchling | ACES | Hatchling is a software tool designed for simulating and analyzing population dynamics in ecological studies, particularly focusing on early life stages of organisms such as fish, amphibians, and invertebrates. It allows researchers to model various environmental factors affecting the survival and growth of hatchlings in different ecosystems. | Population Dynamics, Ecology, Simulation, Environmental Factors | Environmental Biology, Biological Sciences | Research Tool | Documentation, Uses, and more |
| hdf | Anvil ACES |
HDF (Hierarchical Data Format) is a flexible and extensible file format for storing and managing large amounts of data. It supports various data types, attributes, and metadata, making it suitable for a wide range of scientific and engineering applications. | Data Management, File Format, Data Visualization, Api | Data Management, Other Computer & Information Sciences | File Format | Documentation, Uses, and more |
| hdf-eos | ACES | HDF-EOS (Hierarchical Data Format - Earth Observing System) is a software library developed by NASA for managing and processing Earth science data in the HDF (Hierarchical Data Format) format. | Data Management, Data Processing, Earth Science, Geospatial Data | Earth & Environmental Sciences, Physical Sciences | Library | Documentation, Uses, and more |
| hdf-eos5 | ACES | HDF-EOS5 is a software library developed by NASA that provides tools and interfaces for working with EOS (Earth Observing System) data in the Hierarchical Data Format (HDF5) format. It is specifically designed for the management and analysis of Earth science data collected by various NASA missions. | Nasa, Earth Observing System, Data Management, Data Analysis, Hdf5 Format | Earth & Environmental Sciences, Natural Sciences | Data Management & Analysis | Documentation, Uses, and more |
| hdf5 | Anvil ACES DeltaAI Expanse Delta Stampede3 |
HDF5 (Hierarchical Data Format version 5) is a file format and a suite of tools developed by the HDF Group for managing and storing large and complex data. It is designed to store and organize large amounts of data efficiently, enabling fast data access and sharing. | File Format, Data Management, Data Storage, Data Sharing, High-Performance Computing | Computational Science, Other Computer & Information Sciences | Library/Tool | Documentation, Uses, and more |
| hdf5-parallel | DeltaAI Delta |
HDF5 Parallel is an extension of the HDF5 library that allows for parallel I/O operations, enabling efficient data access and manipulation in high-performance computing environments. | HDF5, Parallel Computing, Data Management, High Performance Computing | High-Performance Computing, Data Management | Library | Documentation, Uses, and more |
| hdf5_18 | Expanse | HDF5 is a file format and set of tools for managing complex data. It is designed to store and organize large amounts of data and is widely used in scientific computing. | Data Management, File Format, Scientific Computing | Data Science, Computer Science | Library | Documentation, Uses, and more |
| heffte | ACES | HeFFTe is a high-performance Fast Fourier Transform (FFT) library designed for distributed memory systems. It leverages advanced algorithms to optimize FFT computations on large datasets, making it suitable for scientific computing applications. | FFT, High Performance Computing, Distributed Computing, Scientific Computing | High-Performance Computing, Numerical Analysis | Library | Documentation, Uses, and more |
| help2man | ACES | help2man is a tool that can generate simple man pages from the '--help' and '--version' output of other commands. | Documentation, Man Pages, Automation | Software Engineering, Systems & Development, Engineering & Technology | Utility | Documentation, Uses, and more |
| hf-datasets | ACES | Documentation, Uses, and more | ||||
| hh-suite | ACES | HH-suite is a software package for sensitive protein sequence searching based on profile hidden Markov models. It includes tools for the alignment of protein sequences, detecting remote homologs, and predicting protein structures. | Protein Sequence Searching, Profile Hidden Markov Models, Protein Structure Prediction | Bioinformatics, Biological Sciences | Computational Software | Documentation, Uses, and more |
| highfive | Stampede3 | Documentation, Uses, and more | ||||
| highway | ACES | HighWay is an open-source statistical software tool designed for the identification of driver genes and pathways in cancer based on the analysis of somatic mutations across a cohort of tumor samples. | Bioinformatics, Computational Biology, Statistical Analysis | Bioinformatics, Biological Sciences | Statistical Tool | Documentation, Uses, and more |
| hipify | ACES | Hipify is a tool that converts CUDA code to HIP (Heterogeneous-compute Interface for Portability) code, allowing developers to port their applications from NVIDIA GPUs to AMD GPUs. | CUDA, HIP, GPU programming, Portability | Computer Science, Software Engineering | Conversion Tool | Documentation, Uses, and more |
| hiredis | ACES | Hiredis is a minimalistic C client library for the Redis database, offering a simple interface to interact with Redis servers from C-based applications. It aims to maintain an API that is both high-performance and easy to use, providing basic functionality to communicate with Redis servers. | Redis, Database, C Library | Computer Science, Computer & Information Sciences | Library | Documentation, Uses, and more |
| hisat2 | ACES Delta |
HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA) against the general human population (as well as against a single reference genome). It builds on HISAT and Bowtie, allowing for significantly improved performance and new capabilities. | Alignment, Ngs, Genomics, Transcriptomics | Biology, Biological Sciences | Alignment Tool | Documentation, Uses, and more |
| hmmer | ACES Stampede3 |
Hmmer is a software suite used for protein sequence analysis based on profile hidden Markov models (HMMs). It is widely used for searching sequence databases for homologs of protein sequences, identifying conserved protein domains, and annotating protein sequences based on sequence alignment. | Bioinformatics, Computational Biology, Proteomics, Sequence Analysis | Bioinformatics, Biological Sciences | Bioinformatics Tool | Documentation, Uses, and more |
| horovod | ACES | Horovod is a distributed deep learning training framework for TensorFlow, Keras, PyTorch, and MXNet. It significantly improves the speed and scale of distributed deep learning training. | Deep Learning, Distributed Training, Machine Learning, Gpu Acceleration, High Performance Computing | Machine Learning, Computer & Information Sciences | Library/Framework | Documentation, Uses, and more |
| hpc-x | ACES | hpc-x is a high-performance computing (HPC) software package designed to provide optimized libraries, tools, and compilers for scientific computing on HPC systems. It aims to enhance the performance and efficiency of parallel computing applications on modern HPC architectures. | Hpc, High-Performance Computing, Scientific Computing, Parallel Computing | Engineering & Technology | Hpc Tools | Documentation, Uses, and more |
| hpctoolkit | Anvil | HPCToolkit is a performance analysis tool for high-performance computing applications. It provides a comprehensive suite of tools for profiling, tracing, and analyzing the performance of parallel applications. | performance analysis, profiling, high-performance computing, parallel computing | Computer Science | Analysis Tool | Documentation, Uses, and more |
| hpl | ACES | The High Performance Linpack (HPL) benchmark is a tool for analyzing and ranking the performance of computer systems, particularly supercomputers. It measures the floating-point rate of execution for solving a dense system of linear equations. HPL is widely used to assess and compare the computational performance of High Performance Computing (HPC) systems. | Hpc, Benchmarking, Performance Analysis | Infrastructure & Instrumentation, Engineering & Technology | Benchmarking Tool | Documentation, Uses, and more |
| hprc_utils | ACES | hprc_utils is a collection of utility tools for managing and analyzing High Performance Computing (HPC) environments and workflows. | Hpc, High Performance Computing, Utility Tools | Engineering & Technology | Tool | Documentation, Uses, and more |
| htop | DeltaAI Delta |
htop is an interactive system-monitor process-viewer for Unix systems. It provides a detailed overview of system performance and resource usage in a visually appealing and user-friendly interface. | System Monitoring, Process Viewer, Resource Usage | Systems, Engineering & Technology | Monitoring Tool | Documentation, Uses, and more |
| htseq | ACES | HTSeq is a Python library that provides efficient tools to work with high-throughput sequencing data. It offers functionalities to process and analyze sequence data from RNA-Seq experiments, particularly for quantification of gene and transcript expression levels. | Bioinformatics, RNA-Seq, High-Throughput Sequencing, Gene Expression, Sequence Data | Bioinformatics, Biological Sciences | Bioinformatics Tool | Documentation, Uses, and more |
| htslib | ACES Delta |
HTSlib is a C library for processing high-throughput sequencing data in the form of SAM, BAM, and CRAM formats. It allows for efficient reading, writing, and manipulation of such files, as well as various operations such as format conversion, indexing, and retrieval of specific sequences. | Bioinformatics, Sequencing Data, File Format Processing, C Library | Genomics, Biological Sciences | Data Processing | Documentation, Uses, and more |
| httpx | ACES | Documentation, Uses, and more | ||||
| huggingface_hub | ACES | The Hugging Face Hub is a platform for sharing and discovering machine learning models and datasets. It provides tools for model versioning, collaboration, and integration with various machine learning frameworks. | Machine Learning, Natural Language Processing, Deep Learning, Model Hub, Datasets | Machine Learning, Natural Language Processing | Library | Documentation, Uses, and more |
| humann | ACES | HUMAnN (HMP Unified Metabolic Analysis Network) is a tool for efficiently and accurately profiling the presence and abundance of microbial pathways in a community from metagenomic shotgun sequencing data. It combines sequence alignment and gene activity profiling to quantify the presence of pathway modules. | Metagenomics, Microbiome, Pathway Analysis, Bioinformatics | Biological Sciences | Analysis Tool | Documentation, Uses, and more |
| hunspell | ACES | Hunspell is a spell checker and morphological analyzer software designed for languages with rich morphology and complex word compounding. | Spell Checker, Morphological Analyzer, Language Support | Computational Linguistics, Other Computer & Information Sciences | Utility | Documentation, Uses, and more |
| hwloc | Anvil ACES Expanse KyRIC |
hwloc, the Portable Hardware Locality (hwloc), is an open-source hierarchical machine topology library used to provide abstract representation of the hierarchical topology of modern architectures. | Machine Topology, Hardware Architecture, System Software | Computer Science, Computer & Information Sciences | Library | Documentation, Uses, and more |
| hydra | ACES | Documentation, Uses, and more | ||||
| hyper-shell | Anvil | hyper-shell is a command-line terminal replacement that aims to enhance the user experience and productivity through various features and customizations. | Terminal Emulator, Productivity Tool, Command-Line Interface | Computer & Information Sciences | Command-Line Tool | Documentation, Uses, and more |
| hyperopt | ACES | Hyperopt is a Python library for optimizing over arbitrary search spaces. The main goal of Hyperopt is to provide a flexible and expressive architecture for an optimization workforce, including hyperparameter optimization, machine learning and statistics. | Optimization, Machine Learning, Statistics | Artificial Intelligence, Computer & Information Sciences | Library | Documentation, Uses, and more |
| hypershell | Anvil | Documentation, Uses, and more | ||||
| hypothesis | ACES | Hypothesis is a property-based testing tool for Python that helps in finding edge cases and identifying bugs by generating test data based on properties and invariants. | Python Testing Tool, Property-Based Testing, Automated Test Generation | Computer Science, Computer & Information Sciences | Property-Based Testing Tool | Documentation, Uses, and more |
| hypre | ACES Stampede3 |
HYPRE (High Performance Preconditioners) is a library of high performance preconditioners and solvers for the solution of large, sparse linear systems of equations on massively parallel computers. It provides scalable algorithms for solving large-scale scientific and engineering applications. | Preconditioners, Solvers, Linear Systems, Sparse Matrices | Applied Mathematics, Mathematics | Computational Software | Documentation, Uses, and more |
| iaf2 | ACES | Documentation, Uses, and more | ||||
| iccifort | ACES | iccifort is a software tool that provides the Intel C++ and Fortran compilers for high-performance computing applications. These compilers are designed to optimize code performance for Intel processors. | Compiler, High-Performance Computing, Optimization | Engineering & Technology | Programming Tool | Documentation, Uses, and more |
| icon | ACES | Documentation, Uses, and more | ||||
| icu | ACES | ICU (International Components for Unicode) is a mature, widely used set of C/C++ and Java libraries providing Unicode and Globalization support for software applications. ICU is utilized in a vast array of applications, operating systems, and devices to provide multilingual support. | Unicode Support, Globalization, Localization, Internationalization, Unicode Libraries | Software Engineering, Computer & Information Sciences | Libraries | Documentation, Uses, and more |
| icu4c | DeltaAI KyRIC |
ICU (International Components for Unicode) is a mature, widely used set of C/C++ and Java libraries providing Unicode and Globalization support for software applications. ICU is widely portable and gives applications the same results on all platforms and between C/C++ and Java software. | Unicode, Globalization, Cross-Platform, Libraries | Software Engineering, Computer & Information Sciences | Development | Documentation, Uses, and more |
| idev | Stampede3 | idev is a compiler wrapper that simplifies the use of Intel's data parallel C++ (DPC++) compiler for offloading computations to GPUs. | Compiler Wrapper, Dpc++ Compiler, Gpu Offloading | Computer Science, Computer & Information Sciences | Tool | Documentation, Uses, and more |
| idl | Expanse Stampede3 |
IDL (Interactive Data Language) is a programming language used for data analysis, visualization, and application development. It provides a comprehensive set of tools for scientific research and data processing. | Software, Data Analysis, Data Visualization, Scientific Research | Data Analysis, Physical Sciences | Programming Language | Documentation, Uses, and more |
| igprof | ACES | igprof is a lightweight, portable, and flexible performance profiling tool for C, C++, and Fortran applications. It provides insights into code performance and helps identify hotspots for optimization, with a focus on low-overhead and accurate measurements. | Profiler, Performance Analysis, Code Optimization, Software Development | Software Engineering, Engineering & Technology | Tool | Documentation, Uses, and more |
| iimpi | ACES | IIMPI (Isobaric Ion Mobility Mass Spectrometry with Peak Integration) is a software tool specifically designed for analyzing ion mobility-mass spectrometry data with a focus on accurate peak integration in the presence of isobaric co-elution. | Ion Mobility-Mass Spectrometry, Peak Integration, Data Analysis | Bioinformatics, Biological Sciences | Analytical Tool | Documentation, Uses, and more |
| ijulia | ACES | iJulia is an interactive notebook interface for the Julia programming language, enabling users to create and share documents that contain live code, equations, visualizations, and narrative text. | Julia, Notebooks, Interactive Computing, Data Science, Scientific Computing | Computational Science, Data Science | Interactive Notebook | Documentation, Uses, and more |
| imageio | ACES | Imageio is a Python library that provides an easy interface to read and write a wide range of image and video file formats. It allows for simple, high-level access to image data from Python code. | Python Libraries, Image Processing, Data Visualization | Applied Computer Science, Computer & Information Sciences | Python Library | Documentation, Uses, and more |
| imagej | ACES | ImageJ is a public domain, Java-based image processing program developed at the National Institutes of Health. It is widely used for scientific image analysis and visualization. | Image Processing, Scientific Tool, Java-Based, Open-Source | Computational Biology, Biochemistry and Molecular Biology | Image Processing Software | Documentation, Uses, and more |
| imagemagick | ACES Delta |
ImageMagick is a free and open-source software suite for creating, editing, composing, or converting bitmap images. | Image Processing, Graphics Editing, Conversion Tool | Image Processing, Computer & Information Sciences | Utility | Documentation, Uses, and more |
| imagenet | ACES Delta |
Documentation, Uses, and more | ||||
| imake | ACES | imake is a software tool that automates the construction of imakefiles, which are used with the make utility in software development projects. It simplifies the process of generating makefiles for building software projects, allowing developers to focus on writing code rather than manually creating build configurations. | Build Automation, Software Development, Build Configuration | Software Engineering, Systems & Development, Engineering & Technology | Automation Tool | Documentation, Uses, and more |
| imath | ACES | iMath is a comprehensive computational software for mathematical modeling, simulation, and analysis. It provides a user-friendly interface for performing various mathematical and statistical computations. | Mathematics, Computational Software, Simulation, Data Analysis | Mathematics | Mathematical Modeling & Analysis Software | Documentation, Uses, and more |
| imb | KyRIC | IMB stands for In-Memory Database benchmark. It is a benchmarking tool specifically designed to evaluate the performance of in-memory databases. | Benchmarking, In-Memory Databases | Computer & Information Sciences | Tool | Documentation, Uses, and more |
| imbalanced-learn | ACES | Imbalanced-learn is a Python library designed to tackle the problem of imbalanced datasets in machine learning. It provides a set of tools and techniques to deal with classification tasks where the distribution of classes is skewed, with one class significantly more frequent than the others. | Imbalanced Datasets, Machine Learning, Classification Tasks, Python Library, Over-Sampling, Under-Sampling, Ensemble Techniques | Artificial Intelligence & Intelligent Systems, Computer & Information Sciences | Python Library | Documentation, Uses, and more |
| imkl | ACES | imkl is a open-source software library for creating and managing knowledge graphs for various applications in artificial intelligence, data science, and information retrieval. | Software Library, Knowledge Graph, Artificial Intelligence, Data Science, Information Retrieval | Computer & Information Sciences, Artificial Intelligence & Intelligent Systems | Open-Source | Documentation, Uses, and more |
| imkl-fftw | ACES | imkl-fftw is a library that combines Intel Math Kernel Library (IMKL) with FFTW (Fastest Fourier Transform in the West) for high-performance computation of Fourier transforms on Intel architectures. | Software Library, Math Library, Mathematical Computation, Fourier Transforms, High-Performance Computing | Mathematics | Mathematical Computation | Documentation, Uses, and more |
| iml | ACES | Interpretable Machine Learning | Machine Learning, Interpretability, Model Explanation | Computer & Information Sciences | R Package | Documentation, Uses, and more |
| impi | Anvil ACES |
impi is a high-performance message passing library that provides asynchronous messaging and queuing functionalities for parallel computing applications. | Message Passing Library, Parallel Computing, Asynchronous Messaging | High-Performance Computing, Engineering & Technology | Communication Library | Documentation, Uses, and more |
| impute2 | Delta | IMPUTE2 is a tool for imputing ungenotyped markers in large-scale genome-wide association studies. | Genotype Imputation, Genome-Wide Association Studies, Bioinformatics | Genetics, Biological Sciences | Tool | Documentation, Uses, and more |
| infernal | ACES | Infernal is a software for searching DNA sequence databases for RNA structure and sequence similarities. It is used to align RNA sequences to RNA sequence and structural models. | RNA Sequence Analysis, Bioinformatics, Sequence Alignment | Bioinformatics, Biological Sciences | Command-line tool | Documentation, Uses, and more |
| init_opencl | KyRIC | init_opencl is a software library that is used to initialize OpenCL platforms and create OpenCL contexts for parallel computing applications. | Software, Compiler, Library, Hpc | Computer & Information Sciences | Software Development | Documentation, Uses, and more |
| inputproto | DeltaAI | A package that provides the headers used to compile Xlib clients. | Software Development, Headers, Xlib | Computer & Information Sciences | Library | Documentation, Uses, and more |
| inspector | KyRIC | Inspector is a software tool used for monitoring and analyzing various aspects of computer systems and networks to detect and prevent security breaches or performance issues. | Monitoring, Security, Network Analysis | Computer Science, Computer & Information Sciences | Security Software | Documentation, Uses, and more |
| intel compiler | ACES Expanse KyRIC Jetstream2 |
The Intel Compiler is a suite of high-performance compilers from Intel for various programming languages, including C, C++, and Fortran. It is designed to maximize application performance on Intel architecture-based processors. | Compiler, Optimization, Performance, Debugging | Computer Science, Computer & Information Sciences | Development Tools | Documentation, Uses, and more |
| intel oneapi compiler | Stampede3 | Intel oneAPI Compiler is a suite of compilers and tools designed to optimize performance across various architectures, including CPUs, GPUs, and FPGAs. It supports multiple programming languages, including C, C++, Fortran, and SYCL. | compiler, performance optimization, multi-language, parallel programming, Intel | Computer Science, Software Engineering | Compiler | Documentation, Uses, and more |
| intel(r) mpi library | Stampede3 | Intel MPI Library is a high-performance implementation of the Message Passing Interface (MPI) standard, designed for parallel programming in distributed computing environments. | MPI, Parallel Computing, High-Performance Computing, Distributed Systems | Computer Science | Library | Documentation, Uses, and more |
| intel-compilers | ACES | Intel Compilers are a suite of optimizing compilers for C, C++, and Fortran programming languages, designed to enhance performance on Intel architectures. | compilers, performance optimization, C++, Fortran, parallel computing | Computer Science, Software Engineering | Commercial | Documentation, Uses, and more |
| intel-mkl | Anvil | Intel Math Kernel Library (MKL) is a library of optimized math routines for science, engineering, and financial applications. | Mathematics, Performance, Numerical Computing | Applied Mathematics, Numerical Analysis | Library | Documentation, Uses, and more |
| intel-oneapi-compilers | Delta | Intel oneAPI Compilers provide a unified programming model for high-performance computing, enabling developers to optimize applications across various architectures including CPUs and GPUs. | compilers, high-performance computing, Intel, oneAPI, C++, Fortran | Computer Science, Software Engineering | Compiler | Documentation, Uses, and more |
| intel-oneapi-mkl | Delta | Intel oneAPI Math Kernel Library (MKL) provides highly optimized mathematical functions for scientific computing, including linear algebra, fast Fourier transforms, and vector mathematics. | Mathematics, High-Performance Computing, Numerical Libraries | Numerical Analysis, Applied Mathematics | Library | Documentation, Uses, and more |
| intel-parallel-studio | Anvil | Intel Parallel Studio is a suite of development tools for creating high-performance applications. It includes compilers, libraries, and performance analysis tools to optimize code for Intel architectures. | HPC, Parallel Computing, Performance Optimization, Development Tools | Computer Science | Commercial | Documentation, Uses, and more |
| intel/aikit | ACES | Documentation, Uses, and more | ||||
| intel_ipp_ia32 | KyRIC | Intel Integrated Performance Primitives (IPP) for IA-32 architecture provides a set of highly optimized software functions for multimedia processing, data processing, and communications. | HPC, Performance Optimization, Multimedia Processing | Computer Science, Computer and Information Sciences | Library | Documentation, Uses, and more |
| intel_ipp_intel64 | KyRIC | Intel Integrated Performance Primitives (Intel IPP) provides high-performance software libraries that are designed to help developers improve the performance of their applications. Intel IPP offers a wide range of functions that are optimized for Intel architecture, including signal, imaging, cryptography, and data processing algorithms. | Software Development, Performance Optimization, Data Processing, Signal Processing, Image Processing, Cryptography | Software Engineering, Computer & Information Sciences, Systems & Development | Commercial | Documentation, Uses, and more |
| intel_ippcp_ia32 | KyRIC | Intel Integrated Performance Primitives - Cryptography (IPP-Crypto) is a library that provides highly optimized building blocks for a variety of encryption and decryption algorithms on Intel architecture processors. It aims to accelerate cryptographic operations to enhance performance in software applications. | Cryptographic Library, Performance Optimization, Intel Architecture | Computer & Information Sciences | Compiler/Library | Documentation, Uses, and more |
| intel_ippcp_intel64 | KyRIC | Intel Integrated Performance Primitives Cryptography (IPP Cryptography) is a collection of highly optimized cryptographic functions and algorithms developed by Intel for high-performance computing applications. It provides a set of cryptographic functions optimized for Intel processors to enhance the security and performance of cryptographic operations in software. | Cryptography, High-Performance Computing, Intel Processors, Security | Computer & Information Sciences | Optimization Library | Documentation, Uses, and more |
| intelclusterchecker | ACES | Documentation, Uses, and more | ||||
| intelpython | ACES | Documentation, Uses, and more | ||||
| intervaltree | ACES | A Python library for creating and manipulating interval trees, which are useful for storing intervals and performing efficient queries on them. | Python, Data Structures, Interval Trees, Algorithms | Software Engineering, Computer Science | Library | Documentation, Uses, and more |
| intltool | ACES | Intltool is a set of tools to centralize translation of many different file formats using a single language-styled file. | Localization, Translation, Internationalization | Computer Science, Computer & Information Sciences | Localization Tool | Documentation, Uses, and more |
| ior | Delta | ior is a versatile software tool for analyzing and optimizing input/output (I/O) performance in high-performance computing (HPC) systems. It is designed to assess and improve the efficiency of data transfer operations in parallel computing environments. | High-Performance Computing, Parallel Computing, I/O Optimization | Computer Science | Utility Software | Documentation, Uses, and more |
| iozone | Expanse | Iozone is a filesystem benchmark tool that provides a wide range of file I/O performance measurements. It is used to measure the performance of various file operations such as read, write, re-read, and random access. | Benchmarking, File I/O, Performance Testing, Filesystem | Systems, Software Engineering | Benchmarking Tool | Documentation, Uses, and more |
| iperf3 | DeltaAI Delta |
iperf3 is a tool for actively measuring the maximum achievable bandwidth on IP networks. It supports various parameters to customize the testing process and is widely used for network performance testing and tuning. | Network Testing, Bandwidth Measurement, Network Performance | Computer Science, Computer & Information Sciences | Tool | Documentation, Uses, and more |
| ipmitool | Expanse | ipmitool is an open-source utility for managing and configuring devices that support the Intelligent Platform Management Interface (IPMI) specification. It allows users to interact with IPMI-enabled devices to retrieve information, perform system management tasks, and monitor hardware sensors remotely. | System Management, Hardware Monitoring, Remote Administration, Open Source | Computer Science, Engineering & Technology | Utility | Documentation, Uses, and more |
| ipython | ACES | IPython is a powerful interactive command shell that provides a robust and flexible environment for interactive computing. It offers features such as easy-to-use, high-performance tools for parallel computing, data visualization, and data analysis. | Command Shell, Interactive Computing, Data Visualization, Parallel Computing, Data Analysis | Computer Science, Computer & Information Sciences | Development Tools | Documentation, Uses, and more |
| iq-tree | ACES | IQ-TREE is a fast and effective software for phylogenomic inference. It implements a variety of models for DNA and protein sequences, including substitution models, rate heterogeneity, and mixture models. IQ-TREE uses maximum likelihood estimation to construct phylogenetic trees, and offers ultrafast bootstrap approximation to assess the tree accuracy. | Phylogenetics, Bioinformatics, Computational Biology, Phylogenomic Analysis | Systematics & Population Biology, Biological Sciences | Phylogenetic Tree Construction Tool | Documentation, Uses, and more |
| iqtree3 | DeltaAI | IQ-TREE is a fast and effective software for phylogenetic inference based on maximum likelihood (ML) methods. | phylogenetics, maximum likelihood, bioinformatics | Bioinformatics, Phylogenetics | Standalone | Documentation, Uses, and more |
| irkernel | ACES | IRkernel is a kernel for the R programming language that allows users to run R code in Jupyter notebooks, providing an interactive computing environment. | R, Jupyter, Data Science, Interactive Computing | Data Analysis, Statistics and Probability | Kernel | Documentation, Uses, and more |
| isa-l | ACES | ISA-L (Intel Storage Acceleration Library) is a collection of optimized low-level functions used in storage applications. It is specifically designed to offer high-performance data movement and protection functions for storage and data processing workloads, leveraging Intel hardware capabilities. | Optimized Functions, Data Movement, Data Protection, Storage Applications | Computer Science, Engineering & Technology | Library | Documentation, Uses, and more |
| isl | ACES | ISL (Integer Set Library) is a library for manipulating sets and maps of integer points bounded by linear constraints. It provides functions for computing the integer points in a set or projection of a set represented as unions of polyhedra, as wells as their images under affine transformations. | Library, Integer Points, Linear Constraints | Computer Science, Computer & Information Sciences | Library | Documentation, Uses, and more |
| itac | KyRIC Stampede3 |
Intel Trace Analyzer and Collector (ITAC) is a performance analysis tool designed for parallel applications. It provides in-depth performance data to help developers optimize the performance of their parallel code. | Performance Analysis, Parallel Applications, Optimization | Computer & Information Sciences | Compiler | Documentation, Uses, and more |
| itk | ACES | The Insight Segmentation and Registration Toolkit (ITK) is an open-source, cross-platform library that provides advanced image processing algorithms for registering and segmenting multidimensional scientific images. | Image Processing, Medical Imaging, Scientific Images | Medical & Health Sciences, Engineering & Technology | Image Analysis | Documentation, Uses, and more |
| jansson | ACES | Jansson is a C library for encoding, decoding, and manipulating JSON data. It is designed to be efficient, powerful, and easy to use for integrating JSON parsing and generation capabilities into C/C++ applications. | Json, C Library, Data Parsing, Data Manipulation | Software Engineering, Computer & Information Sciences | Data Processing | Documentation, Uses, and more |
| jasper | ACES | JasPer (JPEG-2000 Part-1 Suite) is an open-source software implementation of the JPEG-2000 Part-1 standard. It provides a complete set of tools for encoding and decoding JPEG-2000 streams, including color space conversion, wavelet transforms, quantization, and entropy coding. | Image Processing, Open-Source, Jpeg-2000 | Computer Science, Computer & Information Sciences | Image Processing | Documentation, Uses, and more |
| java | ACES | Java is a widely-used programming language and computing platform that is designed to be fast, secure, and reliable. It is commonly used for building mobile applications, web applications, enterprise applications, and more. | Programming Language, Computing Platform | Software Engineering, Computer & Information Sciences | Compiler | Documentation, Uses, and more |
| jax | ACES | JAX is an open-source software library for high-performance machine learning research, particularly for automatic differentiation, and numerical and scientific computing. | Machine Learning, Numerical Computing, Scientific Computing | Artificial Intelligence, Computer & Information Sciences | Machine Learning | Documentation, Uses, and more |
| jbigkit | ACES | jbigkit is a software library for encoding and decoding images in the JBIG format, which is particularly efficient for bi-level images such as scanned documents. | Image Processing, Compression, JBIG, Library | Software Engineering, Other Computer and Information Sciences | Library | Documentation, Uses, and more |
| jedi | ACES | Documentation, Uses, and more | ||||
| jellyfish | ACES | Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA sequences. It has the capability to efficiently store and query k-mer counts in large sequencing datasets. | K-Mer Counting, DNA Sequences, Sequence Analysis | Computational Biology, Biological Sciences | Bioinformatics Tool | Documentation, Uses, and more |
| jemalloc | ACES | jemalloc is a general-purpose memory allocator implementation designed for high performance in multithreaded applications. It is widely used in the software industry to optimize memory allocation and improve overall performance of applications. | Memory Allocator, Performance Optimization, Multithreading | Software Engineering, Computer & Information Sciences | Memory Allocator | Documentation, Uses, and more |
| jmol | ACES | Jmol is an open-source Java viewer for chemical structures in 3D with features for visualization, analysis, and manipulation of molecular structures. | Molecular Visualization, Molecular Analysis, Chemistry | Physical Chemistry, Inorganic & Nuclear Chemistry, Chemical Sciences | Modeling & Simulation | Documentation, Uses, and more |
| json-c | ACES DeltaAI KyRIC |
Json-c is a C library for encoding, decoding, and manipulating JSON data. It provides functions for parsing JSON input, creating JSON output, manipulating JSON data structures, and validating JSON data. | C Library, Json Encoding, Json Decoding, Data Manipulation | Computer Science, Computer & Information Sciences | Data Processing | Documentation, Uses, and more |
| json-fortran | ACES | json-fortran is a Fortran library for reading and writing JSON data. It provides a simple interface for working with JSON in Fortran applications, allowing users to easily serialize and deserialize data structures. | Fortran, JSON, Data Serialization, Scientific Computing | Computer Science, Software Engineering | Library | Documentation, Uses, and more |
| json-glib | DeltaAI | json-glib is a library that provides a JSON parsing and serialization API for GLib, allowing for easy manipulation of JSON data in C applications. | JSON, GLib, C programming, Data serialization | Software Engineering, Other Computer and Information Sciences | Library | Documentation, Uses, and more |
| jsonc | Stampede3 | Documentation, Uses, and more | ||||
| jsoncpp | ACES | JsonCpp is a C++ library that allows manipulating JSON data structures. It provides features for parsing, generating, and manipulating JSON data in C++ applications. | C++, Json, Library, Data Manipulation | Software Engineering, Computer & Information Sciences | Development Tools | Documentation, Uses, and more |
| judy | ACES | Judy is a C library that provides a collection of functions to efficiently manage data arrays to store and retrieve key/value pairs. | C Library, Data Management, Key/Value Pairs | Other Computer & Information Sciences | Data Management | Documentation, Uses, and more |
| julia | Anvil ACES Delta |
Julia is a high-level, high-performance dynamic programming language for technical computing, with syntax that is familiar to users of other technical computing environments. It provides a sophisticated compiler, distributed parallel execution, numerical accuracy, and extensive mathematical function libraries. | Programming Language, Technical Computing, High-Performance Computing, Scientific Computing, Numerical Analysis | Computer Science, Computer & Information Sciences | Compiler | Documentation, Uses, and more |
| julia_tamu | ACES | Documentation, Uses, and more | ||||
| jupyter | Anvil | Jupyter is an open-source web application that allows you to create and share documents that contain live code, equations, visualizations, and narrative text. It supports over 40 programming languages, including Python, R, and Julia, and is widely used in data science, scientific computing, and machine learning projects. | Data Science, Scientific Computing, Machine Learning | Data Analysis, Computer & Information Sciences | Web Application | Documentation, Uses, and more |
| jupyter-bundle | ACES | Documentation, Uses, and more | ||||
| jupyter-resource-usage | ACES | A Jupyter Notebook extension that provides resource usage statistics for notebooks, including CPU and memory usage. | Jupyter, Resource Monitoring, Data Science, Performance | Data Science, Computer Science | Jupyter Notebook Extension | Documentation, Uses, and more |
| jupyter-server | ACES | Jupyter server is a flexible and extensible tool that allows users to run interactive computational environments in various programming languages. It provides a web-based interface for running Jupyter notebooks, code, and data analysis. | Interactive Computing, Web-Based Interface, Notebooks | Computer Science, Computer & Information Sciences | Compiler | Documentation, Uses, and more |
| jupyter-server-proxy | ACES | A Jupyter server extension that allows users to create proxies for other web services, enabling them to be accessed through Jupyter notebooks. | Jupyter, Web Proxy, Notebook, Data Science | Data Science, Computer Science | Server Extension | Documentation, Uses, and more |
| jupyterhub | ACES | JupyterHub brings the power of Jupyter Notebooks to groups of users. It allows multiple users to access Jupyter Notebooks through a browser, providing a collaborative and interactive environment for data science, scientific computing, and other computational tasks. | Data Science, Collaborative Computing, Notebook Environment, Interactive Computing | Informatics, Analytics & Information Science, Computer & Information Sciences | Collaborative Tool | Documentation, Uses, and more |
| jupyterlab | ACES | JupyterLab is a web-based interactive development environment for Jupyter notebooks, code, and data. It offers a flexible and powerful user interface to work with data, code, and visualization in a seamless manner. | Interactive Computing, Data Visualization, Jupyter Notebooks, Web-Based Interface, Code Editing | Data Analysis, Computer & Information Sciences | Data Science Tool | Documentation, Uses, and more |
| jupyterlmod | ACES | jupyterlmod is an extension for Jupyter Notebooks that allows users to interact with Lmod, the Environment Modules System, directly within the Jupyter environment. It enables users to manage software environments, load and unload modules, and handle environment variables conveniently within Jupyter Notebook. | Jupyter Notebook, Environment Modules, Software Environment Management | Other Natural Sciences | Extension | Documentation, Uses, and more |
| jupyternotebook | ACES | Jupyter Notebook is an open-source web application that allows you to create and share documents that contain live code, equations, visualizations, and narrative text. | Data Science, Machine Learning, Interactive Computing, Visualization | Data Analysis, Computer Science | Web Application | Documentation, Uses, and more |
| kahip | ACES | KaHIP (Karlsruhe High Quality Partitioning) is a family of graph partitioning programs that aims to efficiently compute high-quality graph partitions. It provides several partitioning algorithms to balance computational load and minimize communication overhead. KaHIP is suitable for large-scale parallel applications and is widely used in the field of high-performance computing. | Graph Partitioning, High-Performance Computing, Parallel Computing | Computer Science, Computer & Information Sciences | Utility | Documentation, Uses, and more |
| kaleido | ACES | Kaleido is a high-performance image export engine for Plotly, enabling the generation of static images from interactive visualizations. | Visualization, Image Export, Plotly, High Performance | Computer Science | Library | Documentation, Uses, and more |
| kalign | ACES | Kalign is a fast and accurate multiple sequence alignment algorithm that utilizes the Wu-Manber approximate string matching algorithm to efficiently align large sets of sequences. It is commonly used in bioinformatics for aligning DNA, RNA, and protein sequences. | Bioinformatics, Sequence Alignment, DNA, RNA, Protein, Wu-Manber Algorithm | Computational Biology, Biological Sciences | Bioinformatics Tool | Documentation, Uses, and more |
| kallisto | ACES | kallisto is a program for quantifying abundances of transcripts from RNA-Seq data, using pseudoalignment to quickly determine compatibility of reads with targets, allowing rapid transcript quantification. | RNA-Seq, Transcriptomics, Bioinformatics, Gene Expression Analysis, Computational Biology | Bioinformatics, Biological Sciences | Bioinformatics Tool | Documentation, Uses, and more |
| kblas-gpu | ACES | KBLAS is a GPU-accelerated linear algebra library for high-performance computing (HPC) applications. It provides optimized implementations of basic linear algebra subroutines (BLAS) and dense matrix operations for NVIDIA GPUs. | Linear Algebra, Gpu-Accelerated, Hpc, Parallel Computing | Engineering & Technology | Computational Software | Documentation, Uses, and more |
| kbproto | DeltaAI | The kbproto package provides the core XKB protocol and extension definitions for usage with X11 protocol libraries. | X11 Protocol, Keyboard Properties | Computer Science, Computer & Information Sciences | Protocol | Documentation, Uses, and more |
| keras | Anvil ACES |
Keras is an open-source neural network library written in Python. It is capable of running on top of TensorFlow, Microsoft Cognitive Toolkit, Theano, or PlaidML. Designed with user-friendliness and modularity as its guiding principles, Keras is known for its ease of use and flexibility, allowing users to experiment with deep neural networks. | Neural Networks, Deep Learning, Machine Learning | Artificial Intelligence & Intelligent Systems, Computer & Information Sciences | Library | Documentation, Uses, and more |
| kim-api | ACES | The Knowledgebase for Interatomic Models (KIM) Application Programming Interface (API) is an open framework for the development of interoperable atomistic and multiscale simulation codes. It provides a common interface for atomistic simulations and facilitates the incorporation and sharing of interatomic models. | Computational Software, Hpc Tools | Materials Science, Physical Sciences | Application Programming Interface | Documentation, Uses, and more |
| kineto | ACES | Kineto is a software suite designed for analyzing and simulating the dynamics of mechanical systems. It provides tools for both kinematic and dynamic analysis of systems with rigid bodies, joints, and constraints. Kineto is particularly useful for studying the motion and forces in complex mechanical systems. | Mechanical Engineering, Simulation, Mechanical Systems, Kinematics, Dynamics | Engineering & Technology | Analysis Tool | Documentation, Uses, and more |
| kmcp | ACES | Documentation, Uses, and more | ||||
| kokkos | Stampede3 | Kokkos is a programming model for writing performance portable parallel applications in C++. It allows developers to write code once and run efficiently on multiple types of heterogeneous architectures. | Programming Model, Performance Portability, Parallel Computing | Computer Science, Computer & Information Sciences | Library | Documentation, Uses, and more |
| kraken2 | ACES Delta |
Kraken 2 is a taxonomic sequence classifier that assigns taxonomic labels to short DNA sequences, such as those generated by high-throughput sequencing technologies. | bioinformatics, sequence classification, metagenomics, taxonomy | Bioinformatics, Metagenomics | Command-line tool | Documentation, Uses, and more |
| krb5 | Anvil | Kerberos is a network authentication protocol designed to provide strong authentication for client/server applications through secret-key cryptography. | Authentication, Security, Networking | Computer Science | Library | Documentation, Uses, and more |
| kubernetes | Expanse | Kubernetes is an open-source container orchestration platform designed to automate the deployment, scaling, and management of containerized applications. | Container Orchestration, Cloud Computing, DevOps, Microservices | Software Engineering, Computer and Information Sciences | Open Source | Documentation, Uses, and more |
| lame | ACES | LAME is a high-quality MPEG Audio Layer III (MP3) encoder licensed under the GNU Lesser General Public License (LGPL). It is considered one of the best MP3 encoders available. | Audio Encoding, Mp3, Open-Source | Computer Science, Other Engineering & Technologies | Encoder | Documentation, Uses, and more |
| lammps | Anvil ACES DeltaAI Delta Stampede3 |
LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator) is a classical molecular dynamics code designed for simulating large-scale atomistic systems. It is highly versatile and can be used to model a wide range of materials and complex molecular structures. | Molecular Dynamics, Simulation, Computational Chemistry | Physical Chemistry, Chemical Sciences | Code/Package | Documentation, Uses, and more |
| lasso-python | ACES | Lasso-python is a Python library that provides tools for lasso regression, a linear regression technique that performs variable selection and regularization to improve the model's prediction and interpretability. | Python Library, Machine Learning, Regression Analysis | Statistics & Probability, Mathematics | Library | Documentation, Uses, and more |
| launcher | Anvil | Launcher is a software application that provides a centralized platform for accessing and managing various files, programs, and tools on a computer system. It serves as a customizable tool for organizing shortcuts and quick access to frequently used resources. | Software Management, File Organization, Shortcut Access | System Tool | Documentation, Uses, and more | |
| learning | Anvil | Documentation, Uses, and more | ||||
| leptonica | ACES | Leptonica is an open-source image processing and image analysis library. It provides a wide range of image processing functions and is used for tasks such as image enhancement, binarization, morphology, and more. Leptonica is written in C and provides bindings for various programming languages. | Image Processing, Image Analysis, Open-Source, Library, C | Computer Science, Computer & Information Sciences | Library | Documentation, Uses, and more |
| lerc | ACES | LERC (Limited Error Raster Compression) is an algorithm for raster data compression that provides high compression ratios with minimal loss in data quality. It is commonly used in geospatial applications to reduce storage space and transmission times for large raster datasets. | Compression, Raster Data, Geospatial Applications | Earth & Environmental Sciences, Other Natural Sciences | Algorithm | Documentation, Uses, and more |
| leveldb | ACES | LevelDB is a fast key-value storage library designed by Google that provides an ordered mapping from string keys to string values. It has features like high performance, low latency reads, low write amplification, data compression, and automatic data compaction. LevelDB is written in C++ and is optimized for use in embedded systems and applications requiring persistent storage. | Storage, Database | Software Engineering, Computer & Information Sciences | Library | Documentation, Uses, and more |
| levmar | ACES | Levmar is a library for solving non-linear least squares problems using the Levenberg-Marquardt algorithm. | Optimization, Non-linear least squares, Mathematics, Algorithms | Applied Mathematics, Other Mathematics | Library | Documentation, Uses, and more |
| libaec | ACES | libaec is a C library for lossless image compression. | Image Compression, Lossless Compression | Computational Sciences, Computer & Information Sciences | Compression | Documentation, Uses, and more |
| libaio | ACES KyRIC |
libaio is a library that provides a Linux-native asynchronous I/O facility to applications. It allows applications to perform I/O operations without being blocked, thus improving performance by enabling concurrent I/O operations. | I/O Library, Linux Library, Asynchronous I/O | Software Engineering, Computer & Information Sciences | Operating System Library | Documentation, Uses, and more |
| libarchive | ACES | libarchive is a programming library that can create and read several different streaming archive formats, including most popular tar variants, cpio, and zip. It can also write entry content directly to or read entry content directly from memory, and provides hooks to read and write the entry content as it is processed. Program is available in C and C++. | Programming Library, Archive, Compression, Data Management | Computer Science, Computer & Information Sciences | Data Management | Documentation, Uses, and more |
| libassuan | ACES | libassuan is a library that provides a simple and secure way to handle IPC (Inter-Process Communication) between applications, primarily used in the context of GnuPG. | IPC, Security, GnuPG, Library | Software Engineering, Computer Science | Library | Documentation, Uses, and more |
| libatomic_ops | ACES | Libatomic_ops is a library implementing atomic memory access operations for use in concurrent programming. It provides a number of low-level memory access and synchronization operations which can be used in lock-free data structures and for inter-thread communication without the need for locks. | Concurrent Programming, Atomic Operations, Memory Access, Synchronization | Software Engineering, Computer & Information Sciences | Development Tool | Documentation, Uses, and more |
| libbsd | Anvil DeltaAI KyRIC |
libbsd is a library that provides functions typically found in the BSD operating systems. It aims to offer a more portable solution for developers needing BSD functions on non-BSD systems. | Library, Bsd, Operating System | Software Engineering, Computer & Information Sciences | Library | Documentation, Uses, and more |
| libcerf | ACES DeltaAI |
libcerf is a C library that provides efficient and accurate implementations of complex error functions, along with Dawson, Fresnel, and Voigt functions. The library is designed to facilitate the computation of complex error functions for a wide range of applications in scientific computing. | Error Functions, Scientific Computing, C Library | Applied Mathematics, Mathematics | Library | Documentation, Uses, and more |
| libcint | ACES | Documentation, Uses, and more | ||||
| libcircle | ACES | libcircle is a library designed for parallel programming in C and C++ that simplifies the development of distributed applications. It provides a high-level API for managing communication between processes in a cluster environment. | Parallel Computing, Distributed Systems, C/C++, High Performance Computing | Distributed Computing, Computer Science | Library | Documentation, Uses, and more |
| libdap | ACES | The libdap (Data Access Protocol) library is a software package that provides an implementation of DAP (Data Access Protocol) for accessing and sharing scientific data over the internet. DAP is a protocol that allows users to access and query remote data repositories in a unified and standardized manner. | Data Access, Scientific Data, Internet Protocol | Remote Sensing, Other Computer & Information Sciences | Data Access | Documentation, Uses, and more |
| libde265 | ACES | libde265 is an open-source implementation of the H.265 (HEVC) video codec, designed for efficient video compression and decompression. | Video Codec, HEVC, Open Source, Compression, Multimedia | Computer Science | Library | Documentation, Uses, and more |
| libdeflate | ACES | libdeflate is a library for fast, flexible, and memory-efficient DEFLATE-based compressed data decompression. | Compression, Data Decompression | Computer & Information Sciences | Compression | Documentation, Uses, and more |
| libdivsufsort | ACES | libdivsufsort is a library for constructing suffix arrays and related data structures efficiently. | suffix array, string processing, data structures, algorithm | Algorithms and Data Structures, Computer Science | Library | Documentation, Uses, and more |
| libdrm | ACES | Direct Rendering Manager (DRM) library for interacting with kernel mode-setting (KMS) drivers, particularly the Direct Rendering Infrastructure (DRI) modules in the Linux kernel. | Graphics, Linux, Kernel, Driver | Software Engineering, Computer Science | Library | Documentation, Uses, and more |
| libedit | KyRIC | libedit is an open-source library that provides a readline-like interface for line editing in command-line applications. It is a replacement for GNU Readline used in many Unix-like systems, providing similar functionality but with a more permissive open-source license (BSD-style license). | Library, Command-Line, Line Editing, History, Open-Source | Software Engineering, Computer & Information Sciences | Tool | Documentation, Uses, and more |
| libepoxy | ACES | libepoxy is a library for handling OpenGL function pointer management. It makes it easy to call OpenGL functions and to know when extensions are available. | Opengl, Library, Graphics | Computer Science, Computer & Information Sciences | Development | Documentation, Uses, and more |
| libev | ACES | libev is a high-performance event loop that provides a full-featured alternative to the event loop provided by the standard C library. It is designed for high scalability and low latency applications. | Event Loop, High Performance, Scalable, Low Latency, Operating System Independent | Software Engineering, Computer & Information Sciences | Library | Documentation, Uses, and more |
| libevent | ACES KyRIC |
libevent is a robust event notification library that provides a mechanism to execute a callback function when specific events occur on a file descriptor or after a timeout has been reached. It is designed to be highly efficient and versatile, capable of handling various types of events in a scalable manner. | Event Notification, Callback Functions, Scalable, Efficient | Software Engineering, Computer & Information Sciences | Development | Documentation, Uses, and more |
| libfabric | Anvil ACES DeltaAI Delta KyRIC |
libfabric is a high-performance library for fabric interfaces, designed to abstract fabric communication resources to applications while providing flexibility to applications that need to bypass the fabric interfaces. It provides fabric-agnostic interfaces for communication in high-performance computing (HPC) environments. | Fabric Interfaces, High-Performance Computing, Communication Resources | Computer Science, Engineering & Technology | Communication Library | Documentation, Uses, and more |
| libfdf | ACES | Documentation, Uses, and more | ||||
| libffi | Anvil ACES DeltaAI KyRIC |
libffi is a library that provides a portable, high-level programming interface to various calling conventions. It allows a C function to be called from a language other than C without having to hand-write assembly code. | Library, Portability, Calling Conventions | Software Engineering, Computer & Information Sciences | Development Tool | Documentation, Uses, and more |
| libflame | Anvil | libflame is a portable library for dense matrix computations, providing high-performance implementations of the BLAS and LAPACK interfaces. | Linear Algebra, Matrix Computations, Numerical Computation | Applied Mathematics, Mathematics | Numerical Computing | Documentation, Uses, and more |
| libfontenc | DeltaAI | libfontenc is a library used for encoding font data in X Window System, allowing for the representation of various character sets. | Font Management, X Window System, Character Encoding | Software Engineering, Other Computer and Information Sciences | Library | Documentation, Uses, and more |
| libfyaml | ACES | libfyaml is a C library for parsing and emitting YAML, designed to be fast and simple to use. | YAML, C library, data serialization, configuration management | Software Engineering, Other Computer and Information Sciences | Library | Documentation, Uses, and more |
| libgcrypt | ACES | Libgcrypt is a general-purpose cryptographic library originally based on code from GnuPG. It provides various cryptographic algorithms to secure data and communications. | Cryptography, Security, Encryption | Computer Science, Computer & Information Sciences | Cryptographic Library | Documentation, Uses, and more |
| libgd | ACES DeltaAI |
Libgd is an open-source graphics library. It allows your code to quickly draw images complete with lines, arcs, text, multiple colors, cut and paste from other images, and flood fills. It can generate WBMP files on the fly. It is also compatible with PHP. | Graphics Library, Image Manipulation, Php Library | Image Processing, Other Computer & Information Sciences | Graphics Library | Documentation, Uses, and more |
| libgeotiff | ACES DeltaAI |
Libgeotiff is a library for reading and writing coordinate system information embedded in geotiff files. | Geotiff, Metadata, Coordinates, Geospatial | Earth & Environmental Sciences | File Handling | Documentation, Uses, and more |
| libgit2 | ACES | libgit2 is a portable, pure C implementation of the Git core methods provided as a re-entrant linkable library with a solid API, allowing you to write native speed custom Git applications in any language which supports C bindings. | Version Control System, Git, Library | Software Engineering, Computer & Information Sciences | Version Control System | Documentation, Uses, and more |
| libglu | ACES | libglu is a software library that provides support for building OpenGL applications. It is designed to complement the functionality provided by OpenGL and aids in handling complex geometric shapes, tessellation, and creating polygonal models. | Software Library, Geometry Processing, Computer Graphics | Computer Science, Computer & Information Sciences | Programming Library | Documentation, Uses, and more |
| libglvnd | ACES | libglvnd is the open-source implementation of the vendor-neutral dispatch layer for arbitrating OpenGL API calls between multiple vendors' graphics drivers and the X server. | Graphics, Opengl, Vendor-Neutral Dispatch | Computer Science, Computer & Information Sciences | Graphics Library | Documentation, Uses, and more |
| libgpg-error | ACES KyRIC |
Libgpg-error is a small library that defines common error values for all GnuPG components. It is used by GnuPG and some other packages. | Error Handling, Library, Gnupg | Software Engineering, Computer & Information Sciences | Utility | Documentation, Uses, and more |
| libgpuarray | ACES | libgpuarray is a library that provides a common, numpy-like array object to represent GPU data for array-oriented algorithms in Python. It is designed to work with various libraries whose primary focus is on GPU acceleration, such as Theano or PyCUDA. | Gpu Acceleration, Array-Oriented Algorithms, Python Library | Computer Science, Computer & Information Sciences | Computational Software | Documentation, Uses, and more |
| libgridxc | ACES | libgridxc is a library for evaluating exchange-correlation functionals in density functional theory (DFT) calculations. | Density Functional Theory, Computational Chemistry, High-Performance Computing | Theoretical Chemistry, Computational Chemistry | Library | Documentation, Uses, and more |
| libheif | ACES | libheif is a library for reading and writing High Efficiency Image File Format (HEIF) files, which are used for storing images and image sequences. | Image Processing, HEIF, AVIF, Library | Software Engineering, Computer and Information Sciences | Library | Documentation, Uses, and more |
| libiconv | Anvil ACES KyRIC |
libiconv is a library that provides character set conversion support. It converts text data between different character encoding schemes. | Character Set Conversion, Text Data, Encoding | Other Computer & Information Sciences, Computer & Information Sciences | Conversion Tool | Documentation, Uses, and more |
| libidn | ACES | Libidn is an internationalized domain name library designed to help with the process of converting internationalized domain names to/from ASCII representation. It implements the Stringprep, Punycode and IDNA specifications defined by the IETF (Internet Engineering Task Force). | Software Library, Internationalization, Domain Names | Computer & Information Sciences | Dynamic Link Library (Dll) | Documentation, Uses, and more |
| libidn2 | ACES DeltaAI KyRIC |
Libidn2 is a library that implements the Stringprep, Punycode and IDNA specifications defined by the IETF Internationalized Domain Names (IDN) working group. | Domain Names, Idns, Stringprep, Punycode | Software Engineering, Computer & Information Sciences | Utility | Documentation, Uses, and more |
| libint | ACES | libint is a library for the evaluation of molecular integrals needed in computational chemistry and related fields. It provides efficient and accurate implementations for various types of integrals used in quantum chemistry calculations. | Computational Chemistry, Molecular Integrals, Quantum Chemistry | Physical Chemistry, Chemical Sciences | Computational | Documentation, Uses, and more |
| libjpeg-turbo | ACES DeltaAI |
libjpeg-turbo is a high-speed version of the widely-used JPEG image compression library. It uses SIMD instructions to accelerate JPEG compression and decompression on x86, x86-64, and ARM processors. | Image Compression, Jpeg Compression, Library, Open Source | Image Processing, Computer & Information Sciences | Compression Library | Documentation, Uses, and more |
| libmad | ACES | libmad is a high-quality MPEG audio decoder library that is designed to decode MP3 audio streams efficiently and accurately. | Audio Processing, MPEG, Library, Decoding | Software Engineering, Other Computer and Information Sciences | Library | Documentation, Uses, and more |
| libmd | Anvil DeltaAI |
libmd is a library for molecular dynamics simulations that allows for the integration of equations of motion for particles interacting with different potentials. | Molecular Dynamics, Simulation, Library | Physical Sciences | Computational | Documentation, Uses, and more |
| libmesh | Anvil Stampede3 |
Libmesh is a C++ finite element library designed to provide a framework for the numerical simulation of partial differential equations in high dimensions. It supports 1D, 2D, and 3D mesh generation, provides a wide range of finite element types, and includes solvers for various types of PDEs. | Finite Element Library, Numerical Simulation, Partial Differential Equations | Engineering, Other Mathematics | Library | Documentation, Uses, and more |
| libnsl | ACES | The libnsl library provides an interface for applications to make use of the services provided by the Network Services Layer (NSL). It offers functions that allow applications to communicate over the network using a variety of protocols. | Network Services, Communication, Protocols | Computer Science, Computer & Information Sciences | System Software | Documentation, Uses, and more |
| libogg | ACES | Libogg is a reference implementation of the Ogg bitstream format. It provides a simple, low-level API for working with Ogg bitstreams. | Library, Bitstream, Audio | Computer Science, Computer & Information Sciences | Data Format | Documentation, Uses, and more |
| libopus | ACES | libopus is a high-quality audio codec that is specifically designed for interactive speech and audio transmission over the Internet. It is part of the wider Opus audio codec family, covering a wide range of bitrates and applications. | Audio Codec, Real-Time Communication, Internet Transmission | Engineering & Technology | Documentation, Uses, and more | |
| libpciaccess | ACES KyRIC |
libpciaccess is a library providing generic access to the PCI bus and devices for use in user-space programs. It allows user-space drivers to directly map PCI memory regions, perform bus transactions, and query devices on the PCI bus. | Library, Pci Bus Access, User-Space Drivers | Software Engineering, Computer & Information Sciences | Programming Library | Documentation, Uses, and more |
| libpng | Anvil ACES DeltaAI |
Libpng is the official PNG reference library, used to support the PNG (Portable Network Graphics) format for storing raster images. It provides a set of functions for creating, reading, and manipulating PNG image files. | Image Processing, Graphics Library, Raster Images | Image Processing, Computer & Information Sciences | Data Handling | Documentation, Uses, and more |
| libpressio | ACES | libpressio is a library designed for compressing and decompressing data in scientific computing applications. It provides a flexible framework for integrating various compression algorithms and allows users to easily switch between them. | compression, data science, high-performance computing, scientific computing | Computer Science | Library | Documentation, Uses, and more |
| libpsl | ACES | Libpsl is a C library that provides functions to work with the Public Suffix List (PSL), which is a database of domain suffixes (like .com, .co.uk, etc.) that are under public registry control. | C Library, Domain Management, Public Suffix List | Computer & Information Sciences | System/Library Software | Documentation, Uses, and more |
| libpsml | ACES | Documentation, Uses, and more | ||||
| libpthread-stubs | Anvil DeltaAI |
Documentation, Uses, and more | ||||
| libreadline | ACES | libreadline is a GNU library that provides line-editing capabilities for interactive programs with a command-line interface. It allows users to edit text as they type commands, providing features such as history, editing, and completion of input. | Command-Line Interface, Text Editing, Gnu Library, Interactive Programs | Software Engineering, Computer & Information Sciences | Utility | Documentation, Uses, and more |
| librom | ACES | LibROM is a library for Reduced Order Models (ROMs) that provides tools for model reduction of complex systems in engineering and computational science applications. It offers a range of algorithms and methods to reduce the computational cost of high-fidelity simulations. | Software Library, Model Reduction, Computational Science | Engineering & Technology | Model Reduction Tool | Documentation, Uses, and more |
| librosa | ACES | Librosa is a Python package for music and audio analysis. It provides the building blocks necessary to create music information retrieval systems. | audio analysis, music information retrieval, signal processing, Python | Computer Science, Applied Computer Science | Library | Documentation, Uses, and more |
| librsvg | ACES | Librsvg is a free software library to render SVG files and convert them to other formats using the Cairo rendering engine. | Software Library, Free Software, Svg Rendering, File Conversion | Software Engineering, Computer & Information Sciences | Rendering & Conversion | Documentation, Uses, and more |
| librttopo | ACES | librttopo is a tool for computational topology focusing on persistent homology and topological data analysis. | Computational Topology, Persistent Homology, Topological Data Analysis | Mathematics | Computational Software | Documentation, Uses, and more |
| libsci | DeltaAI Delta |
libsci is a library of optimized scientific routines for high-performance computing (HPC) environments. It provides a collection of mathematical functions and computational kernels tailored for scientific and engineering applications that require high computational efficiency. | Hpc, Scientific Computing, Optimization | Other Mathematics | Mathematics/Computational Software | Documentation, Uses, and more |
| libsci_acc | DeltaAI Delta |
Documentation, Uses, and more | ||||
| libseccomp | ACES KyRIC |
Libseccomp is an open-source library that provides an easy-to-use, platform-independent interface for working with the Linux Kernel's syscall filtering mechanism. It allows developers to filter system calls made by an application, restricting the actions the application can perform at the kernel level. | Syscall Filtering, Linux Kernel, Security | Systems Security, Computer & Information Sciences | Development | Documentation, Uses, and more |
| libsharp2 | ACES | libsharp2 is a library designed for efficient spherical harmonic transforms and related operations, primarily used in cosmology and astrophysics. | spherical harmonics, cosmology, high-performance computing, astrophysics | Cosmology, Astrophysics | Library | Documentation, Uses, and more |
| libsigsegv | KyRIC | libsigsegv is a library for handling page faults in user mode. It provides a convenient and efficient way to establish a handler for memory violations while exploring memory areas. | Library, Memory, Page Fault | Computer Science, Computer & Information Sciences | Utility | Documentation, Uses, and more |
| libsndfile | ACES | libsndfile is a C library for reading and writing files containing sampled sound (such as WAV, AIFF, and AU) through one standard interface. | Audio Processing, File Input/Output, C Library, Audio File Formats | Other Natural Sciences | Audio Processing | Documentation, Uses, and more |
| libsodium | ACES | libsodium is a modern, easy-to-use software library for encryption, decryption, signatures, password hashing, and more. It is a portable, cross-compilable, installable, packageable fork of NaCl, a highly respected cryptographic library developed by Daniel J. Bernstein. | Cryptography, Security, Encryption, Password Hashing | Cryptography, Computer & Information Sciences | Cryptography | Documentation, Uses, and more |
| libsoup | ACES | libsoup is an HTTP client/server library for GNOME. It uses GObjects and the glib main loop, to integrate well with GNOME applications. Features include asynchronous I/O using GMainContext and WebSockets support. | Http, Client/Server, Gnome, Gobjects, Asynchronous I/O, Websockets | Computer Science, Computer & Information Sciences | Http Client/Server Library | Documentation, Uses, and more |
| libspatialindex | ACES | Libspatialindex is an open-source library for spatial indexing methods, designed to provide various spatial index structures which can be used for spatial queries in databases or applications. | Spatial Index, Library, Open-Source | Computer Science, Computer & Information Sciences | Data Processing/Management | Documentation, Uses, and more |
| libspatialite | ACES | libspatialite is an open-source library that extends the core SQLite database engine with spatial SQL capabilities. It allows users to create, manage, and query spatial data in a SQLite database, providing support for spatial functions and geometric data types. | Spatialite, Geospatial, Database, Spatial Data | Computer & Information Sciences | Database Management | Documentation, Uses, and more |
| libstdcompat | ACES | Documentation, Uses, and more | ||||
| libszip | Anvil | libszip is a compression library for large datasets used in scientific computing and research. It provides support for efficient and high-speed compression and decompression of large data files, particularly in formats commonly used in scientific applications. | Compression Library, Scientific Computing, Data Compression, Research Tools | Bioinformatics, Other Natural Sciences | Compression | Documentation, Uses, and more |
| libtasn1 | ACES | libtasn1 is a library developed for ASN.1 and DER manipulation. ASN.1 is a standard interface description language for defining data structures that can be serialized and deserialized in a cross-platform way. | Library, Asn.1, Der, Serialization, Deserialization | Computer Science, Computer & Information Sciences | Development Library | Documentation, Uses, and more |
| libtiff | Anvil ACES DeltaAI |
libtiff is a library for reading and writing TIFF (Tagged Image File Format) files. It provides support for handling images and documents in various uncompressed and compressed formats. | Image Processing, File Format, Library, Tiff, Image Storage | Computer Science, Computer & Information Sciences | Image Processing | Documentation, Uses, and more |
| libtirpc | Anvil ACES Expanse |
libtirpc is an open-source library that provides an implementation of Sun's Transport-Independent RPC (TI-RPC) protocol. | Software Library | Computer Science, Computer & Information Sciences | Development | Documentation, Uses, and more |
| libtommath | ACES | libtommath is a free open-source multiple-precision integer library written in C. It is designed for high-performance arithmetic operations on large integers, making it suitable for cryptographic applications and other mathematical computations. | Mathematics, Cryptography, Multiple-precision arithmetic, C library | Applied Mathematics, Other Mathematics | Library | Documentation, Uses, and more |
| libtool | ACES DeltaAI KyRIC |
Libtool is a generic library support script that manages the creation of static and dynamic libraries on various Unix-like operating systems. | Library Management, Software Development, Compilation | Software Engineering, Engineering & Technology | Utility/Tool | Documentation, Uses, and more |
| libunistring | ACES DeltaAI KyRIC |
libunistring is a C library that provides functions to manipulate Unicode strings and includes functions for encoding conversion, case mapping, normalization, and more. | Unicode, Encoding, String Manipulation, Localization | Software Engineering, Computer & Information Sciences | Computational Software | Documentation, Uses, and more |
| libunwind | ACES DeltaAI |
libunwind is a portable and efficient C programming interface (API) to determine the call-chain of a program. It is primarily used for debugging, performance profiling, and runtime instrumentation. | Debugging, Profiling, Runtime Instrumentation, Call Stack, C Programming | Software Engineering, Engineering & Technology | Development | Documentation, Uses, and more |
| libv8 | Anvil | libv8 is an open-source C++ library that provides a fast and efficient JavaScript engine for embedding in various applications and tools. | Javascript Engine, C++ Library | Software Engineering, Computer & Information Sciences | Programming Library | Documentation, Uses, and more |
| libvdwxc | ACES | libvdwxc is a library for the evaluation of van der Waals exchange-correlation functionals in density functional theory calculations. | Density Functional Theory, Quantum Chemistry, Computational Materials Science | Theoretical Chemistry, Quantum Chemistry | Library | Documentation, Uses, and more |
| libvorbis | ACES | Libvorbis is a free and open-source software library for encoding and decoding audio data compressed with the Vorbis audio codec. It is part of the Xiph.org Foundation's Ogg project and is used for high-quality audio compression. | Audio Codec, Compression, Open-Source | Computer Science, Engineering & Technology | Audio Processing | Documentation, Uses, and more |
| libvori | ACES | libvori is a library for calculating voronoi diagrams. It provides functions for generating voronoi diagrams from a set of points in the plane. | Voronoi Diagrams, Computational Geometry, Library | Other Mathematics, Mathematics | Calculation Tool | Documentation, Uses, and more |
| libwebp | ACES | libwebp is a library for working with the WebP image format. It provides tools to encode, decode, and manipulate images in the WebP format, which is a modern image format that provides both lossy and lossless compression for images on the web. | Image Processing, Compression, Web Development, Library | Software Engineering, Other Computer & Information Sciences | Image Processing | Documentation, Uses, and more |
| libwpe | ACES | libwpe is a library that provides web platform support for Wayland compositors and other clients that need web content rendered on a Wayland surface. | Library, Web Platform Support, Wayland Compositors, Web Content Rendering | Computer & Information Sciences | Library | Documentation, Uses, and more |
| libx11 | Anvil DeltaAI |
libX11 is the X Window System protocol client library which provides an interface to the X Window System core protocol and provides higher-level functions for building window systems on top of the X Window System core. | X Window System, Client Library, Window System Interface, Graphics | Software Engineering, Computer & Information Sciences, Computer Science | Software Development | Documentation, Uses, and more |
| libxau | Anvil DeltaAI |
libXau is a library that provides authentication data for Xlib-based client programs. | Library, Authentication, Xlib | Computer & Information Sciences | Documentation, Uses, and more | |
| libxc | ACES Stampede3 |
LibXC is a library of exchange-correlation functionals for density-functional theory. | Quantum Mechanics, Computational Chemistry | Theoretical Chemistry, Chemical Sciences | Density Functional Theory | Documentation, Uses, and more |
| libxcb | Anvil DeltaAI |
libxcb is a C language library for the X Window System's X protocol, providing a replacement for the traditional Xlib API. It allows for more efficient communication between X clients and the X server by reducing round-trip requests. | X Window System, C Library, X Protocol | Computer Science, Computer & Information Sciences | Programming | Documentation, Uses, and more |
| libxcrypt | DeltaAI | libxcrypt is a library for cryptographic hashing and password hashing, providing modern and secure algorithms for password storage and verification. | Cryptography, Security, Password Hashing, Libraries | Cryptography, Computer Science | Library | Documentation, Uses, and more |
| libxdmcp | Anvil DeltaAI |
libxdmcp is the X Display Manager Control Protocol library. It provides an API for the X Display Manager Control Protocol (XDMCP) for both the client and server side. | X11, Display Manager, Network Protocol | Software Engineering, Computer & Information Sciences | Networking | Documentation, Uses, and more |
| libxext | Anvil | libXext is an extension library for the X Window System that provides additional functionality to the core Xlib library. | X Window System, Graphics, Library | Computer Science, Computer and Information Sciences | Library | Documentation, Uses, and more |
| libxfont | DeltaAI | libXfont is a library used for font management in the X Window System, providing functionalities to load and manage bitmap and scalable fonts. | X Window System, Font Management, Graphics | Computer Science, Software Engineering | Library | Documentation, Uses, and more |
| libxml2 | Anvil ACES DeltaAI KyRIC |
Libxml2 is a software library for parsing, validating, and manipulating XML and HTML documents. It provides a tree-based API for working with XML data and supports various standards such as XML 1.0, XPath, XInclude, XPointer, and XML Catalogs. | Xml, Html, Parsing, Validation, Manipulation | Software Engineering, Computer & Information Sciences | Parsing | Documentation, Uses, and more |
| libxp | DeltaAI | Documentation, Uses, and more | ||||
| libxpm | DeltaAI | libXpm is a library for reading and writing X PixMap (XPM) image files, which are commonly used in X Window System applications. | Image Processing, Graphics, X Window System | Software Engineering, Computer Science | Library | Documentation, Uses, and more |
| libxrender | Anvil | libXrender is a library that provides an interface to the X Rendering Extension, which allows for the rendering of images and shapes in a more efficient manner than traditional X11 methods. | Graphics, Rendering, X11 | Computer Science, Computer and Information Sciences | Library | Documentation, Uses, and more |
| libxscrnsaver | Anvil | libxscrnsaver is a library that provides an X Window System client interface to the X11 MIT-SCREEN-SAVER extension. It allows applications to inhibit the screensaver and screen blanking in a standardized way. | Library, X Window System, Screensaver, Screen Blanking | Computer & Information Sciences | System Library | Documentation, Uses, and more |
| libxslt | Anvil ACES |
Libxslt is the XSLT C library developed for the GNOME project. It is used for transforming XML documents into other formats using XSLT stylesheets. Libxslt is based on libxml2, the XML C parser and toolkit. | Xml, Xslt, C Library, Transformation | Software Engineering, Computer & Information Sciences | Data Processing | Documentation, Uses, and more |
| libxsmm | ACES | libxsmm is a library for small, dense matrix-matrix multiplications developed for modern CPUs. It provides high performance on Intel Architecture CPUs and comes with different optimized code paths tailored for different processor microarchitectures. | Library, Matrix Multiplication, Intel Cpus | Computer Science, Computer & Information Sciences | Optimization Library | Documentation, Uses, and more |
| libyaml | ACES | LibYAML is a YAML 1.1 parser and emitter written in C. It is a library for parsing and emitting YAML data. YAML is a human-readable data serialization format that is commonly used for configuration files and data exchange between languages. LibYAML allows developers to integrate YAML support into their applications. | Yaml, Parser, Emitter, Serialization, Configuration | Computer Science, Computer & Information Sciences, Engineering & Technology | Parsing/Serialization | Documentation, Uses, and more |
| libzip | ACES | libzip is a C library for reading, creating, and modifying zip archives. It provides a simple programming interface for managing zip files. | C Library, Zip Archives, File Management | Computer Science, Computer & Information Sciences | Compression | Documentation, Uses, and more |
| lifelines | ACES | Lifelines is a Python library for survival analysis, reliability, and lifetime data analysis. It provides tools for data preprocessing, estimating survival functions, hazard rates, and confidence intervals, as well as modeling, predicting, and visualizing survival data. | Python Library, Survival Analysis, Lifetime Data Analysis, Reliability Analysis, Data Visualization | Statistical Methods, Statistics & Probability | Python Library | Documentation, Uses, and more |
| likwid | KyRIC | LIKWID is a performance analysis tool suite designed to support HPC/PCP (performance counter profiling) on Intel and AMD processors. It offers a set of command-line tools and libraries that facilitate the collection of performance data and analysis on modern hardware architectures. | Performance Analysis, Hpc, Performance Counter Profiling, Hardware Performance Counters | Performance Evaluation & Benchmarking, Engineering & Technology | Tool | Documentation, Uses, and more |
| lit | ACES | Documentation, Uses, and more | ||||
| littlecms | ACES | LittleCMS is a color management engine that provides simplified and portable fundamentals for the development and integration of color management components into various software applications. | Color Management, Software Development, Image Processing | Software Engineering, Computer & Information Sciences | Library | Documentation, Uses, and more |
| llava-onevision | ACES | Documentation, Uses, and more | ||||
| llvm | ACES Delta |
The LLVM Project is a collection of modular and reusable compiler and toolchain technologies. LLVM is used for developing compiler back-ends, static analysis tools, and JIT compilation engines. | Compiler, Toolchain | Software Engineering, Computer & Information Sciences | Compiler | Documentation, Uses, and more |
| lmdb | ACES | LMDB is an extremely fast, memory-efficient and crash-proof key-value store that is well-suited for embedded applications and high-performance web services. It is written in C and operates directly on memory-mapped files. | Database, Key-Value Store, Memory-Mapped Files | Computer Science, Computer & Information Sciences | Database Management System | Documentation, Uses, and more |
| lmod | ACES DeltaAI Delta Stampede3 |
Lmod is an environment module system that helps users manage their software environment by providing a convenient way to dynamically modify the user's environment through modulefiles. It supports multiple collections of modules that can be easily swapped in and out, allowing users to load the software packages and versions they need for their work. | Module Management, Software Environment, Environment Module System | Infrastructure & Instrumentation, Engineering & Technology | Utility | Documentation, Uses, and more |
| longranger | ACES | Long Ranger is a software package developed by 10x Genomics for analyzing genomic data generated by their Chromium platform. It is specifically designed for processing and analyzing linked-read sequencing data, enabling users to perform tasks such as variant calling and structural variant detection. | Genomics, Bioinformatics, Data Analysis, Sequencing | Bioinformatics, Genomics | Analysis Software | Documentation, Uses, and more |
| lpsolve | ACES | lpsolve is a free linear programming solver based on the revised simplex method. It can solve linear, mixed integer, and quadratic programming problems. | optimization, linear programming, mixed integer programming, solver | Mathematics, Applied Mathematics | Solver | Documentation, Uses, and more |
| lsd2 | ACES | Documentation, Uses, and more | ||||
| lua | ACES Expanse |
Lua is a lightweight, high-level, multi-paradigm programming language designed for embedded use in applications. It is known for its simplicity, efficiency, and flexibility. | Programming Language, Scripting Language, Embedded Systems | Software Engineering, Computer & Information Sciences | Programming Language | Documentation, Uses, and more |
| luajit | Expanse | LuaJIT is a Just-In-Time Compiler for the Lua programming language, designed to improve the performance of Lua code execution. | JIT Compiler, Scripting Language, Performance Optimization | Software Engineering, Other Computer and Information Sciences | Compiler | Documentation, Uses, and more |
| lvm2 | KyRIC | Logical Volume Manager 2 (LVM2) is a system tool for managing logical volumes. It is typically used to manage disk storage space in a more flexible manner than traditional partitioning. | System Tool, Storage Management, Disk Management | Systems, Engineering & Technology | Utility | Documentation, Uses, and more |
| lwgrp | ACES | Documentation, Uses, and more | ||||
| lxml | ACES | lxml is a powerful and feature-rich library for processing XML and HTML in Python. It provides a simple and pythonic API for efficient handling of XML and HTML data. | Python Library, Xml Processing, Html Processing, Data Parsing | Software Engineering, Computer & Information Sciences, Other Computer & Information Sciences | Data Processing | Documentation, Uses, and more |
| lz4 | ACES | LZ4 is a lossless data compression algorithm that offers extremely fast compression and decompression speeds. It is designed to be very efficient in terms of both processing power and memory usage. | Compression, Data Compression, Lossless Compression | Computer Science, Computer & Information Sciences | Utility | Documentation, Uses, and more |
| lzo | ACES | Lempel-Ziv-Oberhumer (LZO) is a data compression algorithm that focuses on high-speed compression and decompression. It offers fast compression and decompression speeds with moderate compression ratios. LZO is commonly used in applications where speed is more critical than achieving the highest compression ratios. | Data Compression, Algorithm, High-Speed | Computer Science, Computer & Information Sciences | Data Processing | Documentation, Uses, and more |
| m4 | ACES DeltaAI KyRIC |
m4 is a general-purpose macro processor designed to be used with any programming language or data file format. It is commonly used to generate source code or text files and is often used as part of the build process for software development. | Macro Processor, Text Processing, Software Development, Build Process | Software Engineering, Computer & Information Sciences | Compiler | Documentation, Uses, and more |
| macs2 | ACES | Model-based Analysis of ChIP-Seq (MACS) version 2 is a tool for identifying transcription factor binding sites and histone modification enrichment from ChIP-Seq data. It uses a dynamic Poisson distribution to effectively capture local biases in the genome while comparing the tag position density profiles between ChIP-Seq data and control samples. | Chip-Seq Analysis, Transcription Factor Binding Sites, Histone Modification, Bioinformatics | Biological Sciences | Command-Line Tool | Documentation, Uses, and more |
| maeparser | ACES | maeparser is a Python library for reading and writing molecular data stored in Maestro files. It provides a simple interface for extracting structural information from Maestro files commonly used in molecular modeling and computational chemistry. | Python Library, Molecular Data, Maestro Files | Chemical Sciences | Library | Documentation, Uses, and more |
| mafft | ACES | MAFFT is a multiple sequence alignment program for amino acid or nucleotide sequences. It offers a range of algorithms and options for improving alignment quality. | Bioinformatics, Sequence Alignment, Phylogenetics | Bioinformatics, Biological Sciences | Bioinformatics Tool | Documentation, Uses, and more |
| magics | ACES | Magics is a software library for visualizing meteorological data. It provides a wide range of graphical elements for the simultaneous representation of 2D and 3D data, including maps, wind fields, trajectories, symbols, etc. Magics is commonly used in weather forecasting, climate research, and meteorological data analysis. | Visualization, Meteorology, Meteorological Data, Weather Forecasting | Atmospheric Sciences, Earth & Environmental Sciences | Library | Documentation, Uses, and more |
| magma | ACES | Magma is a software package designed for computations in algebra, number theory, algebraic geometry, and algebraic combinatorics. It provides a powerful tool for mathematical research and applications. | Mathematics, Algebra, Number Theory, Combinatorics | Algebra & Number Theory, Mathematics | Mathematical Software | Documentation, Uses, and more |
| make | ACES KyRIC |
Make is a build automation tool that automatically builds executable programs and libraries from source code by reading files called Makefiles which specifies how to derive the target program. | Build Automation, Software Development, Programming | Computer Science, Engineering & Technology | Utility | Documentation, Uses, and more |
| makedepend | ACES | makedepend is a tool used in software development to automatically generate dependencies of C source files. It is commonly used in projects utilizing makefiles to track dependencies and streamline the build process. | Software Development, Build Automation, Dependency Management | Software Engineering, Systems & Development, Engineering & Technology | Utility | Documentation, Uses, and more |
| makeinfo | ACES | makeinfo is a program that formats and prints Texinfo documentation. Texinfo is a typesetting syntax used for generating documentation in a variety of output formats such as HTML, DVI, PDF, PostScript, and plain text. | Documentation, Formatting, Texinfo, Build Systems | Computer Science, Other Computer & Information Sciences | Text Processing | Documentation, Uses, and more |
| mako | ACES | Mako is a template library written in Python. It provides a familiar, non-XML syntax that compiles into Python modules for maximum performance. | Template Library, Python, Web Development | Software Engineering, Computer & Information Sciences | Programming | Documentation, Uses, and more |
| mamba | ACES | Mamba is a reimplementation of the high-performance package manager Conda that aims to be much faster in resolving package dependencies. It provides a simple and fast way to manage environments and packages for conda-enabled systems. | Package Manager, Dependency Resolver, Environment Management | Software Engineering, Engineering & Technology | Package Manager | Documentation, Uses, and more |
| map | Stampede3 | Map is a software tool used for creating, visualizing, and analyzing geographical maps. It is commonly used in cartography and geographic information systems (GIS). | Mapping Software, Geographical Analysis, Cartography | Other Natural Sciences | Geospatial Software | Documentation, Uses, and more |
| margo | ACES | Documentation, Uses, and more | ||||
| mariadb | ACES | MariaDB is a popular open source relational database management system (RDBMS) that is a drop-in replacement for MySQL. It is known for its high performance, scalability, and robust SQL support. MariaDB is developed by the original creators of MySQL and is designed for enterprise environments, web applications, and mission-critical systems. | Database Management System, Rdbms, Open Source, Sql | Computer & Information Sciences | Application Software | Documentation, Uses, and more |
| markdown | ACES | Markdown is a lightweight markup language with plain-text formatting syntax. Its design allows it to be converted to many output formats, but it is most commonly used for formatting readme files, for writing messages in online discussion forums, and for creating rich text using a plain text editor. | markup, text formatting, documentation, content creation | Software Engineering, Other Computer and Information Sciences | Markup Language | Documentation, Uses, and more |
| mash | ACES | Mash is a fast and flexible genome distance estimator that can accurately estimate the pairwise genetic distance between genomes. It uses a MinHash dimensionality reduction technique to efficiently compute Jaccard distances between large sets of DNA sequences, enabling rapid genome comparisons. | Genome Distance Estimator, Minhash Technique, Jaccard Distances, DNA Sequences, Genome Comparisons | Genomics, Biological Sciences | Command-line tool | Documentation, Uses, and more |
| mathematica | Stampede3 | Mathematica is a computational software program used in scientific, engineering, mathematical and computing fields. It provides a wide range of tools for symbolic and numerical computations, visualization, data analysis, and programming. | Computational Software, Mathematics, Data Analysis, Programming, Visualization | Mathematics | Mathematical Software | Documentation, Uses, and more |
| matio | ACES | matio is a library for reading and writing MATLAB MAT files in C and Fortran. The library supports reading and writing Level 5 MAT files and supports most of the features of MAT 4 and MAT 5 MAT files. | Matlab Mat Files, C, Fortran | Other Mathematics, Mathematics | Data Management | Documentation, Uses, and more |
| matlab | Anvil ACES Expanse Delta Stampede3 |
MATLAB is a high-performance language for technical computing and visualization. It integrates computation, visualization, and programming in an easy-to-use environment where problems and solutions are expressed in familiar mathematical notation. | Programming Language, Technical Computing, Visualization, Mathematical Notation | Applied Mathematics, Mathematics | Computational Software | Documentation, Uses, and more |
| matplotlib | ACES | Matplotlib is a comprehensive library for creating static, animated, and interactive visualizations in Python. It can be used to generate plots, histograms, power spectra, bar charts, error charts, scatterplots, etc. Matplotlib is highly customizable and offers a wide range of plotting options and styles. | Python Library, Data Visualization, Plotting Library | Computer Science, Computer & Information Sciences | Plotting & Graphing Tool | Documentation, Uses, and more |
| maturin | ACES | Maturin is a Rust-native build system for Python packages that allows users to create wheels for their Python packages written in Rust. It aims to simplify the process of packaging and distributing Python extensions written in Rust, providing a seamless integration between Rust and Python ecosystems. | Python Packaging, Rust Programming Language, Build System, Python Extensions, Package Distribution | Software Development, Computer & Information Sciences | Build System | Documentation, Uses, and more |
| maven | ACES | Apache Maven is a build automation tool used primarily for Java projects. It manages project dependencies and provides a standardized way to build, test, and deploy Java software projects. | Build Automation, Dependency Management, Java Projects | Software Development, Computer & Information Sciences | Development Tool | Documentation, Uses, and more |
| mayavi | ACES | Mayavi is a scientific data visualization tool that integrates seamlessly with Python, providing a powerful interface for 3D visualization of data. | Visualization, Scientific Computing, 3D Graphics, Data Analysis | Computational Science, Computer Science | Visualization Tool | Documentation, Uses, and more |
| mctc-lib | ACES | Documentation, Uses, and more | ||||
| mdi | ACES | Documentation, Uses, and more | ||||
| mdspan | Stampede3 | mdspan is a C++ library that provides a multidimensional array data structure with a fixed size at compile time. It offers a high-performance alternative to traditional dynamically allocated multidimensional arrays. | C++ Library, Multidimensional Array, Data Structure, High-Performance Computing | Computer Science, Computer & Information Sciences | Data Structure | Documentation, Uses, and more |
| mdtest | Delta | MDTest is a file system metadata benchmark that includes tests to measure metadata operations, such as file creates, stat operations, and directory operations. It is often used to assess the metadata performance of parallel file systems. | Benchmarking, File System, Metadata | High-Performance Computing, Computer & Information Sciences | Tool | Documentation, Uses, and more |
| mdtraj | ACES | MDTraj is a Python library that allows users to analyze molecular dynamics trajectories. It provides tools to read, write, and manipulate trajectory data from various simulation packages. | Molecular Dynamics, Trajectory Analysis, Python, Bioinformatics | Molecular Dynamics, Biochemistry and Molecular Biology | Library | Documentation, Uses, and more |
| meep | Anvil | Meep (or MIT Electromagnetic Equation Propagation) is a free finite-difference time-domain (FDTD) simulation software package developed at MIT to model electromagnetic systems. | Simulation, Electromagnetics, Fdtd | Physical Sciences | Computational Software | Documentation, Uses, and more |
| memoryviewer | ACES | MemoryViewer is a software tool used for analyzing and visualizing memory usage and data structures within computer programs. It allows users to track memory allocation, deallocation, and usage patterns to optimize memory management. | Memory Management, Software Development, Performance Analysis | Computer & Information Sciences | Development Tool | Documentation, Uses, and more |
| mercurial | ACES | Mercurial is a free, distributed source control management tool. It efficiently handles projects of any size and offers an intuitive interface. | Version Control, Software Development | Software Development, Computer & Information Sciences | Development Tools | Documentation, Uses, and more |
| mercury | ACES | Documentation, Uses, and more | ||||
| mesa | ACES Delta |
Mesa is an open-source agent-based modeling framework that allows users to create and analyze computational models of complex adaptive systems. | Agent-Based Modeling, Complex Systems, Simulation, Computational Modeling | Other Computer & Information Sciences, Computer & Information Sciences | Framework | Documentation, Uses, and more |
| mesa-glu | Anvil Delta |
mesa-gl is an open-source implementation of the OpenGL specification, a system for rendering interactive 3D graphics, and a widely used and versatile graphics library. mesa-glu is the OpenGL Utility Library (GLU) component of Mesa, providing useful functions for building OpenGL applications. | Graphics, 3D Graphics, Opengl, Graphics Library | Library | Documentation, Uses, and more | |
| meson | ACES DeltaAI |
Meson is an open-source build system meant to be both extremely fast and as user-friendly as possible. | Build System, Software Development, Automation | Computer Science, Computer & Information Sciences | Compiler | Documentation, Uses, and more |
| meson-python | ACES | Meson is a high-productivity build system. It provides a simple syntax for describing how your project is build and a wide range of options to control the build process. | Build System, Automation, Software Development | Software Engineering, Computer & Information Sciences | Build System | Documentation, Uses, and more |
| metaeuk | ACES | MetaEuk is a software tool designed for the identification and annotation of eukaryotic genes from metagenomic data. It utilizes a combination of sequence alignment and machine learning techniques to improve the accuracy of gene predictions in complex environmental samples. | bioinformatics, metagenomics, gene prediction, annotation | Bioinformatics, Computational Biology | Command-line tool | Documentation, Uses, and more |
| metaphlan | ACES | MetaPhlAn is a computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data. It relies on unique clade-specific marker genes to identify and quantify the presence of microbial species in a sample. | Metagenomics, Microbiome, Microbial Ecology, Bioinformatics | Environmental Biology, Biological Sciences | Tool | Documentation, Uses, and more |
| methscan | ACES | Documentation, Uses, and more | ||||
| metis | ACES Stampede3 |
Metis is a computational software library for partitioning graphs, meshes, and hypergraphs. It provides algorithms that can efficiently partition large graphs and meshes while minimizing the edge-cuts and balancing the partition sizes. | Computational Software, Graph Partitioning, Mesh Partitioning, Hypergraph Partitioning | Computer Science, Computer & Information Sciences | Tool | Documentation, Uses, and more |
| mfem | ACES Stampede3 |
MFEM is a lightweight, general, scalable C++ library for finite element methods. Its features include a wide range of finite element spaces, high-order and variable-order discretizations, parallel computing support, and multiple examples and applications. | Finite Element Method, C++ Library, Parallel Computing | Applied Mathematics, Engineering & Technology | Library | Documentation, Uses, and more |
| mfqe | ACES | Documentation, Uses, and more | ||||
| mgard | ACES | MGARD is a software package designed for high-performance data compression, particularly for scientific data. It utilizes multigrid techniques to achieve efficient compression rates while maintaining data integrity. | Data Compression, High-Performance Computing, Scientific Computing | Data Science, Data Compression Techniques | Library | Documentation, Uses, and more |
| micromamba | ACES | micromamba is a lightweight, fast, and flexible package manager for managing environments and packages in Python and other languages. It is designed to be a minimalistic alternative to conda, providing the same functionality with a smaller footprint. | package manager, environment management, Python, cross-platform | Computer Science, Software Engineering | Package Manager | Documentation, Uses, and more |
| miniconda cuquantum | DeltaAI | Documentation, Uses, and more | ||||
| miniconda3 | ACES KyRIC |
Miniconda is a free minimal installer for conda. It is a package management system that simplifies the installation and management of software packages. Miniconda allows users to create environments containing dependencies from a specified list of packages, making it easier to manage different projects with conflicting package requirements. | Package Management, Dependency Management, Software Installation | Computer Science, Computer & Information Sciences | Package Manager | Documentation, Uses, and more |
| miniforge3 | ACES | Miniforge is a community-driven minimal installer for Conda, designed to provide a lightweight and flexible environment for managing packages and environments in Python and other languages. | Conda, Package Management, Environment Management, Python | Bioinformatics, Biological Sciences | Package Manager | Documentation, Uses, and more |
| miniforge3-python | Delta | Miniforge is a community-driven minimal installer for conda, allowing users to create and manage environments with Python and other packages. | Python, Conda, Environment Management, Package Management | Software Engineering, Computer Science | Package Manager | Documentation, Uses, and more |
| miniforge3_datascience | DeltaAI | Documentation, Uses, and more | ||||
| miniforge3_pytorch | DeltaAI | Documentation, Uses, and more | ||||
| miniforge3_tensorflow_cpu | DeltaAI | Miniforge is a community-driven minimal installer for conda, which includes TensorFlow optimized for CPU usage. | conda, TensorFlow, machine learning, CPU optimization | Computer Science, Artificial Intelligence and Intelligent Systems | Package Manager | Documentation, Uses, and more |
| miniforge3_tensorflow_cuda | DeltaAI | Documentation, Uses, and more | ||||
| minimap2 | ACES | Minimap2 is a versatile sequence alignment program that can be used for mapping DNA or cDNA sequences to a reference genome. It is known for its speed and accuracy, making it a popular choice for various bioinformatics applications. | Sequence Alignment, Bioinformatics, Genomics, Computational Biology | Bioinformatics, Biological Sciences | Bioinformatics Tool | Documentation, Uses, and more |
| miniprot | ACES | Miniprot is a software tool for predicting and modeling protein structures, including protein folding, structure prediction, and structural analysis. It is designed to be user-friendly and efficient for researchers working in the field of protein structure prediction and molecular modeling. | Protein Structure Prediction, Molecular Modeling, Protein Folding, Structural Analysis, Bioinformatics | Bioinformatics, Biological Sciences | Prediction & Modeling | Documentation, Uses, and more |
| minizip | ACES | Minizip is a minimalistic, open-source library that provides a simple API to create, read, and update zip files. It is a lightweight solution for working with zip archives in C or C++ projects. | Compression, Archiving, Library, Open Source | Computer Science, Software Engineering | Compression/Archiving | Documentation, Uses, and more |
| minpath | ACES | Documentation, Uses, and more | ||||
| mkfontdir | DeltaAI | mkfontdir is a utility that generates an index of font files in a directory, creating a fonts.scale file that is used by the X Window System to manage fonts. | Font Management, X Window System, Utilities | Software Engineering, Other Computer and Information Sciences | Utility | Documentation, Uses, and more |
| mkfontscale | DeltaAI | mkfontscale is a utility that generates an index of scalable fonts for the X Window System. | Font Management, X Window System, Utilities | Software Engineering, Other Computer and Information Sciences | Utility | Documentation, Uses, and more |
| mkl | KyRIC | Intel Math Kernel Library (Intel MKL) is a highly optimized, thread-safe, mathematical library for performing mathematical, statistical, and data analysis computations. It offers high-performance implementations of BLAS, LAPACK, ScaLAPACK, sparse solvers, FFT, and more for Intel processors. | Mathematical Library, Optimized Computations, Thread-Safe Functions | Computer Science | Computational Software | Documentation, Uses, and more |
| mkl32 | KyRIC | Intel(R) Math Kernel Library for 32-bit applications | Mathematics, Computational Software, Hpc Tools | Other Mathematics | Library | Documentation, Uses, and more |
| mkmod | Stampede3 | Documentation, Uses, and more | ||||
| ml-collections | ACES | A library that provides a collection of utilities for managing configurations in machine learning projects. | Machine Learning, Configuration Management, Python | Machine Learning, Artificial Intelligence and Intelligent Systems | Library | Documentation, Uses, and more |
| ml_dtypes | ACES | Documentation, Uses, and more | ||||
| mmg | ACES | MMG is a software package designed for the generation and adaptation of unstructured meshes in two and three dimensions. It is particularly useful for numerical simulations in scientific computing. | mesh generation, mesh adaptation, scientific computing, numerical simulations | Numerical Methods, Computational Science | Open Source | Documentation, Uses, and more |
| mmseqs2 | ACES | MMseqs2 is a software suite for fast and sensitive sequence searching. It enables ultra-fast and sensitive sequence search and clustering functionality using a versatile and memory-efficient index data structure. | Sequence Searching, Sequence Clustering, Bioinformatics, Computational Biology | Biological Sciences | Sequence Search & Clustering Tool | Documentation, Uses, and more |
| mmseqs2-gpu | ACES | Documentation, Uses, and more | ||||
| moab | ACES | MOAB (Mesh Oriented datABase) is a software library designed for managing and manipulating unstructured mesh data in high-performance computing applications. | mesh management, high-performance computing, scientific computing | High-Performance Computing, Computational Chemistry | Library | Documentation, Uses, and more |
| modtree | Anvil | ModTree is a software tool for the reconstruction of modular trees of mRNA transcripts and alternative splicing events. It is designed to identify and visualize the modular organization of alternative splicing events within a transcriptome. | Transcriptomics, Alternative Splicing, Modular Trees, Data Analysis | Genetics, Biological Sciences | Computational Software | Documentation, Uses, and more |
| modulair | ACES | Documentation, Uses, and more | ||||
| modular | ACES | Documentation, Uses, and more | ||||
| module-git | Expanse | module-git is a version control system designed to efficiently handle large projects, providing powerful branching, merging, and collaboration features. It allows multiple developers to work on the same codebase concurrently and maintain a complete history of changes. | Version Control, Distributed Version Control, Collaboration, Software Development | Documentation, Uses, and more | ||
| module-info | Expanse | module-info is a software tool that provides information about loaded modules and their dependencies in a computing environment. It helps users to manage and troubleshoot software dependencies and configurations. | Software, Dependency Management, Software Configuration | System Information Tool | Documentation, Uses, and more | |
| mold | ACES | Mold is a computational software tool developed for conducting molecular dynamics simulations in the field of biophysics and computational chemistry. It is designed to model the behavior of biomolecules and study their interactions at the atomic level. | Computational Software, Molecular Dynamics, Biophysics, Chemistry | Biophysics, Biological Sciences | Molecular Dynamics Simulator | Documentation, Uses, and more |
| monai | ACES | MONAI (Medical Open Network for AI) is a PyTorch-based, open-source framework for healthcare imaging. It provides domain-optimized foundational capabilities for developing medical imaging deep learning algorithms. MONAI enables the reproducible and scalable research for the development of novel imaging technologies and clinical applications. | Deep Learning, Medical Imaging, Pytorch, Open Source | Biomedical Engineering, Engineering & Technology | Research | Documentation, Uses, and more |
| monitor | Anvil | A monitor is an electronic visual display for computers. It usually consists of a screen, circuitry, and casing. The display device in modern monitors is typically a thin film transistor liquid crystal display (TFT-LCD) or a flat panel LED display, while older monitors used a cathode ray tube (CRT). Monitors are used to display output from the computer's graphics card, allowing users to interact with the computer and its software. | Technology, Display, Computer Hardware | Device | Documentation, Uses, and more | |
| motif | ACES | Motif is a software tool used for motif discovery and motif analysis in biological sequences. It is commonly employed in bioinformatics and computational biology to identify conserved patterns or motifs within nucleotide or protein sequences. | Bioinformatics, Computational Biology, Sequence Analysis | Biological Sciences | Sequence Analysis Tool | Documentation, Uses, and more |
| mpc | Anvil ACES DeltaAI KyRIC |
MPC, short for Multi-Party Computation, is a cryptographic protocol that allows multiple parties to jointly compute a function over their inputs while keeping those inputs private. It ensures data privacy and security in collaborative computations. | Cryptographic Protocol, Secure Computation, Privacy-Preserving, Collaborative Computation | Computer & Information Sciences | Cryptographic Protocol | Documentation, Uses, and more |
| mpfr | Anvil ACES DeltaAI Expanse KyRIC Stampede3 |
The GNU MPFR (Multiple Precision Floating-Point Reliable) library is a C library for arbitrary-precision arithmetic on floating-point numbers that guarantees correctly rounded results. | Arbitrary-Precision Arithmetic, Floating-Point Computation, Mathematical Library | Numerical Analysis, Mathematics | Computational Software | Documentation, Uses, and more |
| mpi | KyRIC | Message Passing Interface (MPI) is a standardized and portable message-passing system designed to enable scalable, parallel computing on a wide variety of parallel computers. It is widely used in the field of high-performance computing (HPC) to develop parallel programs that can run efficiently on distributed memory architectures. | Hpc, Parallel Computing, Message Passing, Scalable Computing | Computer Science, Computer & Information Sciences | Library | Documentation, Uses, and more |
| mpi4py | ACES | MPI for Python (mpi4py) provides bindings of the Message Passing Interface (MPI) standard for the Python programming language. It allows Python programs to directly interact with MPI parallel computation functionalities. | Parallel Computing, Message Passing Interface, Python Library | Computer Science, Computer & Information Sciences, Other Computer & Information Sciences | Python Library | Documentation, Uses, and more |
| mpich | ACES DeltaAI Delta KyRIC |
MPICH is a high-performance and widely portable implementation of the Message Passing Interface (MPI) standard. It enables parallel computing on a wide variety of platforms and architectures. | Mpi Implementation, Parallel Computing, High Performance Computing | Computer Science, Computer & Information Sciences | Library | Documentation, Uses, and more |
| mpich-abi | DeltaAI Delta |
Documentation, Uses, and more | ||||
| mpifileutils | ACES | A collection of utilities for managing files in parallel using MPI. | MPI, Parallel Computing, File Management | Computer Science | Command Line Tool | Documentation, Uses, and more |
| mpip | DeltaAI | mpip is a small utility that helps to install and manage MPI libraries on HPC clusters by simplifying the process of downloading, configuring, building, and installing MPI libraries. | Software Utility, Hpc, Mpi Libraries, Cluster Management, Installation Tool | Engineering & Technology | Documentation, Uses, and more | |
| mpixlate | DeltaAI Delta |
Documentation, Uses, and more | ||||
| mpl | Stampede3 | Documentation, Uses, and more | ||||
| mrbayes | Anvil | MrBayes is a program for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models. It employs Markov chain Monte Carlo methods to estimate the posterior distribution of model parameters. | Bayesian Inference, Phylogenetics, Evolutionary Biology | Systematics & Population Biology, Biological Sciences | Software Tool | Documentation, Uses, and more |
| mrcfile | ACES | mrcfile is a Python library for reading and writing MRC (Medical Research Council) format files, commonly used in electron microscopy and other scientific imaging applications. | Python, Image Processing, Scientific Computing, Electron Microscopy | Bioinformatics, Biological Sciences | Library | Documentation, Uses, and more |
| mrnet | DeltaAI Delta |
MRNET (Mendelian Randomization using Network models) is a software package for performing causal inference through Mendelian randomization and network modeling. It allows researchers to investigate causal relationships between traits by leveraging genetic instrumental variables and network structures. | Causal Inference, Mendelian Randomization, Network Modeling, Genetic Instrumental Variables | Research Tool | Documentation, Uses, and more | |
| mstore | ACES | Documentation, Uses, and more | ||||
| mujoco | ACES | MuJoCo is a physics engine for detailed, efficient and accurate simulation of complex dynamical systems. It is designed for high-fidelity modeling and simulation of computational and robotic systems in various domains. | Physics Engine, Simulation, Robotics | Artificial Intelligence & Intelligent Systems, Engineering & Technology | Physics Engine | Documentation, Uses, and more |
| multichoose | ACES | multichoose is a Python library that implements the concept of multichoose, which calculates the number of ways to choose a certain number of items from a set where each item can be chosen multiple times. | Python Library, Combinatorics, Mathematics | Pure Mathematics, Mathematics | Mathematical Calculation Tool | Documentation, Uses, and more |
| multiprocess | ACES | Documentation, Uses, and more | ||||
| multiqc | ACES | MultiQC is a reporting tool that collects statistics from multiple bioinformatics analyses and generates a single report. It helps in summarizing the output from various bioinformatics tools in a standardized and consolidated format. | Bioinformatics, Computational Biology, Data Analysis, Reporting Tool | Biological Sciences | Visualization Tool | Documentation, Uses, and more |
| mummer | ACES | MUMmer is a system for rapidly aligning entire genomes, whether in complete or draft form. It can also align a wide range of sequences, including protein-coding sequences. | Genome Alignment, Sequence Alignment, Bioinformatics | Computational Biology, Biological Sciences | Bioinformatics | Documentation, Uses, and more |
| mumps | ACES Stampede3 |
MUMPS (MUltifrontal Massively Parallel sparse direct Solver) is a software package for the parallel solution of large sparse systems of linear equations arising from computational science and engineering applications. | Linear Algebra, Sparse Matrices, Computational Science, Engineering | Applied Mathematics, Mathematics | Solver | Documentation, Uses, and more |
| musl | ACES | musl is a lightweight, fast, simple, and secure C library that targets modern Unix systems. It is designed for embedded systems, performance-critical applications, and other resource-constrained environments where a small footprint is essential. | C Library, Embedded Systems, Performance Optimization, Resource-Constrained Environments | Software Engineering, Computer & Information Sciences | C Library | Documentation, Uses, and more |
| mvapich | Stampede3 | MVAPICH (MPI for MVAPICH2) is an open-source MPI implementation that delivers high performance, scalability, and fault tolerance for parallel computing on large HPC systems. It is specifically designed for InfiniBand and Omni-Path architectures. | Hpc, Mpi, Parallel Computing, High Performance Computing | Computer Science, Engineering & Technology | Parallel Computing | Documentation, Uses, and more |
| mvapich-plus | ACES | MVAPICH-Plus is a high-performance implementation of the Message Passing Interface (MPI) standard, designed for high-performance computing (HPC) environments. It is optimized for various interconnects and provides advanced features for performance and scalability. | MPI, High-Performance Computing, Parallel Computing, Networking | High-Performance Computing, Computer Science | Library | Documentation, Uses, and more |
| mvapich-plus-cpu | Stampede3 | Documentation, Uses, and more | ||||
| mvapich-plus-pvc | Stampede3 | Documentation, Uses, and more | ||||
| mvapich2 | Anvil KyRIC |
MVAPICH2 is an open-source MPI implementation for InfiniBand, iWARP, and RoCE communication protocols which delivers high performance and scalability on a wide variety of HPC systems. | Mpi Implementation, High Performance Computing, Infiniband, Open-Source | Computer Science, Physical Sciences | Library/Tool | Documentation, Uses, and more |
| mvapich2-gdr | ACES | MVAPICH2-GDR is a high-performance MPI library designed for NVIDIA GPU Direct RDMA technology, allowing direct data transfers between GPUs and networking adapters without involving the CPU. It is optimized for HPC clusters and large-scale computing environments to achieve low latency and high message rate communication. | Hpc, Mpi Library, Gpu Direct Rdma, High-Performance Computing | High-Performance Computing, Engineering & Technology | Library | Documentation, Uses, and more |
| mygene | ACES | MyGene is a Python package that provides a simple interface to access gene-related data from various public databases, including gene annotations, gene expression data, and more. | bioinformatics, genomics, data retrieval, Python | Bioinformatics, Genetics | Library | Documentation, Uses, and more |
| namd | Anvil ACES Delta Stampede3 |
NAMD (NAnoscale Molecular Dynamics) is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. It is optimized for the simulation of biomolecular systems containing millions of atoms. | Molecular Dynamics, Biomolecular Systems, Parallel Computing, Cuda, Simulation | Biochemistry and Molecular Biology | Computational Software | Documentation, Uses, and more |
| namd-linux-x86_64-multicore | KyRIC | NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. | Molecular Dynamics, Biomolecular Simulation, High-Performance Computing | Biophysics, Biochemistry and Molecular Biology | Simulation Software | Documentation, Uses, and more |
| namd-multicore-cuda | ACES | A parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. | Documentation, Uses, and more | |||
| namd-netlrts-smp-cuda | ACES | NAMD (NAnoscale Molecular Dynamics) is a high-performance molecular dynamics software that simulates large biomolecular systems. This version of NAMD is customized for parallel computing on multicore machines with CUDA support for GPU acceleration. | Molecular Dynamics, Simulation, Biomolecular Systems, Parallel Computing, Cuda, Gpu Acceleration | Bioinformatics, Biological Sciences | Scientific Software | Documentation, Uses, and more |
| namd-verbs-smp-cuda | ACES | A parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. | Documentation, Uses, and more | |||
| nano | ACES DeltaAI |
Nano is a simple and user-friendly text editor for Unix-like systems, designed to be easy to use for beginners while still providing powerful features for advanced users. | Text Editor, Unix, Open Source | Software Development, Computer Science | Text Editor | Documentation, Uses, and more |
| nanoget | ACES | Documentation, Uses, and more | ||||
| nanomath | ACES | Documentation, Uses, and more | ||||
| nasm | ACES DeltaAI |
NASM (Netwide Assembler) is an 80x86 and x86-64 assembler designed for portability and modularity. It supports a range of object file formats, including Linux and Windows executables, and generates code compatible with Intel syntax. | Assembler, Cross-Platform, X86, Programming | Computer Science, Computer & Information Sciences | Assembler | Documentation, Uses, and more |
| nbclassic | ACES | nbclassic is a classic Jupyter Notebook interface that allows users to create and share documents that contain live code, equations, visualizations, and narrative text. | Jupyter, Notebook, Interactive Computing, Data Science | Data Analysis, Data Science | Web Application | Documentation, Uses, and more |
| nbo | Expanse | Natural Bond Orbital (NBO) analysis is a popular method for understanding chemical bonding in molecules. It provides insight into the nature of chemical bonds, bond strengths, and electron delocalization. | Chemistry, Molecular Biology, Computational Chemistry | Physical Chemistry, Chemical Sciences | Molecular Modeling | Documentation, Uses, and more |
| ncbi-vdb | ACES | NCBI-vdb is a collection of software tools for managing data from the NCBI Sequence Read Archive, the GenBank flatfile sequence databases, as well as a framework for loading data into third-party caller software. It provides tools for downloading, validating, transforming, and analyzing biological sequence data. | Bioinformatics, Sequence Data Management, Data Analysis | Bioinformatics, Biological Sciences | Tool | Documentation, Uses, and more |
| nccl | ACES DeltaAI Anvil |
NCCL (NVIDIA Collective Communication Library) is a library of multi-GPU collective communication primitives that are topology-aware and can be used to implement collective communications algorithms within CUDA kernels. | Cuda, Parallel Computing, Multi-Gpu Communication, Gpu Programming, Hpc | Computer Science, Computer & Information Sciences | Parallel Computing | Documentation, Uses, and more |
| nccl-ofi-plugin | DeltaAI | Documentation, Uses, and more | ||||
| ncl | Anvil ACES |
The NCAR Command Language (NCL) is a scripting language designed specifically for the analysis and visualization of scientific data. It is widely used in the atmospheric and related sciences. | Scientific Data Analysis, Data Visualization, Atmospheric Sciences | Environmental Sciences, Earth & Environmental Sciences | Scripting Language | Documentation, Uses, and more |
| nclncarg | Stampede3 | Documentation, Uses, and more | ||||
| nco | Anvil ACES Stampede3 |
NCO (NetCDF Operators) is a suite of programs designed to help manipulate and analyze netCDF and HDF4 files. It provides a range of powerful tools for processing and analyzing climate and weather data stored in netCDF format. | Data Manipulation, Data Analysis, Climate Data, Netcdf, Hdf4 | Environmental Science, Earth & Environmental Sciences | Command-line tool | Documentation, Uses, and more |
| ncurses | Anvil ACES DeltaAI KyRIC |
ncurses is a programming library providing an API that allows the programmer to write text-based user interfaces on a terminal. | Programming Library, Text-Based User Interfaces, Terminal Applications | Computer Science, Computer & Information Sciences | Programming/Development | Documentation, Uses, and more |
| ncview | Anvil Stampede3 |
ncview is a visual browser for netCDF format files used for earth system data. It provides functionalities for viewing, analyzing, and interacting with data stored in netCDF files. | Data Visualization, Netcdf, Earth System Data | Earth and Environmental Sciences | Data Analysis Tool | Documentation, Uses, and more |
| neci | ACES | Documentation, Uses, and more | ||||
| nedit | ACES | Documentation, Uses, and more | ||||
| neper | ACES | Neper is a software tool for generating and manipulating 3D polycrystalline microstructures. It is particularly useful in materials science for simulating the mechanical behavior of materials at the microscale. | microstructure, polycrystalline, materials science, simulation, finite element analysis | Computational Materials Science, Materials Science | Open Source | Documentation, Uses, and more |
| netcdf | ACES Expanse Stampede3 |
NetCDF (Network Common Data Form) is a set of software libraries and self-describing, machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data. | Scientific Data, Data Storage, Data Access, Data Formats, Data Manipulation, Data Visualization | Environmental Data, Other Natural Sciences | Library | Documentation, Uses, and more |
| netcdf-c | Anvil | NetCDF (Network Common Data Form) is a set of software libraries and self-describing, machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data. | Data Format, Scientific Data, Data Access, Data Sharing | Climate and Global Dynamics, Other Natural Sciences | Data Format | Documentation, Uses, and more |
| netcdf-c++4 | ACES | netCDF-C++4 is a C++ interface for netCDF4, which is a software library and file format for storing multidimensional scientific data. It provides an object-oriented programming interface to the netCDF library, allowing users to read and write data stored in netCDF format using C++. | Netcdf, C++ Interface, Scientific Data Storage | Environmental Science, Other Natural Sciences | Data Storage | Documentation, Uses, and more |
| netcdf-cxx | Delta | netcdf-cxx is a C++ interface for the NetCDF data format, which provides implementations to read and write self-describing, machine-independent binary data files. It is designed to simplify the use of NetCDF in C++ applications. | Netcdf, C++ | Earth & Environmental Sciences | Data Processing | Documentation, Uses, and more |
| netcdf-cxx4 | Anvil Delta |
netcdf-cxx4 is a C++ library for accessing netCDF-4 classic and extended model data formats. It provides a high-level interface for reading and writing netCDF-4 data files in C++. | Netcdf, C++, Data Format | Climate Science, Computer & Information Sciences | Data Processing | Documentation, Uses, and more |
| netcdf-fortran | Anvil ACES |
NetCDF-Fortran is a set of Fortran interfaces to the NetCDF library providing an easy-to-use, high-level access to the NetCDF file format for storing and sharing scientific data. | Scientific Data, Fortran Interface, Netcdf Library | Data Analysis, Other Natural Sciences | Programming Interface | Documentation, Uses, and more |
| netcdf4-python | ACES | NetCDF4 is a Python interface to the netCDF version 4 library. NetCDF is a set of software libraries and self-describing, machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data. | Python Library, Netcdf, Scientific Data Handling, Array-Oriented Data, Data Storage & Access | Climate and Global Dynamics, Earth & Environmental Sciences | Library | Documentation, Uses, and more |
| netcdff | Stampede3 | netcdff is a software library for accessing and creating netCDF format data files in Fortran. | Software Library, Fortran, Netcdf | Earth & Environmental Sciences, Natural Sciences | Library | Documentation, Uses, and more |
| netlib-lapack | Anvil | Netlib LAPACK (Linear Algebra PACKage) is a widely-used library for numerical linear algebra. It provides routines for solving systems of simultaneous linear equations, least-squares solutions of linear systems of equations, eigenvalue problems, and singular value problems. | Numerical Computing, Linear Algebra, Library, Numerical Analysis | Applied Mathematics, Computer & Information Sciences | Library | Documentation, Uses, and more |
| netperf | Expanse | Netperf is a network performance benchmarking tool that can be used to measure various aspects of network performance, including throughput and latency. | networking, performance, benchmarking, throughput, latency | Network Performance, Computer Science | Benchmarking Tool | Documentation, Uses, and more |
| nettle | ACES DeltaAI |
Nettle is a cryptographic library that is designed to be low-level and general-purpose, offering several cryptographic algorithms such as AES, ARCFOUR, Blowfish, and MD5. | Cryptography, Security, Library | Cryptography, Computer & Information Sciences, Computer Science | Library | Documentation, Uses, and more |
| networkx | ACES | NetworkX is a Python package for the creation, manipulation, and study of complex networks or graphs. It provides data structures for representing many types of networks, algorithms for analyzing them, and visualization tools to display them. | Python Library, Graph Theory, Network Analysis, Data Visualization | Computer & Information Sciences | Computational Software | Documentation, Uses, and more |
| nextflow | Anvil ACES |
Nextflow is a powerful workflow manager that enables the writing of parallel and scalable computational workflows using native, containerized, or cloud-enabled execution environments. | Workflow Manager, Computational Biology, Data Science | Computational Biology, Biological Sciences | Open Source | Documentation, Uses, and more |
| nf-core | Anvil | NF-core is a collection of community curated Nextflow pipelines available for genomics, transcriptomics, and other bioinformatics analyses. It provides a collection of best practices workflows that are highly optimized, scalable, and easy to use. | Bioinformatics, Workflow Management, Nextflow, Genomics, Transcriptomics | Bioinformatics, Biological Sciences | Data Analysis Tool | Documentation, Uses, and more |
| ngc | Anvil | NGC is a cloud-based hub that provides users with a comprehensive catalog of GPU-optimized software for deep learning, machine learning, and HPC applications. It offers a platform for easy deployment and integration of GPU-accelerated applications in various domains. | Cloud Computing, Deep Learning, Machine Learning, Hpc | Artificial Intelligence and Intelligent Systems | Platform | Documentation, Uses, and more |
| ngc/cuquantum-appliance | DeltaAI | Documentation, Uses, and more | ||||
| nghttp2 | ACES DeltaAI |
nghttp2 is an open-source implementation of the Hypertext Transfer Protocol version 2 (HTTP/2) and its header compression algorithm. The project also include a HTTP/2 server, client, and proxy. | Http/2, Web Protocol, Networking | Computer Science, Computer & Information Sciences | Library | Documentation, Uses, and more |
| nghttp3 | ACES | nghttp3 is an implementation of HTTP/3 and QUIC protocol in C programming language. It provides a low-level API for developers to interact with HTTP/3 and QUIC connections. | Http/3, Quic, Networking, Protocol | Computer Science, Computer & Information Sciences | Protocol | Documentation, Uses, and more |
| ngtcp2 | ACES | ngtcp2 is a C library implementation of the QUIC protocol (IETF draft) for building QUIC servers and clients. | Quic Protocol, C Library, Networking | Networking, Computer & Information Sciences | Library | Documentation, Uses, and more |
| nibabel | ACES | NiBabel is a Python library that provides read and write access to some common medical and neuroimaging file formats, including NIfTI-1, NIfTI-2, and Analyze. It aims to simplify the process of working with neuroimaging data in Python. | Python Library, Neuroimaging, Medical Imaging, File Format, Nifti | Neuroimaging, Biological Sciences | Imaging & Visualization | Documentation, Uses, and more |
| ninja | ACES DeltaAI Stampede3 |
ninja is a small build system with a focus on speed. It differs from other build systems in that it is designed to have its input files generated by a higher-level build system (like CMake) and will not execute commands in parallel by default. | Build System, Software Development, Automation | Software Engineering, Systems & Development, Engineering & Technology | Utility | Documentation, Uses, and more |
| nlohmann_json | ACES | nlohmann_json is a JSON library for modern C++. It provides a simple and efficient way to work with JSON data in C++ programs. | Json Library, C++ | Software Engineering, Computer & Information Sciences | Data Handling | Documentation, Uses, and more |
| nlopt | ACES | NLopt is an open-source library for nonlinear optimization problems. It provides a common interface for several different optimization algorithms, allowing users to easily switch between them. | Optimization, Library, Open-Source | Applied Mathematics, Mathematics | Library | Documentation, Uses, and more |
| nltk | Anvil ACES |
NLTK, or Natural Language Toolkit, is a leading platform for building Python programs to work with human language data. It provides easy-to-use interfaces to over 50 corpora and lexical resources such as WordNet, along with a suite of text processing libraries for classification, tokenization, stemming, tagging, parsing, and semantic reasoning. | Python Library, Text Processing, Natural Language Processing | Informatics, Analytics & Information Science, Computer & Information Sciences | Text Analysis | Documentation, Uses, and more |
| nmad | ACES | nMAD (normalized mean absolute deviation) is a measure of dispersion for a set of data points. It is used to quantify the variability or spread of the data. nMAD is calculated as the mean of the absolute differences between each data point and the mean of the data, divided by a constant factor for normalization. | Statistics, Data Analysis, Data Normalization | Other Mathematics | Measurement Tool | Documentation, Uses, and more |
| nodejs | ACES | Node.js is a JavaScript runtime built on Chrome's V8 JavaScript engine. It enables developers to build scalable network applications using JavaScript on the server side. | JavaScript, Server-Side, Runtime Environment, Event-Driven, Asynchronous | Computer Science, Software Engineering | Open Source | Documentation, Uses, and more |
| nostack | Expanse | nostack is a platform that allows users to visually design and build custom web and mobile applications without writing code. It provides a visual interface for drag-and-drop creation of applications. | Visual Development, No-Code Platform, Application Design, Web Development | Engineering & Technology, Computer & Information Sciences | Development Platform | Documentation, Uses, and more |
| nsight | Expanse | Documentation, Uses, and more | ||||
| nspr | ACES | nspr (Netscape Portable Runtime) provides a platform-neutral API for system level and libc-like functions. nspr is a platform abstraction library for C/C++. It provides many useful APIs for cross-platform development. | Platform-Abstraction, Cross-Platform, Api, System-Level Functions | Software Engineering, Computer & Information Sciences | Library | Documentation, Uses, and more |
| nss | ACES | Network Security Services (NSS) is a set of libraries designed to support cross-platform development of security-enabled client and server applications. It provides a complete open-source implementation of cryptographic libraries supporting Secure Sockets Layer (SSL) and Transport Layer Security (TLS) protocols. | Security, Network, Encryption | Computer & Information Sciences | Security | Documentation, Uses, and more |
| nsync | ACES | Nsync is a command-line tool for synchronizing files and directories between two locations. It allows users to easily mirror data between local and remote locations, ensuring that the contents are up to date in both places. | File Synchronization, Data Mirroring, Command-Line Tool | Computer Science, Engineering & Technology | File Synchronization Tool | Documentation, Uses, and more |
| ntl | ACES | ntl is a high-performance, portable C++ library providing data types for arbitrary length integers and floating-point numbers. It aims to offer efficient implementations for the fundamental algorithms in number theory. | Arbitrary Length Integers, Number Theory, High-Performance Computing, C++ Library | Pure Mathematics, Mathematics | Data Types & Algorithms | Documentation, Uses, and more |
| ntpoly | ACES | Documentation, Uses, and more | ||||
| numactl | Anvil ACES Expanse KyRIC |
Numactl is a set of tools that allows you to have more control over NUMA (Non-Uniform Memory Access) systems. It provides utilities for memory placement and migration of processes and controlling the NUMA policy of a process. | Numa, Memory Management, Performance Optimization | Other Computer & Information Sciences, Engineering & Technology | Tool | Documentation, Uses, and more |
| numba | ACES | Numba is an open-source just-in-time (JIT) compiler that translates a subset of Python and NumPy code into fast machine code. | Jit Compiler, Python Optimization, Numpy Optimization | Computer Science, Computer & Information Sciences | Open-Source | Documentation, Uses, and more |
| numpy | ACES | NumPy is a fundamental package for scientific computing with Python. It contains functionality for multidimensional arrays, high-level mathematical functions such as linear algebra operations, Fourier transformations, and random number generation. NumPy can be utilized to solve linear algebraic equations, perform statistical analysis, create software simulations, and much more. | Scientific Computing, Numerical Computing, Data Analysis, Mathematics | Mathematics, Computer & Information Sciences | Computational Software | Documentation, Uses, and more |
| nvbandwidth | Delta | Documentation, Uses, and more | ||||
| nvhpc | ACES Anvil Delta Jetstream2 |
NVIDIA HPC SDK is a comprehensive, integrated suite of compilers, libraries, and tools for the development and optimization of GPU-accelerated high-performance computing (HPC) applications. | Hpc, Gpu Acceleration, Compilers, Libraries, Development Tools | Computer Science, Computer & Information Sciences | Development Tool | Documentation, Uses, and more |
| nvhpc-byo-compiler | Delta | Documentation, Uses, and more | ||||
| nvhpc-hpcx | Delta | Documentation, Uses, and more | ||||
| nvhpc-hpcx-2.20-cuda12 | Delta | Documentation, Uses, and more | ||||
| nvhpc-hpcx-cuda11 | Delta | Documentation, Uses, and more | ||||
| nvhpc-hpcx-cuda12 | Delta | Documentation, Uses, and more | ||||
| nvhpc-nompi | Delta | Documentation, Uses, and more | ||||
| nvidia | DeltaAI Delta |
NVIDIA Corporation is an American technology company that designs graphics processing units (GPUs) for the gaming, cryptocurrency, and professional markets, as well as system on a chip units (SoCs) for the mobile computing and automotive market. | Graphics Processing Units, High-Performance Computing, Deep Learning, Data Analytics | Computer Science, Computer & Information Sciences | Graphics Processing Units | Documentation, Uses, and more |
| nvidia compilers | Stampede3 | NVIDIA compilers are a suite of compilers provided by NVIDIA for high-performance computing, specifically optimized for NVIDIA GPUs. They support languages such as C, C++, and Fortran, enabling developers to leverage GPU acceleration in their applications. | HPC, GPU Computing, Compilers, CUDA, Parallel Computing | Computer Science | Compiler | Documentation, Uses, and more |
| nvidia hpc sdk | Anvil | The NVIDIA HPC SDK is a comprehensive suite of compilers, libraries, and tools for high-performance computing applications. It supports CUDA, OpenACC, and OpenMP programming models, enabling developers to optimize their applications for NVIDIA GPUs. | HPC, GPU Computing, CUDA, OpenACC, OpenMP | Computer Science, Computer and Information Sciences | Development Tools | Documentation, Uses, and more |
| nvidia-mixed | DeltaAI Delta |
Documentation, Uses, and more | ||||
| nvitop | DeltaAI | Documentation, Uses, and more | ||||
| nvpl-blas | DeltaAI | Documentation, Uses, and more | ||||
| nvpl-fft | DeltaAI | Documentation, Uses, and more | ||||
| nvpl-lapack | DeltaAI | Documentation, Uses, and more | ||||
| nvshmem | ACES | nvshmem is a GPU-accelerated implementation of the OpenSHMEM standard designed for NVIDIA GPUs. It provides a high-performance, parallel programming model for developing applications on GPU clusters. | Gpu-Accelerated, Openshmem, Nvidia Gpus | Computer Science, Computer & Information Sciences, Other Computer & Information Sciences | Library | Documentation, Uses, and more |
| nvtop | ACES Delta |
nvtop is an NVIDIA GPU system monitoring tool with a user-friendly CLI interface. It provides real-time monitoring of GPU utilization, memory usage, temperature, power consumption, and other important metrics. | System Monitoring, Gpu Monitoring, Nvidia Gpu, Command-Line Interface, Performance Optimization | Computer Science, Computer & Information Sciences | Utility | Documentation, Uses, and more |
| nwchem | Anvil Delta Stampede3 |
NWChem is an open-source computational chemistry package designed for high-performance simulations of large-scale molecular systems. It provides various tools and algorithms for both classical and quantum chemical calculations. | Computational Chemistry, High-Performance Computing, Open-Source Software | Chemical Sciences | Computational Chemistry Software | Documentation, Uses, and more |
| ocaml | ACES | OCaml is a general-purpose programming language with an emphasis on expressiveness and safety, featuring a powerful type system and automatic memory management. | Programming Language, Functional Programming, Type Safety, Static Typing | Programming Languages, Software Engineering | Programming Language | Documentation, Uses, and more |
| oclfpga | KyRIC | oclfpga is an OpenCL framework for FPGA acceleration. It allows users to utilize the power of Field-Programmable Gate Arrays (FPGAs) for accelerating applications through OpenCL programming. | Opencl, Fpga, Acceleration | Engineering & Technology | Framework | Documentation, Uses, and more |
| octave | Anvil | Octave is a high-level interpreted language, primarily intended for numerical computations. It provides capabilities for the numerical solution of linear and nonlinear problems and has extensive graphics capabilities for data visualization and manipulation. | Numerical Computations, Data Visualization | Mathematics, Computer & Information Sciences | Numerical Computation Software | Documentation, Uses, and more |
| octopus | Stampede3 | Octopus is a software package designed for the simulation of quantum systems, particularly in the field of condensed matter physics. It allows for the study of various physical phenomena using time-dependent density functional theory (TDDFT) and other quantum mechanical methods. | Quantum Mechanics, Condensed Matter Physics, Simulation Software | Physics, Physical Sciences | Simulation | Documentation, Uses, and more |
| ohpc | KyRIC | OpenHPC is a collaborative, community-driven effort to provide a comprehensive and cohesive open-source HPC stack to the community. Through close collaboration with key stakeholders across the industry, OpenHPC aims to provide a reference collection of open-source HPC software components and best practices to enable the development, testing, and deployment of HPC systems. Ultimately, building on the resecarch outputs from various related fields. | Hpc, High Performance Computing, Open-Source, Collaborative, Community-Driven | Computer Science, Engineering & Technology | Computational Software | Documentation, Uses, and more |
| oneapi | Anvil | OneAPI is a unified programming model that aims to simplify development across diverse architectures such as CPUs, GPUs, FPGAs, and other accelerators. It provides a single programming interface for developers to efficiently target and deploy applications in heterogeneous computing environments. | Heterogeneous Computing, Unified Programming Model, Accelerated Computing, Performance Optimization | Computer Science, Computer & Information Sciences | Unified Programming Model | Documentation, Uses, and more |
| onnx | Anvil ACES |
ONNX (Open Neural Network Exchange) is an open-source format for AI models. It enables interoperability between different frameworks, making it easier to move models between various tools and platforms. | Ai, Machine Learning, Deep Learning | Artificial Intelligence & Intelligent Systems, Computer & Information Sciences | Interoperability Format | Documentation, Uses, and more |
| onnx-runtime | ACES | ONNX Runtime is a high-performance inference engine for deploying machine learning models in production. It supports models in the Open Neural Network Exchange (ONNX) format and is designed to optimize performance across various hardware platforms. | Machine Learning, Inference, ONNX, Cross-platform | Machine Learning, Artificial Intelligence and Intelligent Systems | Inference Engine | Documentation, Uses, and more |
| opari2 | ACES | OPARI2 (OpenMP Parallelizer and Runtime Instrumentation) is a tool for the parallelization and instrumentation of OpenMP programs. It helps to analyze and optimize the performance of parallel codes that use OpenMP directives. | Parallelization, Performance Analysis, Openmp | Computer Science, Computer & Information Sciences | Compiler/Analyzer | Documentation, Uses, and more |
| openbabel | ACES | Open Babel is an open-source chemical toolbox designed to facilitate the interconversion of chemical file formats and the manipulation of chemical data. | Cheminformatics, Molecular Modeling, File Conversion, Open Source | Cheminformatics, Molecular Modeling | Library | Documentation, Uses, and more |
| openblas | Anvil ACES DeltaAI Expanse Delta KyRIC |
OpenBLAS is an open-source implementation of the Basic Linear Algebra Subprograms (BLAS) library with optimized functions for matrix operations and linear algebra computations. It provides fast and efficient routines for common linear algebra operations. | Linear Algebra, Blas Library, Optimized Functions, Open Source | Mathematics, Computer & Information Sciences | Library | Documentation, Uses, and more |
| opencilk | Stampede3 | Documentation, Uses, and more | ||||
| opencv | Anvil ACES Delta |
OpenCV (Open Source Computer Vision Library) is an open-source computer vision and machine learning software library. It provides a wide range of functionalities for real-time computer vision, including image processing, object detection, object tracking, and machine learning algorithms. | Computer Vision, Image Processing, Machine Learning, Open Source | Computer Science, Computer & Information Sciences | Computer Vision Library | Documentation, Uses, and more |
| openexr | ACES | OpenEXR is a high dynamic-range (HDR) image file format developed by Industrial Light & Magic (ILM) for use in computer imaging applications. It is used for the interchange of high-fidelity image data between different software applications. | Image, File Format, High Dynamic-Range, Hdr, Image Data | Engineering & Technology | File Format | Documentation, Uses, and more |
| openfoam | Anvil ACES Stampede3 |
OpenFOAM (Open Source Field Operation and Manipulation) is a free, open-source computational fluid dynamics (CFD) software package developed by the OpenFOAM Foundation. It is widely used for simulating complex fluid flows in various industries and academic research. | Computational Fluid Dynamics, Open-Source Software, Finite Volume Method, Hpc | Fluid Dynamics, Physical Sciences | Computational Software | Documentation, Uses, and more |
| openfold | ACES | openfold is a computational software tool designed for protein folding simulations and structural analysis. It allows researchers to study the folding pathways of proteins and investigate their three-dimensional structures. | Computational Software, Molecular Dynamics Simulations, Protein Folding, Structural Analysis | Biophysics, Biological Sciences | Bioinformatics | Documentation, Uses, and more |
| openimageio | ACES | OpenImageIO is a library for reading and writing images, and a bunch of related functionality, like dealing with image formats and color management. | Image Processing, Color Management, Library, Image Formats, Cross-Platform | Image Processing, Computer & Information Sciences | Computational Software | Documentation, Uses, and more |
| openjdk | Anvil Expanse KyRIC |
OpenJDK (Open Java Development Kit) is a free and open-source implementation of the Java Platform, Standard Edition (Java SE). It is developed under the OpenJDK project as a collaboration between several companies and the open-source community. | Open-Source, Java Development, Software Development, Programming | Software Engineering, Computer & Information Sciences | Compiler | Documentation, Uses, and more |
| openjpeg | ACES | OpenJPEG is an open-source JPEG 2000 codec written in C language. It aims to provide an open-source toolkit for JPEG 2000 encoding and decoding. OpenJPEG is free software licensed under the BSD-2-Clause. | Jpeg 2000 Codec, Image Processing Software, Open-Source Software | Image Processing, Computer & Information Sciences | Codec | Documentation, Uses, and more |
| openldap | Expanse | OpenLDAP is an open-source implementation of the Lightweight Directory Access Protocol (LDAP) that provides a platform-independent, stable, and high-performance LDAP server suite. It is designed to provide robust, scalable, and secure directory services for managing user authentication, access control, and directory information. | Ldap, Directory Services, Authentication, Access Control, Open Source | Applied Computer Science, Computer & Information Sciences | System Software | Documentation, Uses, and more |
| openmc | ACES | OpenMC is a community-developed, open-source code for simulating the transport of neutrons and photons in a variety of materials. It is designed for high-performance computing applications and supports a wide range of geometries and materials. | Monte Carlo, neutron transport, photon transport, high-performance computing, open-source | Computational Methods, Nuclear Engineering | Simulation Software | Documentation, Uses, and more |
| openmm | ACES | OpenMM is a widely-used open-source toolkit for molecular dynamics simulation. It provides a high-performance, flexible, and easy-to-use platform for the development of computationally intensive simulations of biomolecular systems. | Molecular Dynamics, Biomolecular Simulations, Computational Chemistry, Biophysics, Gpu Acceleration | Bioinformatics, Biological Sciences | Molecular Dynamics Software | Documentation, Uses, and more |
| openmpi | Anvil ACES Expanse KyRIC |
OpenMPI is an open-source Message Passing Interface (MPI) library that allows parallel computing on a distributed memory system. It enables high performance computing (HPC) by facilitating communication and coordination between processes running on multiple nodes. | Mpi Library, Parallel Computing, High Performance Computing, Distributed Memory System | Computer Science, Computer & Information Sciences | Development Tools | Documentation, Uses, and more |
| openmpi4 | KyRIC | OpenMPI is an open-source Message Passing Interface implementation that allows for high-performance communication between nodes in a distributed computing environment. | HPC, Parallel Computing, Message Passing, Distributed Systems | Computer Science | Library | Documentation, Uses, and more |
| openpgm | ACES | OpenPGM is an open-source implementation of the Pragmatic General Multicast (PGM) protocol for reliable and scalable multicast communication. It offers high performance and reliability for applications requiring multicast messaging. | Multicast Communication, Network Protocols, Open Source Software | Artificial Intelligence, Computer & Information Sciences | Networking | Documentation, Uses, and more |
| openpyxl | ACES | openpyxl is a Python library for reading and writing Excel (xlsx) files. It allows for the manipulation of Excel spreadsheets, enabling users to create, modify, and extract data from Excel files programmatically. | Python, Excel, Spreadsheet, Data Manipulation, Open Source | Computational Sciences, Computer Science | Library | Documentation, Uses, and more |
| openscenegraph | ACES | OpenSceneGraph (OSG) is an open-source high-performance 3D graphics toolkit that is widely used in the fields of virtual reality, simulation, visualization, and gaming. It provides a powerful scene graph API for rapid development of interactive 3D graphics applications. | 3D Graphics, Virtual Reality, Simulation, Visualization, Gaming | Visualization and Human-Computer Systems, Engineering & Technology | Library | Documentation, Uses, and more |
| opensees | Stampede3 | OpenSees is an open-source software framework developed for simulating the seismic response of structural and geotechnical systems. It is widely used in civil engineering for earthquake engineering research, structural analysis, and performance-based design. | Simulation, Finite Element Analysis, Earthquake Engineering, Structural Analysis, Geotechnical Engineering | Civil Engineering, Engineering & Technology | Finite Element Analysis (Fea) | Documentation, Uses, and more |
| openshmemx | DeltaAI Delta |
OpenSHMEMX is a portable implementation of the OpenSHMEM API designed to provide a high-performance, flexible, and scalable parallel programming model for symmetric multiprocessing (SMP) and massively parallel processing systems. It extends the original OpenSHMEM and aims to simplify the development of parallel applications. | Parallel Programming, High-Performance Computing, Distributed Memory Programming | Computer Science, Computer & Information Sciences | Parallel Programming Library | Documentation, Uses, and more |
| openssh | KyRIC | OpenSSH is a suite of secure networking utilities based on the SSH protocol, providing encrypted communication sessions over a computer network using the SSH protocol. It offers secure remote login, secure file transfer, and public key authentication functionalities. | Ssh, Secure Networking, Utilities | Computer Science, Computer & Information Sciences | Utility | Documentation, Uses, and more |
| openssl | Anvil ACES DeltaAI KyRIC |
OpenSSL is a robust, commercial-grade, and full-featured toolkit for the Transport Layer Security (TLS) and Secure Sockets Layer (SSL) protocols. It is also a general-purpose cryptography library. | Cryptography, Security, Encryption, Networking | Cryptography, Computer & Information Sciences, Other Computer & Information Sciences | Toolkit | Documentation, Uses, and more |
| opensubdiv | ACES | OpenSubdiv is an open-source library that provides high-performance subdivision surface evaluation on massively parallel hardware. It generates high-quality surfaces, enabling detailed and complex geometry to be efficiently rendered and animated. | Subdivision Surface, Rendering, Animation | Computer Science, Computer & Information Sciences | Graphics | Documentation, Uses, and more |
| operating system provided modules | KyRIC | Documentation, Uses, and more | ||||
| opt-einsum | ACES | opt-einsum is a Python library for optimizing the computation of Einstein summation convention expressions, enabling efficient tensor contractions in high-performance computing applications. | tensor computation, optimization, high-performance computing, scientific computing, machine learning | Computer Science, Applied Computer Science | Library | Documentation, Uses, and more |
| optax | ACES | Optax is a gradient processing and optimization library for JAX, designed to facilitate the implementation of various optimization algorithms and gradient transformations. | Optimization, Machine Learning, JAX, Gradient Descent | Artificial Intelligence, Machine Learning | Library | Documentation, Uses, and more |
| optix | ACES | OptiX is a GPU-accelerated ray tracing engine from NVIDIA that provides a programmable ray tracing pipeline for developers to build high-performance ray tracing applications. | Ray Tracing, Gpu-Accelerated, Real-Time Rendering | Computer Science, Computer & Information Sciences | Gpu Software | Documentation, Uses, and more |
| optuna | ACES | Optuna is an open-source hyperparameter optimization framework to automate hyperparameter search with a variety of flexible and powerful features for machine learning model training. | Machine Learning, Hyperparameter Optimization, Automated Machine Learning, Optimization Framework | Artificial Intelligence, Computer & Information Sciences | Library | Documentation, Uses, and more |
| orca | ACES KyRIC |
Orca is a flexible, efficient, and powerful quantum chemistry software written by Frank Neese and co-workers. It provides accurate and reliable computational simulations of molecular structures and properties based on quantum mechanical methods. | Quantum Chemistry, Computational Chemistry, Quantum Mechanics | Physical Chemistry, Chemical Sciences | Quantum Chemistry Software | Documentation, Uses, and more |
| osi | ACES | OSI (Open System Interconnection) is a conceptual framework that standardizes the functions of a telecommunication or computing system into seven abstraction layers. It facilitates communication between different systems by defining a set of protocols to be used at each layer. | Networking, Communication, Protocol, Standardization | Computer Science, Computer & Information Sciences | Networking Software | Documentation, Uses, and more |
| osmesa | Delta | Documentation, Uses, and more | ||||
| osu | KyRIC | Documentation, Uses, and more | ||||
| osu-micro-benchmarks | ACES Delta |
OSU Micro-Benchmarks is a suite of parallel micro-benchmarks written in C with MPI and OpenMP implementations, designed for evaluating the performance of parallel computing systems and HPC networks. | Performance Evaluation, Hpc, Benchmarking | Computer Science, Engineering & Technology | Tool | Documentation, Uses, and more |
| otf2 | ACES | OTF2 is a trace format for event traces. It is mainly used for the scalable and efficient storage, transfer, and analysis of trace data generated by HPC applications. | Trace Format, Event Traces, Hpc Applications | Infrastructure & Instrumentation, Engineering & Technology | Library | Documentation, Uses, and more |
| ovito | Anvil | OVITO (Open Visualization Tool) is a scientific visualization and analysis software for atomistic simulation data. It is designed to visualize and analyze large-scale molecular dynamics and Monte Carlo simulation results. | Visualization, Data Analysis, Molecular Dynamics, Scientific Computing | Materials Science, Computational Materials Science | Visualization Tool | Documentation, Uses, and more |
| p11-kit | ACES | p11-kit is a library to manage PKCS#11 modules. It enables multiple applications to use the same PKCS#11 module in parallel, ensures that applications get access to the same serialized view of the module's state, and handles sharing access to the module state among applications. | Library, Pkcs#11, Module Management | Cryptography, Computer & Information Sciences | Utility | Documentation, Uses, and more |
| p4est | Stampede3 | p4est (parallel framework for dynamic load balancing and adaptive mesh refinement) is a software library that provides support for dynamic load balancing and adaptive mesh refinement in parallel numerical simulations. It is particularly useful for solving partial differential equations on unstructured grids efficiently. | Computational Software, Library | Computer Science, Engineering & Technology | Library | Documentation, Uses, and more |
| p7zip | ACES Expanse |
p7zip is a command-line file archiver that supports the 7z compression format and various other archive formats. It is based on the open-source LZMA compression algorithm. | File Archiver, Compression Software, Command-Line Tool, Open-Source Software | Computer Science, Computer & Information Sciences | Command-line Tool | Documentation, Uses, and more |
| padicotm | ACES | PadicoTM is a parallel discrete element method software package tailored for large-scale simulations of granular and multiphase flows. It is designed to efficiently model the behavior of particulate materials in various engineering and scientific applications. | Dem, Granular Flows, Multiphase Flows, Simulation Software | Engineering & Technology | Computational Software | Documentation, Uses, and more |
| pandoc | ACES | Pandoc is a universal document converter that allows users to convert files from one markup format to another. It supports a wide range of formats including Markdown, HTML, LaTeX, and many others. | document conversion, markup languages, text processing, open source | Computer Science, Computer and Information Sciences | Document Converter | Documentation, Uses, and more |
| pango | ACES DeltaAI |
Pango is a library for layout and rendering of text, with an emphasis on internationalization. It forms the core of text and font handling for the GTK+ toolkit and is used by a variety of other open-source projects, including GNOME desktop environment. | Text Layout, Font Handling, Internationalization | Computer & Information Sciences | Text Processing | Documentation, Uses, and more |
| papi | Anvil ACES DeltaAI Delta KyRIC Stampede3 |
PAPI (Performance Application Programming Interface) is a portable and efficient API that provides a consistent interface and methodology for collecting performance counter data from the underlying hardware. | Performance Monitoring, Api, Hardware Counter | Computer Science | Library | Documentation, Uses, and more |
| parabricks | ACES | Parabricks is a GPU-accelerated toolkit that assists in fast and accurate genomic analysis. It is designed to efficiently process raw sequencing data, such as those generated by DNA sequencing technologies, for tasks like variant calling, mapping, and genome assembly. | Genomic Analysis, DNA Sequencing, Variant Calling, Gpu Acceleration | Genomics, Biological Sciences | Toolkit | Documentation, Uses, and more |
| parafly | Anvil | Parafly is a Python library for parallelizing and distributing task execution across multiple cores or nodes, aimed at improving computational efficiency for high-performance computing applications. | Parallelization, Distributed Computing, Python Library | Computer & Information Sciences | Python Library | Documentation, Uses, and more |
| parafold | ACES | Parafold is a software tool for RNA secondary structure prediction using deep learning models. It utilizes neural networks to predict RNA secondary structures from primary sequences. | RNA Secondary Structure Prediction, Deep Learning, Neural Networks | Bioinformatics, Biological Sciences | Bioinformatics Tool | Documentation, Uses, and more |
| parallel | Anvil ACES DeltaAI Expanse Delta |
GNU Parallel is a command-line tool for Unix-like operating systems that allows the user to execute shell scripts or commands in parallel. It is designed to simplify parallel job execution on single or multiple processors without the need for complex scripting. | Parallel Computing, Command-Line Tool, Task Scheduling | Computer & Information Sciences | Command-Line Tool | Documentation, Uses, and more |
| parallel-netcdf | Anvil DeltaAI Delta Stampede3 |
Parallel-NetCDF is a library providing high-performance I/O in parallel environments for big data applications with large scientific datasets. It offers parallel I/O capabilities for NetCDF files, which are commonly used in climate modeling, weather forecasting, and other scientific disciplines. | High-Performance I/O, Big Data, Parallel Computing | Earth & Environmental Sciences, Physical Sciences | I/O Library | Documentation, Uses, and more |
| parameterized | ACES | Documentation, Uses, and more | ||||
| paraview | Anvil ACES Delta |
ParaView is an open-source, multi-platform data analysis and visualization application. It is designed to handle large data sets and offers a wide range of visualization techniques to analyze and interact with the data. | Visualization, Data Analysis, Open-Source, Multi-Platform | Data Visualization, Physical Sciences, Engineering & Technology, Natural Sciences, Computer & Information Sciences, Other Natural Sciences | Data Visualization | Documentation, Uses, and more |
| parmetis | ACES Stampede3 |
ParMETIS is an MPI-based parallel graph partitioning and sparse matrix ordering library designed for efficiently solving large, sparse graph problems. It provides high-performance graph partitioning, matrix reordering, and fill-reducing matrix ordering capabilities for a wide range of scientific computing applications. | Graph Partitioning, Sparse Matrix Ordering, Scientific Computing, Parallel Computing | Computer Science, Computer & Information Sciences | Computational Tool | Documentation, Uses, and more |
| parpack | Stampede3 | PARPACK is a software library for solving large scale eigenvalue problems. It is specifically designed to compute a few eigenvalues and corresponding eigenvectors of large sparse matrices. | Eigenvalue Problems, Sparse Matrices, Numerical Linear Algebra | Numerical Linear Algebra, Mathematics | Library | Documentation, Uses, and more |
| parsl | ACES | Parsl is a parallel scripting library for Python that allows users to easily write parallel applications and workflows, enabling efficient execution of tasks across various computing resources. | parallel computing, workflow management, Python, HPC, data science | High-Performance Computing, Computer Science | Library | Documentation, Uses, and more |
| pasa | ACES | PASA (Program to Assemble Spliced Alignments) is a software tool designed for the alignment and assembly of transcript sequences, particularly useful in the context of RNA-Seq data analysis. | RNA-Seq, Transcriptome, Alignment, Bioinformatics | Computational Biology, Genomics | Command Line Tool | Documentation, Uses, and more |
| patch | Delta KyRIC |
The `patch` utility is a tool used to apply changes to files based on a diff file, which contains the differences between two versions of a file or set of files. | version control, file management, diff, software development | Software Engineering, Other Computer and Information Sciences | Command-line tool | Documentation, Uses, and more |
| patchelf | ACES | PatchELF is a simple utility for modifying the dynamic linker and run-time library paths in executable files. | Dependency Management, Executable Modification, Dynamic Linker Paths | Systems and Development, Computer & Information Sciences | Library Management | Documentation, Uses, and more |
| patsy | ACES | Documentation, Uses, and more | ||||
| pblat | ACES | pblat (Parallel BLAT) is a software tool that efficiently aligns biological sequences to a reference genome by using the BLAT algorithm in a parallel computing framework. It is specifically designed for high-throughput sequence analysis tasks, offering improved speed and scalability for large-scale genomic analyses. | Bioinformatics, Sequence Alignment, Genomics, Parallel Computing | Genomics, Biological Sciences | Sequence Analysis Tool | Documentation, Uses, and more |
| pciutils | Expanse | pciutils is a set of utilities for displaying information about PCI buses in the system and devices connected to them. It provides various tools for configuration, diagnostics, and monitoring of PCI devices in Linux systems. | Pci Management, System Utilities, Linux Tools | Systems, Computer & Information Sciences | Command-Line Tool | Documentation, Uses, and more |
| pcre | Anvil ACES DeltaAI |
Perl Compatible Regular Expressions (PCRE) is a library for pattern matching with regular expressions. It implements the functionality of the regular expression library in Perl and provides support for Perl-style regular expressions in many programming languages. | Regular Expressions, Pattern Matching, Library | Biology, Computer & Information Sciences | Runtime Library | Documentation, Uses, and more |
| pcre2 | ACES DeltaAI KyRIC Stampede3 |
PCRE2 is a C library implementing Perl-compatible regular expressions. It is a reimplementation of PCRE but with a different API that is designed to be compatible with Perl 5. It provides a regular expression matching engine that supports Perl-style patterns while also providing some features not found in Perl, such as matching up to 2^16 code units. | Regular Expressions, Text Processing, Pattern Matching | Biology, Computer & Information Sciences | C Library | Documentation, Uses, and more |
| pdal | ACES | PDAL is an open-source library for point cloud processing and data management. It offers a variety of tools and pipelines for manipulating geospatial data in the form of point clouds. | Point Cloud, Geospatial Data, Lidar, Gis, Data Processing | Remote Sensing, Other Natural Sciences | Point Cloud Processing | Documentation, Uses, and more |
| pdt | ACES | Program Database Toolkit (PDT) is a framework for analyzing source code written in several programming languages and for making rich program knowledge accessible to developers, analysts, and creating tools for source code understanding. | Software, Programming, Source Code, Analysis | Computer & Information Sciences | Tools | Documentation, Uses, and more |
| pdtoolkit | KyRIC | PDT (Program Database Toolkit) from the University of Oregon — A framework for analyzing source code (C, C++, Fortran, etc.) and exposing program structure to static/dynamic analysis tools. It's commonly paired with TAU for HPC performance instrumentation, so given your work on HPC clusters, this might be the one you're asking about. | Static Analysis, Source Code Parsing | Development library | Documentation, Uses, and more | |
| perftools | DeltaAI | Perftools is a collection of performance analysis tools designed to help developers optimize their software by identifying performance bottlenecks and areas for improvement. It includes a suite of profiling tools that can be used to analyze CPU and memory usage, as well as identify hotspots in code. | Performance Analysis, Optimization, Profiling | Engineering & Technology | Performance Analysis Tools | Documentation, Uses, and more |
| perftools-base | DeltaAI Delta |
perftools is a collection of performance analysis tools for Linux-based systems. perftools-base is the base package of perftools which includes basic performance analysis tools for profiling CPU and memory usage. | Performance Analysis, Profiling, Linux | Computer & Information Sciences | Tool | Documentation, Uses, and more |
| perftools-lite | DeltaAI | Perftools lite is a set of performance analysis tools designed for lightweight profiling and tracing of applications. It provides insights into the performance of software applications to help optimize and improve efficiency. | Performance Analysis, Profiling, Tracing | Computer Science, Computer & Information Sciences | Software Tool | Documentation, Uses, and more |
| perftools-lite-events | DeltaAI | Perftools Lite (PTL) provides a framework for lightweight performance analysis of parallel applications. It allows users to collect and analyze performance data to identify bottlenecks and optimize code performance. PTL focuses on event-based performance analysis to monitor and measure the execution behavior of parallel applications. | Performance Analysis, Parallel Applications, Optimization | Computer & Information Sciences | Compiler/Profiler | Documentation, Uses, and more |
| perftools-lite-gpu | DeltaAI | Perftools-lite-gpu is a lightweight performance analysis tool designed for GPU applications. It allows developers to analyze the performance of their GPU-accelerated applications by providing insightful metrics and visualizations. | Performance Analysis, Gpu Applications, Metrics, Visualization | Engineering & Technology | Performance Analysis Tool | Documentation, Uses, and more |
| perftools-lite-hbm | DeltaAI | PerfTools-Lite-HBM is a performance analysis tool specifically designed for profiling applications running on High Bandwidth Memory (HBM) systems. It provides insights into memory access patterns, cache behavior, and overall performance characteristics of HBM-enabled applications. | Performance Analysis, Memory Profiling, Hbm Systems, High Bandwidth Memory, Optimization | Engineering & Technology | Profiler | Documentation, Uses, and more |
| perftools-lite-loops | DeltaAI | The perftools-lite-loops software is a performance monitoring tool that focuses on analyzing loop-level performance in applications. It is designed to provide detailed insights into loop optimizations, dependencies, and potential performance bottlenecks in code. | Performance Monitoring, Optimization, Debugging | Computer & Information Sciences | Analysis Tool | Documentation, Uses, and more |
| perftools-preload | DeltaAI | perftools-preload is a tool designed to optimize and profile code performance by collecting runtime statistics, such as CPU utilization, memory usage, and function call traces. It is particularly useful for identifying performance bottlenecks and optimizing code for improved efficiency. | Performance Optimization, Code Profiling, Software Performance, Debugging | Computer Science, Computer & Information Sciences | Tool | Documentation, Uses, and more |
| perl | Anvil ACES DeltaAI KyRIC |
Perl is a high-level, general-purpose, interpreted, dynamic programming language known for its powerful text-processing features and used for a wide range of tasks including web development, system administration, and network programming. | Programming Language, Text Processing, Scripting, Web Development, System Administration | Bioinformatics, Computer & Information Sciences | Programming Language | Documentation, Uses, and more |
| perl-bioperl | Anvil | BioPerl is a collection of Perl modules that facilitate the development of Perl scripts for bioinformatics applications. | bioinformatics, perl, sequence analysis, genomics, molecular biology | Computational Biology, Biological Sciences | Library | Documentation, Uses, and more |
| perl-bundle-cpan | ACES | A collection of Perl modules that can be installed using CPAN, providing a convenient way to manage Perl dependencies. | Perl, CPAN, Package Management | Computer Science, Software Engineering | Library | Documentation, Uses, and more |
| perl-bundle1-cpan | ACES | A collection of Perl modules and libraries available on CPAN (Comprehensive Perl Archive Network) bundled together for easy installation and management. | Software Bundle, Perl Modules, Code Libraries | Computer & Information Sciences | Programming Libraries | Documentation, Uses, and more |
| perl-bundle2-cpan | ACES | perl-bundle2-cpan is a Perl module that allows for the installation of multiple CPAN modules in one go, making it easier to manage dependencies and streamline the process of installing Perl modules. | Perl, Cpan, Dependency Management, Module Installation | Computer Science, Computer & Information Sciences | Package | Documentation, Uses, and more |
| petsc | Anvil ACES DeltaAI Delta Stampede3 |
PETSc, the Portable, Extensible Toolkit for Scientific Computation, is a suite of data structures and routines for the scalable (parallel) solution of scientific applications modeled by partial differential equations. | Scientific Computing, Computational Science, Numerical Analysis | Applied Mathematics, Natural Sciences | Library | Documentation, Uses, and more |
| petsc4py | ACES | petsc4py is a Python wrapper for the Portable, Extensible Toolkit for Scientific Computation (PETSc), which provides a suite of data structures and routines for the scalable (parallel) solution of scientific applications modeled by partial differential equations. | HPC, Scientific Computing, Python, Numerical Methods | Applied Mathematics, Numerical Methods | Library | Documentation, Uses, and more |
| pfft | ACES | Documentation, Uses, and more | ||||
| phdf5 | Stampede3 | ph5util provides utilities for reading, writing, and manipulating PHDF5 files. PHDF5 is a parallel I/O file format based on the HDF5 file format and is used for storing large datasets efficiently across distributed storage systems. | Parallel I/O, Phdf5, Hdf5, Large Datasets | Computer & Information Sciences | File Format | Documentation, Uses, and more |
| phylip | ACES | PHYLIP (Phylogeny Inference Package) is a software package for inferring phylogenies (evolutionary trees) from DNA or protein sequences. | phylogenetics, bioinformatics, evolutionary biology | Bioinformatics, Evolutionary Biology | Standalone | Documentation, Uses, and more |
| physics-tenpy | ACES | TeNPy (short for ‘Tensor Network Python’) is a Python library for the simulation of strongly correlated quantum systems with tensor networks. Description Source: https://pypi.org/project/physics-tenpy/ |
Documentation, Uses, and more | |||
| picard | Anvil ACES Delta |
Picard is a set of command line tools for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF. It is primarily used for processing and analyzing next-generation sequencing (NGS) data in genomics. | Bioinformatics, Ngs, Hts, Sequencing Data, Sam, Bam, Vcf | Genomics, Biological Sciences | Command Line Tool | Documentation, Uses, and more |
| pigz | ACES Expanse |
pigz, which stands for parallel implementation of gzip, is a compression utility that uses multiple processors and cores to compress files quickly and efficiently. It is compatible with gzip and gunzip, allowing for seamless integration with existing gzip workflows. | Compression, Parallel Processing, Utility, Command-Line Tool | Computer Science, Computer & Information Sciences | Utility | Documentation, Uses, and more |
| pillow | ACES | Pillow is a powerful Python Imaging Library (PIL) replacement that adds image processing capabilities to your Python interpreter. | Image Processing, Python Library | Applied Computer Science, Computer & Information Sciences, Software Engineering, Systems & Development | Library | Documentation, Uses, and more |
| pillow-simd | ACES | pillow-simd is an optimized fork of Python imaging library (PIL) with SIMD support, designed to enhance image processing capabilities with improved performance. | Image Processing, Python Library, Optimization | Software Engineering, Computer & Information Sciences | Image Processing | Documentation, Uses, and more |
| pioman | ACES | Pioman is a Python package that provides tools for parallel input and output (IO) management. It aims to optimize IO performance in high-performance computing (HPC) environments by enabling efficient reading and writing of large datasets. Pioman is particularly useful for scientific simulations and data analysis workflows that involve heavy IO operations. | Python Library, Hpc Tool, Io Management | Computer & Information Sciences | Library | Documentation, Uses, and more |
| pipenv | ACES | Pipenv is a packaging tool for Python that aims to bring the best of all packaging worlds (bundled, required, and development dependencies) to the Python world. It manages dependencies, virtual environments, and simplifies the process of managing Python projects. | Python, Dependency Management, Virtual Environments, Development Tools | Computer Science, Software Engineering | Package Management | Documentation, Uses, and more |
| pixi | ACES | Documentation, Uses, and more | ||||
| pixman | Anvil ACES DeltaAI |
Pixman is a low-level software library for pixel manipulation, providing software acceleration for numerous rendering operations. It is used primarily by projects requiring high-quality rendering such as the X server, Cairo, the GTK+ toolkit, and more. | Pixel Manipulation, Rendering, Software Library, Performance | Software Development, Computer & Information Sciences | Graphics Library | Documentation, Uses, and more |
| pkg-config | ACES | pkg-config is a helper tool used when compiling applications and libraries. It helps to manage compiler and linker flags for libraries in the system. It simplifies the process of compiling and linking against libraries. | Compilation, Library Management, Build Process | Computer Science, Engineering & Technology | Utility | Documentation, Uses, and more |
| pkgconf | ACES DeltaAI KyRIC |
pkgconf is a package configuration system. It helps to provide a uniform and system-agnostic API for the management of build and link flags. It replaces the functionality of pkg-config. | Package Configuration, Build Flags, Link Flags, System-Agnostic | Software Engineering, Computer & Information Sciences | Package Configuration | Documentation, Uses, and more |
| pkgconfig | ACES | pkg-config is a helper tool used when compiling applications and libraries. It helps in specifying compilation options by providing the compiler options needed to use a library. It also provides information about installed libraries. | Compilation, Library Management, Software Development | Software Engineering, Engineering & Technology | Tool | Documentation, Uses, and more |
| plink | ACES | PLINK (whole-genome association analysis toolset) is an open-source whole genome association analysis toolset designed to perform a range of basic, large-scale analyses in a computationally efficient manner. It enables users to carry out a variety of tasks, such as quality control, data management, and statistical analysis of genotypic data. | Genetic Analysis, Genomic Data Analysis, Gwas, Genetic Epidemiology | Genetics, Biological Sciences | Tool | Documentation, Uses, and more |
| plotly.py | ACES | Plotly.py is an open-source Python graphing library that makes interactive, publication-quality graphs online. It allows users to create interactive plots and dashboards using Python, with a high degree of customization and interactivity. | Data Visualization, Graphing Library, Python Library | Statistics, Computer & Information Sciences | Graphing Library | Documentation, Uses, and more |
| plumed | ACES DeltaAI Delta |
PLUMED is an open-source library for free energy calculations in molecular dynamics simulations. It allows for the easy and flexible implementation of enhanced sampling techniques and the calculation of various collective variables. | Molecular Dynamics, Enhanced Sampling, Free Energy Calculations, Collective Variables | Chemistry, Biological Sciences | Library | Documentation, Uses, and more |
| ply | ACES | Ply is a pure-Python implementation of the popular Lex and Yacc parsing tools. It is designed to simplify the process of writing lexers and parsers in Python, providing a high-level, object-oriented interface that makes it easy to define grammars directly in the code. | Parser, Lexer, Python, Parsing | Software Engineering, Computer & Information Sciences | Library | Documentation, Uses, and more |
| pmi | DeltaAI Delta |
PMI is a low-level API (Application Programming Interface) designed for managing processes in an HPC environment. It is primarily used to manage resources, handle process launch and communication, and manage job execution within parallel computing frameworks, such as those using MPI (Message Passing Interface) for distributed computing. | Distributed Systems, Job Scheduling, Parallel Computing | Computer Science | Documentation, Uses, and more | |
| pmix | ACES KyRIC |
The Process Management Interface (PMIx) is an abstract interface for managing the data and resources associated with managing parallel processes. It provides a framework and services for coordinating data exchange and interaction amongst parallel processes in high-performance computing environments. | Process Management, Parallel Computing, High-Performance Computing, Data Exchange, Resource Management, Scalability | Computer Science, Engineering & Technology | Hpc Tool | Documentation, Uses, and more |
| pnetcdf | ACES Stampede3 |
PnetCDF is a parallel I/O library for accessing NetCDF files in parallel. It is specifically designed to address the scalability and performance limitations of serial NetCDF I/O by providing parallel I/O support. | Parallel I/O, Netcdf Files, Scalability, Performance | High-Performance Computing, Physical Sciences | I/O Library | Documentation, Uses, and more |
| pocl | ACES Delta |
Portable Computing Language (pocl) is an open-source implementation of the OpenCL standard which aims to provide a portable programming layer for execution on various devices including CPUs, GPUs, and FPGAs. It enables developers to write parallel programs that can be executed efficiently across different hardware platforms. | Opencl, Parallel Computing, Hardware Acceleration | Computer Science, Computer & Information Sciences | Development Tools | Documentation, Uses, and more |
| poetry | ACES | Poetry is a dependency management and packaging tool for Python projects. It allows you to declare and manage project dependencies, create virtual environments, build and publish packages, and more. | Dependency Management, Packaging, Python | Computer Science, Computer & Information Sciences | Package Manager | Documentation, Uses, and more |
| polars | ACES | Polars is a fast DataFrame library implemented in Rust and designed for performance and ease of use in data manipulation and analysis. | DataFrame, Data Analysis, Performance, Rust, Python | Computer Science, Software Engineering | Library | Documentation, Uses, and more |
| poppler | ACES | Poppler is a software utility library that is used to render PDF documents. It is a PDF rendering library based on the xpdf-3.0 code base. It provides various command-line utilities for working with PDF files as well. | Pdf Rendering, Pdf Manipulation, Pdf Parsing | Software Engineering, Computer & Information Sciences | Library | Documentation, Uses, and more |
| popt | KyRIC | popt is a C library for parsing command line options. | Command Line Options, C Library | Computer & Information Sciences | Command Line Option Parser | Documentation, Uses, and more |
| portmidi | ACES | PortMidi is a portable MIDI input/output library designed for use with C, C++, and other programming languages. It provides a simple interface for MIDI communication across various platforms. | MIDI, Audio, Cross-platform, Library | Computer Science | Library | Documentation, Uses, and more |
| postgresql | ACES | PostgreSQL is a powerful, open-source relational database management system known for its reliability, robustness, and performance. It offers advanced features such as multi-version concurrency control, point-in-time recovery, and full ACID compliance. | Database Management, Relational Database, Open Source, Data Management | Database Management, Computer Science | Database Management System | Documentation, Uses, and more |
| pov-ray | ACES | POV-Ray (Persistence of Vision Raytracer) is a high-quality three-dimensional graphics tool that creates stunning photorealistic images using ray tracing techniques. It is a free, open-source software package that allows users to design detailed scenes using a specialized scripting language. | 3D Graphics, Ray Tracing, Open-Source, Visualization | Visualization and Human-Computer Systems, Computer Science | Visualization Software | Documentation, Uses, and more |
| pplacer | ACES | pplacer is a phylogenetic placement tool that places query sequences on a fixed reference phylogenetic tree while simultaneously estimating their likelihoods. It is particularly useful for analyzing large collections of short reads, such as those generated from next-generation sequencing technologies. | Phylogenetic Analysis, Sequence Placement, Phylogenetic Tree, Likelihood Estimation | Biological Sciences | Tool | Documentation, Uses, and more |
| prank | ACES | PRANK is a probabilistic multiple sequence alignment program for DNA, codon and amino-acid sequences. It constructs multiple alignments by aligning sequences pairwise based on local alignment and phylogenetic information. | Sequence Alignment, Bioinformatics, Genomics, Phylogenetics | Genetics, Biological Sciences | Computational Software | Documentation, Uses, and more |
| precice | Stampede3 | preCICE is a coupling library for multi-physics simulations, enabling the interaction between different simulation codes in a flexible and efficient manner. | multi-physics, coupling, simulation, high-performance computing | Numerical Simulation, Multi-Physics Simulation | Library | Documentation, Uses, and more |
| prgenv | DeltaAI Delta |
Documentation, Uses, and more | ||||
| prgenv-amd | Delta | Documentation, Uses, and more | ||||
| prgenv-aocc | Delta | Documentation, Uses, and more | ||||
| prgenv-cray-amd | Delta | Documentation, Uses, and more | ||||
| prgenv-gnu | DeltaAI Delta |
The prgenv-gnu is a programming environment module that provides the GNU compiler collection (GCC) for compiling and running codes. It sets up the environment variables needed to compile and run programs using the GNU compilers. | Programming Environment, Gnu Compiler Collection (Gcc) | Computer & Information Sciences, Software Engineering, Systems & Development | Compiler | Documentation, Uses, and more |
| prgenv-gnu-amd | Delta | Documentation, Uses, and more | ||||
| prgenv-nvidia | DeltaAI Delta |
prgenv-nvidia is a software environment that provides compilers and tools optimized for NVIDIA GPUs, allowing users to develop and execute GPU-accelerated applications efficiently. | Software Environment, Compilers, Gpu Computing, Nvidia | Computational Science, Computer & Information Sciences | Compiler | Documentation, Uses, and more |
| printproto | DeltaAI | Documentation, Uses, and more | ||||
| prodigal | ACES | Prodigal is a microbial gene finding program that identifies protein-coding regions in microbial genomes. It uses a combination of intrinsic and extrinsic signals to accurately predict genes in bacterial and archaeal genomes. | Gene Prediction, Microbial Genomes | Biological Sciences | Bioinformatics | Documentation, Uses, and more |
| proj | Anvil ACES DeltaAI Stampede3 |
PROJ is a standard Unix filter function designed to convert geographic longitude and latitude coordinates into Cartesian coordinates. It is widely used in geospatial applications for coordinate transformation and map projection. | Geospatial, Coordinate Transformation, Map Projection | Other Natural Sciences | Coordinate Transformation Tool | Documentation, Uses, and more |
| prokka | ACES | Prokka is a software tool for rapid prokaryotic genome annotation. It annotates bacterial, archaeal, and viral genomes quickly and easily. Prokka performs a comprehensive annotation that includes gene prediction, functional annotation, and other genomic features. | Genome Annotation, Bioinformatics, Genomics | Genetics, Biological Sciences | Annotation Tool | Documentation, Uses, and more |
| protobuf | Anvil ACES |
Protocol buffers are a language- and platform-neutral extensible mechanism for serializing structured data. It enables you to define data structures in a JSON-like format and automatically generate code to serialize and deserialize them in a variety of languages. | Serialization, Data Interchange, Code Generation | Software Engineering, Computer & Information Sciences | Library | Documentation, Uses, and more |
| protobuf-python | ACES | protobuf-python is a Python library for Protocol Buffers, Google's language-neutral, platform-neutral extensible mechanism for serializing structured data. | Data Serialization, Binary Encoding, Data Validation, Structured Data, Extensible | Software Engineering, Computer & Information Sciences | Serialization | Documentation, Uses, and more |
| prrte | ACES | PRRTE (Proactive Resilience and Real-Time Executor) is a fault tolerance framework designed to provide fault tolerance capabilities to complex, high-performance computing (HPC) applications. It focuses on enabling applications to run to completion in the presence of faults by providing various resilience strategies. | Fault Tolerance, Hpc, Resilience, Real-Time Execution | Computer Science, Engineering & Technology | Framework | Documentation, Uses, and more |
| prun job launch utility | KyRIC | Documentation, Uses, and more | ||||
| psutil | ACES | psutil is a cross-platform library for process and system monitoring in Python. It provides an interface for retrieving information on running processes and system utilization (CPU, memory, disks, network, sensors) in a portable way. | Python, Monitoring, System Utilities, Cross-Platform | Applied Computer Science, Other Computer and Information Sciences | Library | Documentation, Uses, and more |
| psycopg2 | ACES | Psycopg is a popular PostgreSQL database adapter for the Python programming language. It provides a robust, efficient, and well-supported interface for interacting with PostgreSQL databases from Python applications. | Python Library, Database Adapter, Postgresql, Data Management | Computer Science, Computer & Information Sciences | Database Adapter | Documentation, Uses, and more |
| ptex | ACES | A high-quality Japanese typesetting system based on TeX that is specifically optimized for the Japanese language. | Typesetting, Tex, Japanese Language | Languages & Literature, Humanities | Typesetting Software | Documentation, Uses, and more |
| pugixml | ACES | pugixml is a lightweight C++ XML processing library that consists of a simple and intuitive API. It is designed to be easy to integrate with other projects and provides efficient and fast XML parsing capabilities. | Xml Processing, C++ Library, Xpath, Parsing | Software Engineering, Computer & Information Sciences | Xml Processing | Documentation, Uses, and more |
| puk | ACES | PM2 is an umbrella software suite for high-performance runtime systems. Modules may be installed and used together or separately. | Documentation, Uses, and more | |||
| pukabi | ACES | Pukabi is a bioinformatics tool used for analyzing and visualizing phylogenetic trees. | Bioinformatics, Phylogenetics, Tree Visualization | Biological Sciences | Documentation, Uses, and more | |
| pulp | ACES | PuLP is a Python library for modeling linear programming problems. It allows users to describe optimization problems in a natural way and provides a simple interface to various solvers. | Optimization, Linear Programming, Mathematics, Python | Optimization, Mathematics | Library | Documentation, Uses, and more |
| py-cpuinfo | ACES | py-cpuinfo is a Python library to get CPU information by parsing data from /proc/cpuinfo. It provides information about the CPU and its features. | Python Library, System Information, Cpu Information | Software Engineering, Computer & Information Sciences | Python Library | Documentation, Uses, and more |
| py-cutadapt | Anvil | py-cutadapt is a Python package for preprocessing high-throughput sequencing data. It trims adapter sequences, removes low-quality bases, and filters out reads that do not meet specified quality thresholds. | Bioinformatics, Sequencing Data Processing, Python Package | Genomics, Biological Sciences | Bioinformatics Tool | Documentation, Uses, and more |
| py-cython | DeltaAI KyRIC |
Py-Cython is a compiler for writing C extensions for the Python language. It allows for combining Python and C code seamlessly to improve performance and efficiency. | Compiler, Python Library, Performance Optimization | Computer & Information Sciences | Development Tool | Documentation, Uses, and more |
| py-flit-core | DeltaAI | A core library for building and packaging Python projects using the Flit tool. | Python, Packaging, Build Tools | Computer Science, Software Engineering | Library | Documentation, Uses, and more |
| py-gpaw | Anvil | GPAW is an open-source software package for electronic structure calculations based on density functional theory (DFT). It uses the real-space grid method and is designed for high-performance computing environments. | DFT, Quantum Mechanics, Computational Chemistry, High-Performance Computing | Computational Materials Science, Quantum Chemistry | Scientific Software | Documentation, Uses, and more |
| py-htseq | Anvil | Py-htseq is a high-throughput sequencing (HTS) analysis tool in Python designed to process and analyze mapped sequence data, particularly for RNA-seq experiments. It facilitates gene expression analysis by counting reads that align to features in the reference genome or transcriptome. | Hts Analysis, RNA-Seq, Sequence Data Processing, Gene Expression, Transcriptomics | Bioinformatics, Biological Sciences | Sequence Analysis Tool | Documentation, Uses, and more |
| py-meson-python | DeltaAI | Documentation, Uses, and more | ||||
| py-mpi4py | Anvil | py-mpi4py is a Python interface to the Message Passing Interface (MPI) standard for parallel computing, allowing users to utilize MPI functionality within Python scripts and applications. | Python, Mpi, Parallel Computing | Computer Science, Computer & Information Sciences | Library | Documentation, Uses, and more |
| py-numpy | DeltaAI | NumPy is a fundamental package for scientific computing in Python. It provides support for arrays, matrices, and a variety of mathematical functions to operate on these data structures. | Python, Scientific Computing, Data Analysis, Numerical Computation | Applied Mathematics, Other Mathematics | Python Library | Documentation, Uses, and more |
| py-packaging | DeltaAI | A Python library for packaging Python projects, providing tools for building, distributing, and installing packages. | Python, Packaging, Development, Open Source | Computer Science, Software Engineering | Library | Documentation, Uses, and more |
| py-pip | DeltaAI | py-pip is the official installer for Python packages from the Python Package Index (PyPI). It is used to install and manage software packages written in Python. | Package Management, Python, Software Installation | Software Engineering, Computer & Information Sciences, Systems & Development | Package Management | Documentation, Uses, and more |
| py-pyproject-metadata | DeltaAI | Documentation, Uses, and more | ||||
| py-setuptools | DeltaAI KyRIC |
Setuptools is a package development process library designed to facilitate development and distribution of Python projects. It provides a common approach for managing project dependencies, packaging, and installation processes. | Python, Package Development, Distribution, Dependency Management | Computer Science, Computer & Information Sciences | Package Management | Documentation, Uses, and more |
| py-wheel | DeltaAI | Documentation, Uses, and more | ||||
| py3dmol | ACES | Py3Dmol is a Python library that provides a simple way to use the 3Dmol.js molecular viewer in Jupyter notebooks or Python scripts. It enables interactive visualization of molecular structures and is particularly useful for educational purposes and research in chemistry, biochemistry, and structural biology. | Molecular Visualization, Python Library | Chemical Sciences, Biological Sciences | Python Library | Documentation, Uses, and more |
| pyberny | ACES | Documentation, Uses, and more | ||||
| pybigwig | ACES | pyBigWig is a Python interface for working with BigWig files, a binary format for efficiently storing genome-wide signal data. | Bigwig Files, Genome-Wide Signal Data, Python Interface | Genomics, Biological Sciences | Library | Documentation, Uses, and more |
| pybind11 | ACES | pybind11 is a lightweight header-only library that exposes C++ types in Python and vice versa, mainly to create Python bindings for C++ libraries. It provides seamless interoperability between C++11 and Python without the need for boilerplate code or external tools. | Software Development, Python Library, C++ Integration, Header-Only Library | Software Engineering, Computer & Information Sciences | Interoperability | Documentation, Uses, and more |
| pybiolib | ACES | Documentation, Uses, and more | ||||
| pycairo | ACES | Pycairo is a set of Python bindings for the Cairo graphics library. It allows Python applications to use the powerful vector graphics capabilities provided by Cairo for creating high-quality 2D graphics and illustrations. | Python, Graphics, 2D Graphics, Illustrations | Software Engineering, Computer & Information Sciences | Visualization Library | Documentation, Uses, and more |
| pychemps2 | ACES | Documentation, Uses, and more | ||||
| pycuda | ACES | PyCUDA is a Python library that enables easy access to NVIDIA's CUDA parallel computation API directly from Python. It allows for seamless integration of GPU computation into Python code, providing a high-level interface to CUDA operations. | Python Library, Gpu Computing, Parallel Processing | Computer Science, Computer & Information Sciences | Python Library | Documentation, Uses, and more |
| pycurl | ACES | pycurl is a Python interface to the cURL library, allowing for easy HTTP requests and data transfer. | Python, Networking, HTTP, Data Transfer | Applied Computer Science, Software Engineering | Library | Documentation, Uses, and more |
| pydantic | ACES | Pydantic is a data validation and settings management library in Python that provides data validation using Python type annotations. It enforces type hints at runtime, allowing you to define JSON-like data structures with Python types. | Python Library, Data Validation, Settings Management | Software Engineering, Computer & Information Sciences | Library | Documentation, Uses, and more |
| pydicom | ACES | pydicom is a Python library for working with DICOM files and data. It provides tools for reading, modifying, and writing DICOM files, as well as accessing DICOM data elements and metadata. | Python Library, Dicom Data, Medical Imaging | Medical & Health Sciences | Library | Documentation, Uses, and more |
| pyem | ACES | Documentation, Uses, and more | ||||
| pyfaidx | ACES | pyfaidx is a Python library that enables efficient random access to genome FASTA files in both uncompressed and gzipped formats. It provides a simple interface for indexing and querying sequences from FASTA files. | Python Library, Genome Analysis, Bioinformatics | Bioinformatics, Biological Sciences | Genomics | Documentation, Uses, and more |
| pyfr | ACES | PyFR is an open-source Python-based framework for solving fluid dynamics problems on many-core architectures. | Fluid Dynamics, Finite Element Method, Computational Fluid Dynamics, High-Performance Computing | Fluid Dynamics, Physical Sciences | Framework | Documentation, Uses, and more |
| pygame | ACES | Pygame is a set of Python modules designed for writing video games. It provides functionalities like creating windows, drawing shapes, handling images, sounds, and events, making it easier to develop games and multimedia applications. | Game Development, Multimedia, Python, Open Source | Software Engineering, Computer Science | Library | Documentation, Uses, and more |
| pygobject | ACES | PyGObject is a Python module that enables developers to access GObject-based libraries in Python. It allows Python code to interact with and use functionalities provided by libraries written in the GObject introspection format. | Python, Programming, Gobject-Based Libraries, Development | Computer Science, Computer & Information Sciences | Python Library | Documentation, Uses, and more |
| pylauncher | Stampede3 | Documentation, Uses, and more | ||||
| pyopengl | ACES | PyOpenGL is a cross-platform open source Python binding to OpenGL and related APIs that provides access to high-performance 2D and 3D graphics rendering capabilities. It allows developers to utilize the full feature set of OpenGL within Python applications. | Graphics, Opengl, Python, 2D, 3D, Rendering | Computer Science, Computer & Information Sciences | Library | Documentation, Uses, and more |
| pyproj | ACES | Pyproj is a Python interface to the PROJ library for cartographic projections and coordinate transformations. | Python Library, Geospatial Analysis, Cartographic Projections, Coordinate Transformations | Geospatial Science, Earth & Environmental Sciences | Geospatial Analysis Software | Documentation, Uses, and more |
| pyqt-builder | ACES | Documentation, Uses, and more | ||||
| pyqt5 | ACES | PyQt5 is a comprehensive set of Python bindings for the Qt application framework developed by Riverbank Computing. It allows Python programmers to create desktop applications with rich graphical user interfaces (GUIs) using Qt tools and libraries. | Python, Gui, Qt, Desktop Applications | Software Engineering, Computer & Information Sciences | Library | Documentation, Uses, and more |
| pyrosetta | ACES | PyRosetta is a Python-based interface to the Rosetta molecular modeling suite, which is widely used for protein structure prediction and design. | bioinformatics, computational biology, molecular modeling, protein design | Bioinformatics, Molecular Modeling | Library | Documentation, Uses, and more |
| pysam | ACES | Pysam is a Python module that provides access to read, write, manipulate, and analyze SAM/BAM files used in bioinformatics. It allows seamless integration of SAMtools, a set of utilities for interacting with and post-processing short DNA sequence read alignments in SAM, BAM, or CRAM format. | Bioinformatics, Sequence Analysis, Sam/Bam Files, Python Module | Bioinformatics, Biological Sciences | Library | Documentation, Uses, and more |
| pyscf | ACES | Documentation, Uses, and more | ||||
| pytensor | ACES | PyTensor is a Python library for tensor operations and computations. It provides a high-level interface for handling multi-dimensional arrays and performing various tensor manipulations. | Python Library, Tensor Operations, Scientific Computing | Computer Science, Computer & Information Sciences | Scientific Computing | Documentation, Uses, and more |
| pytesseract | ACES | Pytesseract is a Python wrapper for Google's Tesseract-OCR Engine. It allows for easy integration of Tesseract OCR functionality in Python scripts. | Ocr, Text Recognition, Image Processing | Artificial Intelligence, Computer & Information Sciences | Ocr Library | Documentation, Uses, and more |
| pytest | ACES | Pytest is a testing framework that makes it easy to write simple and scalable tests in Python. It is a popular testing framework used for testing Python programs and libraries. | Testing, Python, Framework | Computer Science, Computer & Information Sciences | Testing Framework | Documentation, Uses, and more |
| pytest-flakefinder | ACES | pytest-flakefinder is a Pytest plugin that helps in detecting flaky tests by running them multiple times and analyzing the results. It identifies tests that fail intermittently due to non-deterministic behavior. | Pytest Plugin, Test Automation, Flaky Test Detection | Software Engineering, Systems & Development, Engineering & Technology | Plugin | Documentation, Uses, and more |
| pytest-rerunfailures | ACES | pytest-rerunfailures is a plugin for the pytest testing framework that automatically reruns failed test cases to improve test reliability. | Software Testing, Python Libraries, Programming Tools | Software Engineering, Systems & Development, Engineering & Technology | Library | Documentation, Uses, and more |
| pytest-shard | ACES | pytest-shard is a pytest plugin that allows test execution to be split across multiple workers for faster test runs. It enables parallel test execution by distributing the test load among several processes. | Pytest, Testing, Parallelization | Computer Science, Computer & Information Sciences | Python Library | Documentation, Uses, and more |
| pytest-xdist | ACES | pytest-xdist is a plugin for pytest that extends it with distributed testing capabilities. It allows for parallel execution of tests across multiple CPUs on the same machine or multiple machines, potentially reducing the overall test suite execution time. | Pytest, Testing, Distributed Computing, Parallel Execution | Computer Science, Computer & Information Sciences | Python Library | Documentation, Uses, and more |
| pythia | ACES | Pythia is a software package for event generation for high-energy collisions, implementing a number of hard scattering models for hadron collisions. It is commonly used in theoretical physics and high-energy physics research. | Event Generation, High-Energy Collisions, Theoretical Physics, Particle Physics | Particle & High-Energy Physics, Physical Sciences | Scientific Software | Documentation, Uses, and more |
| python | Anvil ACES DeltaAI Delta KyRIC |
Python is a high-level, interpreted programming language known for its simplicity and readability. It supports multiple programming paradigms and has a vast ecosystem of libraries and frameworks. | Programming Language, Interpreted Language, High-Level Language | Software Engineering, Computer & Information Sciences, Systems & Development | Language | Documentation, Uses, and more |
| python-bundle-pypi | ACES | Python-bundle-pypi is a collection of Python package bundles available on the Python Package Index (PyPI). These bundles consist of multiple Python libraries and utilities grouped together for convenience in installation and usage. | Python, Package, Pypi, Library, Utilities | Computer & Information Sciences | Utility | Documentation, Uses, and more |
| python-isal | ACES | Python bindings for Intel Storage Acceleration Library (ISAL) that provides optimized functions for storage protocols and data transformation. | Python Library, Data Transformation, Storage Protocols | Computer Science, Computer & Information Sciences | Python Library | Documentation, Uses, and more |
| python-venv | DeltaAI | A tool for creating isolated Python environments, allowing users to manage dependencies for different projects independently. | Python, Virtual Environment, Dependency Management | Computer Science, Software Engineering | Library | Documentation, Uses, and more |
| python-xxhash | ACES | A Python wrapper for the xxHash algorithm, which is known for its high speed and good distribution properties. | hashing, performance, data integrity, Python | Software Engineering, Other Computer and Information Sciences | Library | Documentation, Uses, and more |
| python3 | Expanse Stampede3 |
Python3 is a versatile, high-level programming language that is known for its readability and simplicity. It supports multiple programming paradigms such as object-oriented, imperative, functional, and procedural programming. Python3 has a comprehensive standard library and a large ecosystem of third-party packages, making it suitable for a wide range of applications. | Programming Language, Scripting Language | Computer Science, Computer & Information Sciences, Other Computer & Information Sciences | Interpreter | Documentation, Uses, and more |
| python37 | Expanse | Python 3.7 is a widely-used high-level programming language known for its readability and versatility. It supports multiple programming paradigms and is extensively used in scientific computing, data analysis, artificial intelligence, and web development. | programming, scripting, data analysis, machine learning, web development | Software Engineering, Computer Science | Programming Language | Documentation, Uses, and more |
| python_cacher | Stampede3 | python_cacher is a Python package for caching function results and improving computational efficiency by storing and retrieving expensive function calls. | Python Library, Function Caching, Computational Efficiency | Computer & Information Sciences | Library | Documentation, Uses, and more |
| pytorch | Anvil ACES |
PyTorch is an open-source machine learning library used for numerical computations and building deep learning models. | Machine Learning, Deep Learning, Numerical Computation, Neural Networks | Artificial Intelligence & Intelligent Systems, Computer & Information Sciences | Machine Learning Framework | Documentation, Uses, and more |
| pytorch-bundle | ACES | Documentation, Uses, and more | ||||
| pytorch-conda | Delta | A package that provides a conda environment for PyTorch, a popular deep learning framework. | Deep Learning, Machine Learning, Artificial Intelligence, Data Science | Computer Science, Artificial Intelligence and Intelligent Systems | Library | Documentation, Uses, and more |
| pytorch-geometric | ACES | PyTorch Geometric is a library for deep learning on irregular structures such as graphs, point clouds, and manifolds. It provides a set of tools to easily implement graph neural networks and other related models. | Deep Learning, Graph Neural Networks, Machine Learning, PyTorch | Computer Science, Artificial Intelligence and Intelligent Systems | Python Library | Documentation, Uses, and more |
| pytorch-lightning | ACES | PyTorch Lightning is a lightweight wrapper around PyTorch that helps to organize PyTorch code and decouple the science code from the engineering code, making it easier to scale and maintain. | Deep Learning, Machine Learning, PyTorch, Framework | Machine Learning, Deep Learning | Python Library | Documentation, Uses, and more |
| pyyaml | ACES | PyYAML is a YAML parser and emitter for Python. It supports YAML 1.2 specification and can parse and emit YAML data quickly and efficiently. | Yaml, Parser, Emitter | Other Computer & Information Sciences, Computer & Information Sciences | Data Serialization | Documentation, Uses, and more |
| pyzmq | ACES | PyZMQ is a Python library that provides bindings for ZeroMQ. ZeroMQ is a high-performance asynchronous messaging library that allows you to build distributed applications. | Python Library, Messaging Library, Distributed Applications, Asynchronous Messaging | Computer & Information Sciences | Programming Library | Documentation, Uses, and more |
| qca | ACES | QCA (Qualitative Comparative Analysis) is a comparative analytical method primarily used in the social sciences to analyze data sets involving categorical variables. It is a method for studying the relationships between the presence and absence of conditions and an outcome of interest. | Qualitative Data Analysis, Comparative Analysis, Social Sciences | Social Sciences | Analytical Software | Documentation, Uses, and more |
| qchem | Stampede3 | Q-Chem is a comprehensive quantum chemistry software package that provides a wide range of capabilities for electronic structure calculations, including methods for molecular geometry optimization, vibrational analysis, and excited state calculations. | Quantum Chemistry, Computational Chemistry, Electronic Structure, Molecular Modeling | Chemistry, Quantum Chemistry | Commercial | Documentation, Uses, and more |
| qcint | ACES | Documentation, Uses, and more | ||||
| qemu | Anvil ACES |
QEMU is a generic and open-source machine emulator and virtualizer that supports executing different operating systems and programs on a host operating system. It provides full system simulation, allowing users to run virtual machines with various architectures (x86, ARM, PowerPC, etc.) on a wide range of host platforms. QEMU can be used for various purposes such as development, testing, debugging, and virtualization. | Virtualization, Emulation, System Development | Biology, Computer & Information Sciences | Virtual Machine Emulator | Documentation, Uses, and more |
| qgis | Anvil ACES |
QGIS is a free and open-source cross-platform desktop geographic information system (GIS) application that supports viewing, editing, and analysis of geospatial data. | Gis, Mapping, Geospatial, Open Source | Geographic Information Science, Earth & Environmental Sciences | Geo-Spatial Software | Documentation, Uses, and more |
| qhull | ACES | Qhull computes the convex hull, Delaunay triangulation, Voronoi diagram, halfspace intersection about a point, furthest-site Delaunay triangulation, and furthest-site Voronoi diagram. | Computational Geometry, Libraries, Mesh Generation, Geometry Processing | Computer Science, Other Mathematics | Libraries | Documentation, Uses, and more |
| qiime2 | ACES | QIIME 2 is an open-source bioinformatics platform for performing microbiome analysis. It provides a comprehensive suite of tools for analyzing and visualizing microbial communities from amplicon sequencing data. | Microbiome, Bioinformatics, Sequencing | Bioinformatics | Analysis Software | Documentation, Uses, and more |
| qiskit | ACES | Qiskit is an open-source quantum computing software development framework that provides tools for creating, simulating, and executing quantum programs. | Quantum Computing, Open Source, Simulation, IBM | Quantum Computing, Quantum Algorithms | Library | Documentation, Uses, and more |
| qjson | ACES | QJson is a Qt-based library that maps JSON data to QVariant objects. It allows for easy JSON serialization and deserialization in Qt applications. | Json, Qt, Serialization, Deserialization | Computer & Information Sciences | Serialization/Deserialization | Documentation, Uses, and more |
| qmsolve | ACES | Documentation, Uses, and more | ||||
| qorts | ACES | Documentation, Uses, and more | ||||
| qscintilla | ACES | QScintilla is a port to Qt of Neil Hodgson's Scintilla editing component. It provides a rich text editing features and is commonly used for source code editing in integrated development environments (IDEs) and text editors. | Text Editing, Source Code Editing, Ides | Software Engineering, Engineering & Technology | Text Editor | Documentation, Uses, and more |
| qt | Anvil | Qt is a cross-platform C++ framework for application development. It provides a comprehensive set of libraries and tools for building graphical user interfaces, as well as for developing applications with network support, database integration, and more. | C++ Framework, Application Development, Cross-Platform, Graphical User Interface, Network Programming, Database Integration | Computer Science, Engineering & Technology | Framework | Documentation, Uses, and more |
| qt5 | ACES Stampede3 |
Qt is a comprehensive cross-platform C++ application framework that is widely used for developing application software with a graphical user interface (GUI), and also used for developing non-GUI programs such as command-line tools and consoles for servers. It allows developers to write code once and deploy it across various desktop, mobile, and embedded operating systems without rewriting the codebase. Qt5 is the latest version of the Qt development framework. | Software Development, Cross-Platform, Gui Development, C++ Framework | Computer Science, Engineering & Technology | Application Development | Documentation, Uses, and more |
| qt5webkit | ACES | Qt 5 Webkit is a module for the Qt 5 framework that allows developers to integrate web content into their applications. It provides a web rendering engine based on the open-source WebKit engine, allowing Qt applications to display and interact with web content. | Web Content Integration, Ui Development, Qt Framework | Computer Science, Computer & Information Sciences | Library | Documentation, Uses, and more |
| qt6 | ACES | Qt 6 is a cross-platform application framework that is widely used for developing application software with a graphical user interface (GUI) as well as non-GUI programs such as command-line tools and consoles for servers. | GUI, Cross-platform, Framework, C++ | Computer Science, Software Engineering | Application Framework | Documentation, Uses, and more |
| qtkeychain | ACES | QtKeychain is a Qt API to store passwords securely | Password Management, Security | Software Engineering | Library | Documentation, Uses, and more |
| qualimap | ACES | QualiMap is a quality control tool for high-throughput sequencing data. It provides a user-friendly interface to assess the quality of sequencing data generated by platforms such as Illumina, Roche 454, and Ion Torrent. QualiMap offers both basic and advanced quality metrics to help researchers evaluate the accuracy and reliability of their sequencing data. | Quality Control, High-Throughput Sequencing, Data Analysis | Bioinformatics, Biological Sciences | Quality Control Tool | Documentation, Uses, and more |
| quantum espresso | Stampede3 | Quantum ESPRESSO is an integrated suite of computer codes for electronic-structure calculations and materials modeling at the nanoscale. | Quantum Mechanics, Computational Physics, Materials Science | Physics, Condensed Matter Physics | Open Source | Documentation, Uses, and more |
| quantum machine 9 (qm9) | ACES | Documentation, Uses, and more | ||||
| quantum-espresso | Anvil | Quantum ESPRESSO is an integrated suite of computer codes for electronic-structure calculations and materials modeling at the nanoscale. | Quantum Mechanics, Materials Science, Computational Physics | Chemistry, Condensed Matter Physics | Package | Documentation, Uses, and more |
| quantum_espresso | Anvil | Quantum ESPRESSO is an integrated suite of open-source computer codes for electronic-structure calculations and materials modeling at the nanoscale. | Quantum Mechanics, Materials Science, Computational Physics | Physics, Condensed Matter Physics | Open-source | Documentation, Uses, and more |
| quantumespresso | ACES | Quantum ESPRESSO is an integrated suite of computer codes for electronic structure calculations and materials modeling at the nanoscale. | Quantum Mechanics, Materials Science, Computational Physics | Chemistry, Condensed Matter Physics | Package | Documentation, Uses, and more |
| quast | ACES | QUAST (Quality Assessment Tool for Genome Assemblies) is a software tool used for evaluating and comparing genome assemblies. It generates various metrics and statistics to assess the quality and accuracy of genomic assemblies. | Genome Assembly, Bioinformatics, Quality Assessment | Genomics, Biological Sciences | Stand-Alone Tool | Documentation, Uses, and more |
| quda | ACES | QUDA (Quda) is a library for solving quantum chromodynamics (QCD) problems on GPUs, providing high-performance implementations of lattice QCD algorithms. | GPU computing, quantum chromodynamics, high-performance computing | Quantum Field Theory, Quantum Chromodynamics | Library | Documentation, Uses, and more |
| qwt | ACES | Qwt is a robust library for developing Qt applications that require 2D plotting and data visualization. It provides a set of classes and functions for creating various types of plots and graphs with different customization options. | 2D Plotting, Data Visualization, Qt Applications | Engineering & Technology | Libraries | Documentation, Uses, and more |
| r | Anvil ACES DeltaAI Delta KyRIC Jetstream2 |
R is a free software environment for statistical computing and graphics. It compiles and runs on a wide variety of UNIX platforms, Windows, and MacOS. | Statistical Computing, Data Analysis, Statistical Graphics | Computer Science | Statistical Software | Documentation, Uses, and more |
| r-bundle-bioconductor | ACES | Bioconductor is an open-source software project that provides tools for the analysis and comprehension of high-throughput genomic data. | bioinformatics, genomics, R, data analysis | Computational Biology, Biological Sciences | Library | Documentation, Uses, and more |
| r-bundle-cran | ACES | A collection of R packages that are available on CRAN (Comprehensive R Archive Network) for various statistical and graphical techniques. | R, Statistical Computing, Data Analysis, Visualization | Statistics, Statistical Computing | Library | Documentation, Uses, and more |
| r_tamu | ACES | r_tamu is a simulation software for thermal and mechanical unit operations in chemical engineering. | Simulation Software, Chemical Engineering, Thermal Unit Operations, Mechanical Unit Operations | Chemical Engineering, Engineering & Technology | Engineering & Technology | Documentation, Uses, and more |
| racon | ACES | Racon is a consensus module for correcting errors in long reads generated by third-generation sequencing technologies. It utilizes both a partially ordered de Bruijn graph and a fuzzy pairwise aligner to achieve high accuracy error correction. | Bioinformatics, Sequence Analysis, Genomics | Genomics, Biological Sciences | Bioinformatics Tool | Documentation, Uses, and more |
| raja | ACES | Documentation, Uses, and more | ||||
| rapidjson | ACES | RapidJSON is a fast JSON parser and generator for C++ with both SAX/DOM styles. It is designed to be highly memory efficient and is self-contained with no external dependencies. | Json, C++, Parser, Generator, Sax, Dom, Memory Efficient | Software Engineering, Computer & Information Sciences | Library | Documentation, Uses, and more |
| rapids | ACES | RAPIDS is a suite of open-source software libraries and APIs built on NVIDIA CUDA for executing end-to-end data science and analytics pipelines entirely on GPUs. It allows for faster processing and analysis of big data. | Data Science, Analytics, Gpu Computing | Computer Science, Computer & Information Sciences | Data Science | Documentation, Uses, and more |
| rapidsai | Anvil | RAPIDS AI is an open-source suite of software libraries and APIs built on CUDA for accelerating data science and analytics pipelines. | GPU Computing, Data Science, Machine Learning, Analytics | Computer Science, Data Science | Library | Documentation, Uses, and more |
| rapsearch2 | ACES | RapSearch2 is a high-performance sequence alignment tool designed for rapid and sensitive alignment of protein sequences against large databases. | bioinformatics, sequence alignment, high-performance computing | Computational Biology, Bioinformatics | Command-line tool | Documentation, Uses, and more |
| rastair | ACES | Documentation, Uses, and more | ||||
| rasterio | ACES | Rasterio is a Python library for reading and writing geospatial raster datasets. It is built on the capabilities of the GDAL (Geospatial Data Abstraction Library) and provides easy access to the functionalities for opening, reading, and writing geospatial raster data formats. | Python Library, Geospatial Data, Raster Data, Gdal, Remote Sensing | Geospatial Science, Earth & Environmental Sciences | Data Processing/Analysis | Documentation, Uses, and more |
| rattler-build | ACES | Documentation, Uses, and more | ||||
| raven | ACES | Documentation, Uses, and more | ||||
| ray-project | ACES | Ray is a flexible, high-performance distributed execution framework that makes it easy to scale Python applications from a single machine to a cluster. | Distributed Computing, Parallel Processing, Machine Learning, Python | Distributed Systems, Artificial Intelligence and Intelligent Systems | Framework | Documentation, Uses, and more |
| rclone | Anvil ACES Expanse |
Rclone is a command-line program to manage files on cloud storage. It is a powerful tool that supports various cloud storage services and allows users to sync files between different storage locations. | Cloud Storage, File Synchronization, Command-Line Tool | Computer Science | Data Management | Documentation, Uses, and more |
| rdflib | ACES | RDFLib is a Python library for working with RDF (Resource Description Framework) data. It allows users to create, parse, modify, serialize, and query RDF graphs. | Rdf, Python Library | Computer Science, Computer & Information Sciences | Data Management | Documentation, Uses, and more |
| rdkit | ACES | RDKit is an open-source toolkit for cheminformatics that provides a wide range of functionality for cheminformatics, including molecular modeling, cheminformatics, and machine learning tools. | Cheminformatics, Molecular Modeling, Cheminformatics Toolkit | Chemical Sciences, Natural Sciences | Toolkit | Documentation, Uses, and more |
| re2 | ACES | RE2 is a fast, safe, thread-friendly, and efficient regular expression library. It provides better performance than many widely used regular expression libraries by using automata theory, generating linear-time matching algorithms. | Regular Expression, Library, Performance, Thread-Safe | Software Engineering, Computer & Information Sciences | Tool | Documentation, Uses, and more |
| re2c | ACES DeltaAI |
re2c is a tool for writing fast and flexible lexer/scanner programs. It translates regular expressions into deterministic finite automata (DFA) and compiles them into C/C++ code. This allows for efficient lexical analysis of input streams. | Lexer, Scanner, Regular Expressions, Dfa | Software Engineering, Computer & Information Sciences | Tool | Documentation, Uses, and more |
| readline | Anvil DeltaAI KyRIC |
GNU Readline is a free software library that provides line-editing and history capabilities for interactive programs with a command-line interface. It allows users to edit command lines as they are typed in, recall and re-edit previous input, and perform basic character manipulations. | Gnu, Command Line Interface, Interactive Programs, Line Editing, History Manipulation | Software Engineering, Computer & Information Sciences | Command Line Tool | Documentation, Uses, and more |
| redis | ACES | Redis is an open-source, in-memory data structure store that can be used as a database, cache, and message broker. It supports various data structures such as strings, hashes, lists, sets, sorted sets with range queries, bitmaps, hyperloglogs, geospatial indexes with radius queries, and streams. | Database, Cache, Message Broker | Database Management, Computer & Information Sciences | Data Store | Documentation, Uses, and more |
| redis-py | ACES | redis-py is a Python client library for Redis, a popular in-memory data store. It allows Python developers to easily interact with a Redis database to store and retrieve data. | Python Library, Database Interaction, In-Memory Data Store, Data Persistence | Computer Science, Computer & Information Sciences | Client Library | Documentation, Uses, and more |
| reframe | ACES | ReFrame is a Python library for writing tests for High Performance Computing (HPC) systems. It provides a functional testing framework designed to support a variety of different HPC systems. | Hpc, Python Library, Testing Framework | Engineering & Technology | Software Development | Documentation, Uses, and more |
| relion | ACES Anvil |
Relion is a stand-alone computer program that employs an empirical Bayesian approach to refinement of (multiple) 3D reconstructions or 2D class averages in electron cryo-microscopy (cryo-EM). | Cryo-Em, Image Processing, 3D Reconstruction, Macromolecular Complexes | Biochemistry and Molecular Biology | Image Processing | Documentation, Uses, and more |
| remora | Stampede3 | Remora is a lightweight and extensible Python library for parallel and distributed computing workflows. It simplifies the process of distributing tasks across multiple workers and managing dependencies in a distributed environment. | Python Library, Parallel Computing, Distributed Computing | Computer & Information Sciences | Parallel & Distributed Computing | Documentation, Uses, and more |
| renderproto | Anvil | Documentation, Uses, and more | ||||
| rioxarray | ACES | rioxarray is a Python package that extends xarray to add geospatial capabilities by making use of rasterio for I/O operations with raster data. It enables reading and writing spatial raster data with ease and integrates seamlessly with xarray for analysis and manipulation of these geospatial datasets. | Python Library, Geospatial Data, Raster Data, Data Processing | Earth & Environmental Sciences | Python Package | Documentation, Uses, and more |
| rising | ACES | RISING (Rapidly Installed Systems Engineering) is an open-source systems engineering tool that focuses on automating the system development process. It provides a framework for designing, integrating, and verifying complex systems with an emphasis on modularity, reusability, and maintainability. | Systems Engineering, Automation, Modularity, Reusability, Maintainability | Software Engineering, Systems & Development, Engineering & Technology | Systems Engineering | Documentation, Uses, and more |
| rnaquast | ACES | RNAQuast is a quality assessment tool for de novo transcriptome assembly pipelines. It evaluates the quality of transcriptome assemblies by comparing them to a reference genome and measures various metrics to assess the completeness, correctness, and compatibility of the assembly. | Bioinformatics, Transcriptome Analysis, Quality Assessment, Genomics | Biological Sciences | Quality Assessment Tool | Documentation, Uses, and more |
| rocm-smi | ACES | rocm-smi is a command-line program that allows users to monitor and manage AMD Radeon Open Compute (ROCm) System Management Interface (SMI) enabled GPUs. It provides detailed information about the current state of the GPUs and enables users to manage various aspects of the GPUs such as power management, fan speed control, temperature monitoring, and more. | Gpu Management, Performance Monitoring, System Management Interface, Amd Radeon, Rocm | Computer Science, Engineering & Technology | Command-Line Interface | Documentation, Uses, and more |
| root | ACES | ROOT is an open-source data analysis framework used by high-energy physics (HEP) experiments. It provides a range of tools for data manipulation, visualization, statistical analysis, and storage. ROOT is written in C++ and offers a scripting language called ROOT/CINT that allows for quick prototyping and interactive analysis. | Data Analysis, Visualization, High-Energy Physics, Data Manipulation, Statistical Analysis | Particle & High-Energy Physics, Physical Sciences | Library | Documentation, Uses, and more |
| rosetta | ACES | Rosetta is a software suite for modeling macromolecules, including protein folding, protein-protein interactions, and protein-ligand docking. It provides tools for predicting and designing protein structures, protein-protein interactions, and protein-ligand binding. | bioinformatics, computational biology, structural biology, molecular modeling | Bioinformatics, Structural Biology | Application | Documentation, Uses, and more |
| rpmrebuild | ACES | A tool for rebuilding RPM packages from existing RPM files. | RPM, Package Management, Linux, Software Development | Computer Science, Software Engineering | Command Line Tool | Documentation, Uses, and more |
| rsem | ACES | RSEM (RNA-Seq by Expectation Maximization) is a software package for estimating gene and isoform expression levels from RNA-Seq data. It quantifies the abundances of transcripts by calculating maximum likelihood estimates based on the Expectation-Maximization algorithm. | RNA-Seq, Transcriptomics, Gene Expression, Bioinformatics | Genomics, Biological Sciences | Computational Tool | Documentation, Uses, and more |
| rseqc | ACES | RSeQC provides a number of standalone modules to check quality of RNA-Seq experiments, from raw data to the final result. | RNA-Seq, Quality Control, Gene Expression Analysis | Bioinformatics, Biological Sciences | Tool | Documentation, Uses, and more |
| rstudio | Anvil Expanse Jetstream2 |
RStudio is an integrated development environment (IDE) for R, a programming language and environment widely used for statistical computing and graphics. RStudio provides an intuitive and productive user interface for R, allowing users to efficiently write, execute, and debug R code. | Ide, Statistical Computing, Data Visualization, Programming | Statistics, Other Natural Sciences | Ide | Documentation, Uses, and more |
| ruamel.yaml | ACES | ruamel.yaml is a YAML 1.2 loader/dumper package for Python. It is a superset of the PyYAML library and it includes round-trip parsing (which allows for preserving comments and formatting when loading and then emitting the YAML data). | Yaml, Parser, Dumper, Python | Software Engineering, Computer & Information Sciences | Data Serialization | Documentation, Uses, and more |
| ruby | ACES | Ruby is a dynamic, object-oriented programming language focused on simplicity and productivity. It has an elegant syntax that is easy to read and write, making it a popular choice for web development and scripting. | Programming Language, Scripting Language, Web Development | Computer Science | Programming | Documentation, Uses, and more |
| rust | ACES | Rust is a multi-paradigm system programming language focused on safety, speed, and concurrency. | Programming Language, System Programming, Concurrency | Software Engineering, Computer & Information Sciences | Compiler | Documentation, Uses, and more |
| safestringlib | ACES | A library for safe string handling in C/C++ to prevent buffer overflows and other vulnerabilities. | C, C++, Security, Library | Software Engineering | Library | Documentation, Uses, and more |
| safetensors | ACES | Documentation, Uses, and more | ||||
| salmon | ACES | Salmon is a wicked-fast program to provide quantification of transcript expression from RNA-seq data. | RNA-Seq, Transcript Expression Quantification | Genetics, Biological Sciences | Tool | Documentation, Uses, and more |
| samtools | Anvil ACES Delta |
Samtools is a suite of programs for interacting with high-throughput sequencing data generated in sequence alignment/map (SAM) format, such as those produced by the Short Read Mapping (SHRiMP) or Burrows-Wheeler Aligner (BWA) aligners. It allows various operations on SAM/BAM files, including indexing, sorting, merging, and manipulating sequence alignments. | Sequence Analysis, Genomics, Bioinformatics | Bioinformatics, Biological Sciences | Command Line Tool | Documentation, Uses, and more |
| sanitizers4hpc | DeltaAI Delta |
sanitizers4hpc is a toolset designed for detecting and removing memory errors and data races in high-performance computing (HPC) applications. It offers various sanitizers to enhance the reliability and performance of parallel programs. | Memory Errors, Data Races, Hpc Applications | Computer Science, Engineering & Technology | Tool | Documentation, Uses, and more |
| sanitytool | Stampede3 | Sanitytool is a software tool designed for ensuring the sanity and quality of software code by performing various checks and validations. It helps in identifying potential issues, bugs, and vulnerabilities in the codebase, ensuring a higher level of code quality and reliability. | Software Quality Assurance, Code Analysis, Automated Testing, Continuous Integration | Software Engineering, Systems & Development, Engineering & Technology | Quality Assurance Tool | Documentation, Uses, and more |
| scafacos | ACES | SCAFACOS (Single-Cell Analysis Framework for Assessing Clonal Outcomes of Signaling) is a computational tool designed for analyzing single-cell signaling data and inferring clonal outcomes in cellular systems. It is specifically tailored for studying cellular heterogeneity and clonal dynamics in response to signaling pathways. | Computational Tool, Single-Cell Analysis, Signaling Pathways, Clonal Dynamics | Cell Biology, Biological Sciences | Data Analysis Tool | Documentation, Uses, and more |
| scalapack | ACES | ScaLAPACK (Scalable LAPACK) is a parallel version of LAPACK (Linear Algebra PACKage) for distributed memory machines. It is designed to efficiently solve large-scale problems in numerical linear algebra using parallelism. | Linear-Algebra, Numerical-Computing, Distributed-Computing, Parallel-Computing | Other, Physical Sciences | Library | Documentation, Uses, and more |
| scalasca | ACES KyRIC |
Scalasca is a software toolset for analyzing the performance behavior of parallel applications and specifically for identifying potential performance bottlenecks. It assists users in optimizing the performance of their parallel applications by providing scalable and usable performance data. | Performance Analysis, Parallel Applications, Performance Optimization, Mpi Applications, Visualization | Software Engineering, Systems & Development, Computer & Information Sciences | Performance Analysis Tool | Documentation, Uses, and more |
| scalene | ACES | Scalene is a high-performance, high-precision CPU, GPU, and memory profiler for Python. It provides detailed insights into the performance of Python code, allowing developers to identify bottlenecks and optimize their applications effectively. | profiling, performance, Python, development, optimization | Computer Science, Software Engineering | Profiling Tool | Documentation, Uses, and more |
| schrodinger | ACES | Schrodinger is a leading provider of advanced molecular simulations and quantum chemistry software for Life Sciences and Materials Research. The software suite offers a wide range of tools for drug discovery and materials science applications. | Molecular Simulations, Quantum Chemistry, Drug Discovery, Materials Research | Chemistry, Chemical Sciences | Commercial | Documentation, Uses, and more |
| scikit-bio | ACES | scikit-bio is a Python library for bioinformatics that provides tools for biological data manipulation, analysis, and visualization. It offers functionality for working with biological sequence data, phylogenetic trees, and related metadata. | Bioinformatics, Python Library, Biological Data Analysis, Sequence Analysis | Bioinformatics, Biological Sciences | Library | Documentation, Uses, and more |
| scikit-build | ACES | Scikit-build is an improved build system generator for CPython C/C++/Fortran/Cython extensions. It provides better support for CMake and enables you to easily build Python packages containing C++, C, Fortran, or Cython code. | Python Library, Build System, Cmake Integration | Computer Science, Computer & Information Sciences | Library | Documentation, Uses, and more |
| scikit-build-core | ACES | scikit-build-core is a core library for building Python packages with CMake, designed to simplify the process of creating Python extensions and modules. | Python, CMake, Packaging, Build Tools | Computer Science, Software Engineering | Library | Documentation, Uses, and more |
| scikit-cuda | ACES | scikit-cuda is a Python library that provides a Python interface to Nvidia's CUDA parallel computation API. It aims to make GPU programming more accessible to Python developers by providing GPU-accelerated linear algebra operations and other numerical algorithms. | Python Library, Gpu Programming, Numerical Algorithms, Linear Algebra, Cuda Api | High-Performance Computing, Computer & Information Sciences | Python Library | Documentation, Uses, and more |
| scikit-image | ACES | scikit-image is an open-source image processing library for the Python programming language that is designed to work with NumPy arrays. It provides a collection of algorithms for image processing, segmentation, feature extraction, and more. | Image Processing, Python Library | Image Analysis, Computer & Information Sciences | Library | Documentation, Uses, and more |
| scikit-learn | ACES | Scikit-learn is a machine learning library for the Python programming language. It features various classification, regression, and clustering algorithms including support vector machines, random forests, gradient boosting, k-means, and DBSCAN, among others. Scikit-learn is designed to interoperate with the Python numerical and scientific libraries NumPy and SciPy. | Machine Learning, Python Library | Artificial Intelligence & Intelligent Systems, Computer & Information Sciences | Libraries | Documentation, Uses, and more |
| scipy-bundle | ACES | The scipy-bundle is a comprehensive collection of scientific computing tools built on top of the SciPy library. It includes a wide range of modules and packages for numerical processing, optimization, statistics, integration, interpolation, signal processing, and more. | Scientific Computing, Numerical Processing, Statistics, Optimization, Signal Processing | Computer & Information Sciences, Other Computer & Information Sciences | Scientific Computing | Documentation, Uses, and more |
| scons | ACES | SCons is an open-source software construction tool implemented in Python. It is designed to replace traditional build tools like Make with a more powerful and flexible build system. | Build Tool, Software Construction, Automation, Python | Software Development, Engineering & Technology | Build Tool | Documentation, Uses, and more |
| score-p | ACES | Score-P is a performance measurement infrastructure designed to analyze and optimize the performance of parallel and distributed applications. It provides a set of measurement and analysis tools to assess the performance, scalability, and behavior of parallel applications. | Software, Performance Measurement, Parallel Computing, Distributed Computing | Computer Science, Engineering & Technology | Tool | Documentation, Uses, and more |
| scorep | KyRIC | Score-P is a tool for profiling and tracing of parallel applications. It provides a comprehensive performance analysis framework for HPC applications, allowing developers to identify bottlenecks and optimize their code. | Performance Analysis, Profiling, Tracing, HPC | Computer Science | Performance Analysis Tool | Documentation, Uses, and more |
| scotch | ACES Stampede3 |
Scotch is a software package and library for graph and mesh partitioning, ordering, and clustering. It is designed to efficiently distribute data and computations across distributed memory parallel computers. | Graph Partitioning, Mesh Partitioning, Parallel Computing, Distributed Memory | Software Engineering, Systems & Development, Computer & Information Sciences | Library | Documentation, Uses, and more |
| sdl2 | ACES | Simple DirectMedia Layer is a cross-platform development library designed to provide low level access to audio, keyboard, mouse, joystick, and graphics hardware via OpenGL and Direct3D. It is used by video playback software, emulators, and popular games including Valve's Steam. | Development, Multimedia, Graphics, Input-Output | Software Development, Engineering & Technology | Development | Documentation, Uses, and more |
| sdl2_image | ACES | SDL2_image is an image loading library that is part of the Simple DirectMedia Layer (SDL) project. It allows developers to load various image formats into SDL surfaces and textures, making it easier to work with images in multimedia applications and games. | image processing, graphics, SDL, multimedia | Software Development, Computer Science | Library | Documentation, Uses, and more |
| sdl2_mixer | ACES | SDL2_mixer is a simple multi-channel audio mixer library for use with SDL2. It provides support for various audio formats and allows for easy mixing of multiple audio sources. | audio, SDL, game development, multimedia | Computer Science, Software Engineering | Library | Documentation, Uses, and more |
| sdl2_ttf | ACES | SDL2_ttf is a library that provides TrueType font support for the Simple DirectMedia Layer (SDL) library. It allows developers to render text using TrueType fonts in their SDL applications. | graphics, font rendering, SDL, game development | Software Engineering, Other Computer and Information Sciences | Library | Documentation, Uses, and more |
| sdsc | Expanse | SDSC (San Diego Supercomputer Center) is an organized research unit of the University of California, San Diego that provides cyberinfrastructure resources and services to researchers in the fields of computational science, data analytics, bioinformatics, and more. SDSC supports a wide range of scientific disciplines by offering high-performance computing resources, data storage solutions, software tools, consulting services, and training programs. | Supercomputing, Research Support, Data Analytics, Cyberinfrastructure | Computer & Information Sciences, Other Computer & Information Sciences, Engineering & Technology, Other Engineering & Technologies, Training, Infrastructure & Instrumentation | Documentation, Uses, and more | |
| sdsl-lite | ACES | SDSL-lite is a lightweight C++ library for the implementation of succinct data structures, which are space-efficient representations of data that allow for fast access and modification. | Data Structures, C++, Succinct Data Structures, Algorithms | Algorithms, Computer Science | Library | Documentation, Uses, and more |
| seaborn | ACES | Seaborn is a Python data visualization library based on matplotlib. It provides a high-level interface for creating attractive and informative statistical graphics. | Python Library, Data Visualization, Statistical Graphics | Statistics, Computer & Information Sciences | Library | Documentation, Uses, and more |
| sentencepiece | ACES | SentencePiece is an unsupervised text tokenizer and detokenizer mainly for Neural Network-based text generation systems where the vocabulary size greatly affects the model performance. | Text Tokenizer, Neural Network, Text Generation | Computer Science, Computer & Information Sciences | Library/Tool | Documentation, Uses, and more |
| sepp | ACES | SEPP (Satz per Partial Parsimony) is a software tool for aligning short DNA reads to a reference alignment in phylogenetic studies. It employs a phylogenetic placement strategy to assign reads to the reference tree in a computationally efficient manner. | Phylogenetics, DNA Alignment, Phylogenetic Placement | Bioinformatics, Biological Sciences | Bioinformatics Tool | Documentation, Uses, and more |
| seqkit | ACES | SeqKit is a cross-platform, ultrafast, and handy sequenced data manipulation toolkit. It allows users to quickly manipulate sequences in fasta/fastq format, including filtering, splitting, removing duplicates, converting formats, and extracting sequences. SeqKit is designed to be efficient and user-friendly for handling large-scale sequencing data. | Sequence Manipulation, Fasta, Fastq | Bioinformatics, Biological Sciences | Bioinformatics | Documentation, Uses, and more |
| seqlib | ACES | Documentation, Uses, and more | ||||
| seqtk | ACES | Seqtk is a fast and lightweight tool for processing sequences in the FASTA or FASTQ format. It is designed for handling large sequence data efficiently. | bioinformatics, sequence processing, FASTA, FASTQ, data manipulation | Bioinformatics, Biological Sciences | Command-line tool | Documentation, Uses, and more |
| serf | ACES | Serf is a decentralized solution for cluster membership, failure detection, and orchestration. It is lightweight and highly available, providing a mechanism for event broadcasting and key/value storage. | Cluster Management, Orchestration, Decentralized System | Engineering & Technology | Documentation, Uses, and more | |
| settarg | ACES DeltaAI Delta Stampede3 |
Settarg is a command-line utility designed for setting target specific optimizations in C/C++ compilers. It helps in specifying optimization flags tailored for a particular CPU architecture to improve performance. | Compilers, Optimization, Performance Enhancement, Command-Line Tool | Command-Line Utility | Documentation, Uses, and more | |
| setuptools | ACES | Setuptools is a package development process library designed to facilitate packaging Python projects. It allows developers to specify project metadata, declare project dependencies, and create distributable packages that can be easily installed using the Python package manager, pip. | Python Packaging, Package Management, Dependency Management | Software Engineering, Computer Science | Library | Documentation, Uses, and more |
| setuptools-rust | ACES | Setuptools-Rust is a Python library that extends the Setuptools build system, allowing you to build and distribute Rust packages from Python projects seamlessly. It simplifies the integration of Rust code into Python projects, making cross-language development easier and more efficient. | Python Library, Build System, Rust Integration | Software Engineering, Systems & Development, Computer & Information Sciences | Plug-In/Extension | Documentation, Uses, and more |
| shadow | KyRIC | Shadow is a versatile network simulator that is designed with the aim of providing not only an efficient and scalable simulation framework but also powerful and flexible scripting engines to automate complex simulations. | Network Simulation, Scripting, Simulation Framework | Computer Science, Computer & Information Sciences | Network Simulator | Documentation, Uses, and more |
| shap | ACES | SHAP (SHapley Additive exPlanations) is a unified approach to explain the output of any machine learning model. It connects game theory with local explanations, attributing the impact of each feature on a model's predictions. | Explainability, Interpretability, Machine Learning, Model Explanation | Artificial Intelligence & Intelligent Systems, Computer & Information Sciences | Python Library | Documentation, Uses, and more |
| shapely | ACES | Shapely is a Python library for manipulation and analysis of planar geometric objects. It is based on the widely deployed GEOS (the engine of PostGIS) and JTS (from which GEOS is ported) libraries. | Python Library, Geospatial Analysis, Geometric Objects | Geographic Information Science, Earth & Environmental Sciences | Python Library | Documentation, Uses, and more |
| shared | Expanse | Shared is a cloud-based collaboration platform that allows users to share files, documents, and information with team members or external collaborators. It provides a centralized location for real-time collaboration, file storage, version control, and communication. | Collaboration Platform, Cloud-Based Software, File Sharing, Communication, Version Control | Other | Cloud-Based Platform | Documentation, Uses, and more |
| siesta | ACES Stampede3 |
Siesta is a computer program that performs electronic structure calculations based on density-functional theory. It is especially designed for tight-binding and ab-initio calculations in materials science. | Electronic Structure Calculations, Density-Functional Theory, Materials Science | Condensed Matter Physics, Physical Sciences | Material Science | Documentation, Uses, and more |
| silo | Stampede3 | Documentation, Uses, and more | ||||
| simple-dftd3 | ACES | Documentation, Uses, and more | ||||
| singularity | KyRIC | Singularity is an open-source container platform designed to create, run, and manage containers for scientific and high-performance computing (HPC) workloads. It focuses on providing secure and portable environments for researchers and developers. | Containerization, Scientific Computing, Hpc, Research | High-Performance Computing, Computer & Information Sciences, Engineering & Technology | Platform | Documentation, Uses, and more |
| singularitypro | Expanse | SingularityPro is a container platform that allows users to create, deploy, and manage containers for high-performance computing (HPC) environments. It is designed to provide users with a flexible and scalable solution for running applications in isolated environments. | Container Platform, Hpc, High-Performance Computing | Engineering & Technology | Container Platform | Documentation, Uses, and more |
| sionlib | ACES KyRIC |
Sionlib is a library that provides an I/O interface for scientific data stored in self-describing Hierarchical Data Format (HDF5) files, often used in high-performance computing applications. It offers functionalities for reading and writing data, metadata management, and dataset manipulation, making it a valuable tool for handling complex scientific data structures. | I/O Interface, Scientific Data, Hdf5 Files | High-Performance Computing, Computer Science | Library | Documentation, Uses, and more |
| sip | ACES | SIP (Session Initiation Protocol) is a protocol used for initiating, maintaining, and terminating real-time sessions that include voice, video, and messaging applications. | Communication, Networking, Protocol, Real-time | Networking, Computer Science | Protocol | Documentation, Uses, and more |
| slepc | ACES | SLEPc (Scalable Library for Eigenvalue Problem Computations) is a software library for the solution of large scale sparse eigenvalue problems. | Eigenvalue Problems, Sparse Matrices, Parallel Computing | Numerical Linear Algebra, Other Mathematics | Numerical Computing | Documentation, Uses, and more |
| slurm | Expanse | Slurm is an open-source workload manager designed for Linux clusters of all sizes. It provides job scheduling, prioritization, and management capabilities to maximize the efficiency of cluster resources. | Workload Manager, Cluster Management, High-Performance Computing | Computer Science, Engineering & Technology | Workload Manager | Documentation, Uses, and more |
| slurm-env | Delta | slurm-env is a tool that helps manage environment variables for SLURM job scripts. SLURM, which stands for Simple Linux Utility for Resource Management, is an open-source job scheduler for Linux clusters. | Slurm, Job Scheduler, Environment Variables, Linux Clusters | Engineering & Technology | Utility Tool | Documentation, Uses, and more |
| smithwaterman | ACES | Smith-Waterman is an algorithm used for local sequence alignment in bioinformatics, particularly for comparing protein or nucleotide sequences. | bioinformatics, sequence alignment, local alignment, algorithm | Bioinformatics | Algorithm | Documentation, Uses, and more |
| smv | ACES | Documentation, Uses, and more | ||||
| snakemake | ACES | Snakemake is a workflow management system that aims to improve the reproducibility and traceability of computational workflows. It allows users to define workflows in a human-readable and Python-based domain-specific language. | Workflow Management, Reproducibility, Traceability, Bioinformatics, Computational Biology, Data Science | Bioinformatics, Other Computer & Information Sciences | Software | Documentation, Uses, and more |
| snappy | ACES | Snappy is a fast compressor/decompressor for big data. It aims for very high speeds and reasonable compression levels. Snappy is widely used in many large-scale data processing frameworks. | Compression, Big Data, Data Processing | Computer & Information Sciences | Data Processing Tool | Documentation, Uses, and more |
| sox | ACES | SoX (Sound eXchange) is a command-line utility that converts various formats of computer audio files in to other formats. It can also apply various effects to the audio. | Audio Processing, Sound Conversion, Command Line Tool | Sound Processing, Audio Engineering | Utility | Documentation, Uses, and more |
| spack | ACES KyRIC |
Spack is a flexible package management tool designed to support multiple versions of software, compilers, libraries, and tools on a wide range of platforms and configurations. It helps users easily install, uninstall, and manage software and dependencies in a reproducible and customizable way. | Package Management, Software Installation, Dependency Management, Hpc, Scientific Computing | High Performance Computing, Other Computer & Information Sciences | Utility | Documentation, Uses, and more |
| spacy | ACES | spaCy is a free, open-source library for advanced Natural Language Processing (NLP) in Python. It is designed with the goal of facilitating easy implementation of state-of-the-art NLP techniques. | Nlp, Natural Language Processing, Python Library | Artificial Intelligence & Intelligent Systems, Computer & Information Sciences | Library | Documentation, Uses, and more |
| spades | ACES | SPAdes (St. Petersburg genome assembler) is a de novo genome assembly software tool designed for single-cell and multi-cell bacterial genome projects. It uses a combination of de Bruijn graph and mismatch correction algorithms to assemble highly accurate and contiguous draft genomes. | Genome Assembly, Bioinformatics, Computational Biology | Bioinformatics, Biological Sciences | Bioinformatics Tool | Documentation, Uses, and more |
| spark | Anvil ACES Expanse |
Apache Spark is an open-source distributed computing system that provides an interface for programming entire clusters with implicit data parallelism and fault tolerance. | Distributed Computing, Big Data, Data Processing | Computer Science, Computer & Information Sciences | Distributed Computing System | Documentation, Uses, and more |
| sparsehash | ACES | sparsehash is a C++ library that provides several hash-map implementations. These implementations are designed to be very space-efficient, but still allow fast lookups. | C++ Library, Hash-Map Implementations | Software Engineering, Computer & Information Sciences | Data Structure | Documentation, Uses, and more |
| spfft | ACES | Documentation, Uses, and more | ||||
| spglib | ACES | spglib is a software library for finding and manipulating the crystal symmetries written in C. It is primarily used for crystallography and solid-state physics research. | Crystallography, Solid-State Physics | Condensed Matter Physics, Physical Sciences | Computational Software | Documentation, Uses, and more |
| spglib-python | ACES | Spglib-python is a Python wrapper for the C library Spglib, which is a library for finding and manipulating spacegroup symmetry. It provides a wide range of functionalities for crystallography and solid-state physics calculations. | Crystallography, Solid State Physics | Condensed Matter Physics, Physical Sciences | Python Library | Documentation, Uses, and more |
| spice-server | Anvil | Documentation, Uses, and more | ||||
| spin | ACES | Documentation, Uses, and more | ||||
| spython | ACES | Spython is a software tool that combines the functionalities of the Python programming language with specific features tailored for scientific computing, data analysis, and visualization tasks. It aims to streamline the workflow for researchers and scientists by providing an integrated environment for code development, data manipulation, and result visualization. | Scientific Computing, Data Analysis, Visualization, Python Programming, Research Tools | Computer & Information Sciences, Other Mathematics, Other Natural Sciences | Scientific Computing Tool | Documentation, Uses, and more |
| sqlalchemy | ACES | SQLAlchemy is a SQL toolkit and Object-Relational Mapping (ORM) system for the Python programming language. | Python, Database, ORM, SQL | Software Engineering, Database Systems | Library | Documentation, Uses, and more |
| sqlite | Anvil ACES DeltaAI KyRIC Stampede3 |
SQLite is a C-language library that implements a small, fast, self-contained, high-reliability, full-featured, SQL database engine. SQLite is the most widely deployed SQL database engine in the world. The source code for SQLite is in the public domain. | Relational Database, Sql, Database Management | Computer Science, Computer & Information Sciences | Library | Documentation, Uses, and more |
| squashfs | KyRIC | SquashFS is a compressed read-only filesystem for Linux. It enables efficient storage of files, in a compressed format, with a focus on high compression ratios. | Filesystem, Compression, Read-Only | Computer Science, Computer & Information Sciences | Filesystem | Documentation, Uses, and more |
| sra-toolkit | ACES | The SRA Toolkit is a collection of tools for working with data from the Sequence Read Archive (SRA). It allows users to download, convert, and manipulate sequencing data. | bioinformatics, sequencing, data processing, genomics | Biology, Genomics | Command-line tool | Documentation, Uses, and more |
| sratoolkit | Anvil Expanse |
The SRA Toolkit is a collection of tools for working with data in the Sequence Read Archive (SRA). It allows users to download, convert, and manipulate sequencing data from the SRA. | bioinformatics, genomics, data processing | Biology, Genomics | Command-line tool | Documentation, Uses, and more |
| sst-core | ACES | SST (Structural Simulation Toolkit) Core is a framework for developing high-performance simulations of complex systems, particularly in the field of computer architecture and systems. | Simulation, High Performance Computing, Computer Architecture, Systems Modeling | Systems, Computer Science | Simulation Framework | Documentation, Uses, and more |
| ssw | ACES | Documentation, Uses, and more | ||||
| star | ACES Delta |
STAR (Spliced Transcripts Alignment to a Reference) is a RNA-seq read aligner that maps RNA-seq data to a reference genome to identify splice junctions between exons. It is particularly useful for mapping reads that span multiple exons, thereby aiding in the analysis of alternative splicing events. | Software, RNA-Seq, Read Aligner, Splice Junctions, Alternative Splicing | Genetics, Biological Sciences | Alignment Tool | Documentation, Uses, and more |
| starpu | ACES | StarPU is a runtime system designed for heterogeneous multicore machines with accelerators. It offers a unified runtime system that can handle multi-threading, task parallelism, data management, and data locality management. StarPU is specifically tailored for dense numerical linear algebra operation kernels and iterative solvers. | Runtime System, Heterogeneous Computing, Multicore Architectures | Other | Hpc Tool | Documentation, Uses, and more |
| stat | DeltaAI Delta |
Stat is a statistical software package designed for data analysis, statistical modeling, hypothesis testing, and visualization. | Statistics, Data Analysis, Statistical Modeling, Hypothesis Testing, Visualization | Systems, Mathematics | Data Analysis Tool | Documentation, Uses, and more |
| statsmodels | ACES | Statsmodels is a Python module that provides classes and functions for the estimation of many different statistical models, as well as for conducting statistical tests, and statistical data exploration. It also includes machine learning algorithms, such as clustering algorithms and supervised learning models. | Statistics, Data Analysis, Machine Learning, Python | Data Science, Statistics & Probability | Data Analysis & Statistics | Documentation, Uses, and more |
| strace | ACES | strace is a diagnostic, debugging and instructional userspace utility for Linux. It is used to monitor and tamper with interactions between processes and the Linux kernel, which include system calls, signal deliveries, and changes of process state. | Debugging, Diagnostic, Monitoring | Systems, Computer & Information Sciences | Diagnostic Tool | Documentation, Uses, and more |
| stringtie | ACES | StringTie is a software for transcript assembly and quantification of RNA-Seq data. It is designed to efficiently assemble and quantify full-length transcripts representing multiple splice variants for each gene locus. | RNA-Seq, Transcript Assembly, Transcript Quantification | Biological Sciences | Transcriptomics Tool | Documentation, Uses, and more |
| subread | ACES | subread is a software package for processing next-generation sequencing data, including read mapping and quantification of gene and genomic feature expression levels. It is designed to efficiently handle large volumes of sequencing data with high accuracy and speed. | Ngs, Bioinformatics, Sequencing, Alignment | Bioinformatics, Biological Sciences | Ngs Analysis | Documentation, Uses, and more |
| subversion | ACES Expanse |
Subversion (SVN) is an open-source version control system that allows users to manage files and directories, track changes in the source code, and collaborate with team members on software development projects. | Version Control, Software Development, Collaboration, Teamwork | Computer Science | Development Tools | Documentation, Uses, and more |
| suitesparse | ACES Stampede3 |
SuiteSparse is a suite of sparse matrix algorithms and solvers available in the form of libraries that are designed to efficiently handle sparse matrices commonly encountered in numerical computations. | Sparse Matrix, Algorithms, Numerical Computations | Numerical Analysis, Other Mathematics | Computational Software | Documentation, Uses, and more |
| sundials | ACES Stampede3 |
SUNDIALS (Suite of Nonlinear and Differential/Algebraic Equation Solvers) is a software package for the solution of large-scale, time-dependent nonlinear differential/algebraic systems. | Software, Numerical Integration, Differential Equations, Algebraic Equations, Scientific Computing | Numerical Analysis, Other Mathematics | Library | Documentation, Uses, and more |
| superlu | ACES | SuperLU is a software package for solving large, sparse, nonsymmetric systems of linear equations on high-performance computers. It is based on the LU factorization with partial pivoting and triangular solution of the linear system. | Linear Algebra, Sparse Matrix, Direct Solver, Computational Science | Applied Mathematics, Mathematics | Solver Library | Documentation, Uses, and more |
| superlu_dist | ACES | SuperLU_DIST is a parallel direct solver for large sparse systems of linear equations. It is designed for distributed memory parallel computers and can solve general, unsymmetric, linear systems Ax = b. | Linear Solver, Sparse Systems, Parallel Computing | Applied Mathematics, Mathematics | Library | Documentation, Uses, and more |
| swig | Anvil ACES DeltaAI Stampede3 |
SWIG (Simplified Wrapper and Interface Generator) is a software development tool that connects programs written in C and C++ with scripting languages such as Perl, Python, Ruby, Tcl, and more. It simplifies the process of creating interfaces for these languages, enabling developers to easily incorporate C/C++ code into their scripting language-based projects. | Software Development, Programming Tool, Scripting Languages, Interface Generator | Computer Science, Computer & Information Sciences, Software Engineering, Systems & Development | Interface Generator | Documentation, Uses, and more |
| syclomatic | ACES | Documentation, Uses, and more | ||||
| sympy | ACES | SymPy is a Python library for symbolic mathematics that aims to become a full-featured computer algebra system. It provides capabilities for symbolic computation, algebraic manipulation, calculus, equation solving, and more. | Symbolic Mathematics, Computer Algebra System, Mathematics, Python Library | Pure Mathematics, Mathematics | Scientific Computing | Documentation, Uses, and more |
| synthcity | ACES | SynthCity is a software for urban simulation and modeling that allows researchers to simulate various aspects of urban environments and study the effects of different urban planning strategies. It provides a platform for detailed spatial analysis and scenario planning. | Urban Planning, Simulation Software, Spatial Analysis, Scenario Planning, Data Visualization | Library | Documentation, Uses, and more | |
| sz | Stampede3 | Documentation, Uses, and more | ||||
| szip | ACES | szip is a compression tool specifically designed for scientific data sets. It is optimized for enhancing the performance of reading and writing data stored in the HDF5 file format by reducing the file size. szip uses a lossless compression algorithm to achieve data compression while maintaining data integrity. | Compression Tool, Scientific Data Sets, Hdf5 File Format | Computer Science | Utility | Documentation, Uses, and more |
| tabixpp | ACES | Documentation, Uses, and more | ||||
| tacc | Stampede3 | TACC (Texas Advanced Computing Center) provides comprehensive advanced computing resources and support services to researchers, enabling them to address some of society's most challenging problems. | High-Performance Computing, Advanced Computing Resources, Visualization, Data Analysis, Storage Solutions, Cloud Computing, Training, Education Programs | Infrastructure & Instrumentation, Engineering & Technology | Hpc Tools | Documentation, Uses, and more |
| tacc tips | Stampede3 | Documentation, Uses, and more | ||||
| talloc | ACES | talloc is a hierarchical, reference counted memory pool system designed for C and C++ programming. It allows for easy memory management and helps prevent memory leaks. | Memory Management, C Programming, C++ Programming | Software Engineering, Other Computer and Information Sciences | Library | Documentation, Uses, and more |
| tar | Anvil Delta KyRIC |
tar is a software utility used for packaging files together into an archive file often referred to as a "tarball". It is commonly used in Unix-like operating systems for creating, storing, and managing files in a single file. | File Archiving, Compression, Terminal | Other, Computer & Information Sciences | File Management | Documentation, Uses, and more |
| tau | KyRIC | Tau is a performance analysis tool for parallel programs, providing insights into the behavior of applications across various HPC platforms. | Software, Compiler, Hpc Tools | High-Performance Computing, Physical Sciences | Commercial | Documentation, Uses, and more |
| tbb | ACES KyRIC |
Intel Threading Building Blocks (TBB) is a widely-used C++ template library for multicore programming that provides rich features for parallel programming. It offers a high-level abstraction for expressing parallelism to help developers create scalable, high-performance applications. | Multicore Programming, Parallel Computing, C++ Library, High Performance Computing | Software Engineering, Computer & Information Sciences | Programming Library | Documentation, Uses, and more |
| tbb32 | KyRIC | Intel Threading Building Blocks (TBB) is a widely used C++ template library developed by Intel for parallel programming on multi-core processors. TBB provides higher-level abstractions for parallelism, making it easier to write code that can take advantage of multicore processors. | Parallel Programming, Multi-Core Processors, C++ Template Library, Intel | Computer & Information Sciences | Library | Documentation, Uses, and more |
| tbl2asn | ACES | tbl2asn is a software tool used for converting tab-delimited files into ASN.1 format for submission to GenBank and other databases. | bioinformatics, data conversion, genomics, sequence submission | Bioinformatics, Genomics | Data Conversion Tool | Documentation, Uses, and more |
| tblis | ACES | Documentation, Uses, and more | ||||
| tcl | Anvil ACES Expanse Delta |
Tool Command Language (Tcl) is a dynamic programming language often used for creating scripts, applications, and embedded control systems. It provides a simple scripting language and a powerful code execution environment for various platforms. | Scripting Language, Dynamic Programming Language, Cross-Platform, Scripting | Software Engineering, Computer & Information Sciences | Language Interpreter | Documentation, Uses, and more |
| tcsh | ACES | Tcsh is a command language interpreter that is based on and compatible with the C shell (csh). It offers extensive customization options and interactive features for command-line users. | Command-Line Interpreter, Shell Scripting, Unix-Like Operating Systems | Operating Systems, Computer & Information Sciences | Language Interpreter | Documentation, Uses, and more |
| tensorboard | ACES | TensorBoard is a suite of web applications for inspecting and understanding the TensorFlow runs and graphs. It enables visualization of TensorFlow graphs, as well as monitoring of training progress and evaluation metrics. | Tensorflow, Deep Learning, Visualization, Model Monitoring | Artificial Intelligence, Computer & Information Sciences | Web Application | Documentation, Uses, and more |
| tensorboardx | ACES | TensorBoardX is a library for visualization and tracking of TensorFlow deep learning models. It enables visualization of training and testing processes, model graphs, scalar values, histograms, images, text, audio, and videos. It extends the functionality of TensorFlow's native TensorBoard with additional features and flexibility. | Visualization, Deep Learning, Tensorflow, Pytorch | Computer Science, Computer & Information Sciences | Library | Documentation, Uses, and more |
| tensorflow | Anvil ACES |
TensorFlow is an open-source machine learning library developed by Google to build and train deep learning models. | Machine Learning, Deep Learning, Neural Networks, Model Training | Artificial Intelligence & Intelligent Systems, Computer & Information Sciences | Machine Learning Framework | Documentation, Uses, and more |
| tensorflow-conda | Delta | TensorFlow is an open-source machine learning framework developed by Google, designed for building and training deep learning models. | Machine Learning, Deep Learning, Artificial Intelligence, Data Science | Computer Science, Artificial Intelligence and Intelligent Systems | Library | Documentation, Uses, and more |
| tensorflow-probability | ACES | TensorFlow Probability is a library for probabilistic reasoning and statistical analysis in TensorFlow. It provides tools for building probabilistic models, performing Bayesian inference, and working with probabilistic distributions. | Machine Learning, Probabilistic Programming, Bayesian Inference, Statistics | Artificial Intelligence, Artificial Intelligence and Intelligent Systems | Library | Documentation, Uses, and more |
| tensorrt | ACES | TensorRT is a high-performance deep learning inference optimizer and runtime for production deployment of deep learning applications. It maximizes runtime performance through optimizations like kernel fusion, layer fusion, and precision calibration. TensorRT also delivers low latency and high throughput for deep learning inference by leveraging GPU hardware. | Deep Learning Inference, Optimization, Gpu Acceleration, Production Deployment | Computer Science, Computer & Information Sciences | Runtime | Documentation, Uses, and more |
| tensorstore | ACES | TensorStore is a library for managing multi-dimensional arrays and tensors with support for various storage backends, including in-memory, disk, and cloud storage. | data management, multi-dimensional arrays, tensor operations, cloud storage | Software Engineering, Other Computer and Information Sciences | Library | Documentation, Uses, and more |
| tesseract | ACES | Tesseract is an open-source OCR (Optical Character Recognition) engine that can be used to extract text from various sources like images, PDFs, and scanned documents. | Ocr, Text Recognition, Open-Source, Cross-Platform | Image Processing, Computer & Information Sciences | Ocr Tool | Documentation, Uses, and more |
| test-drive | ACES | Documentation, Uses, and more | ||||
| texlive | Anvil ACES Stampede3 |
TeX Live is a comprehensive distribution of TeX and related programs, providing a complete environment for typesetting documents. | Typesetting, Document Preparation, LaTeX, Open Source | Computer and Information Sciences, Computer Science | Typesetting System | Documentation, Uses, and more |
| theano | ACES | Theano is an open-source symbolic mathematical library, used for deep learning and numerical computation, that allows you to define, optimize, and evaluate mathematical expressions involving multi-dimensional arrays efficiently. | Mathematical Library, Deep Learning, Numerical Computation | Artificial Intelligence & Intelligent Systems, Computer & Information Sciences | Symbolic Mathematical Library | Documentation, Uses, and more |
| time | ACES | Time is a fundamental quantity used to sequence and compare events. It is a concept which enables the measurement of durations and intervals, and forms the basis of various systems for measuring and quantifying changes. | Time, Measurement, Events, Synchronization | Other | Measurement & Timekeeping | Documentation, Uses, and more |
| tinker | Delta Stampede3 |
Tinker is a software package for molecular modeling and simulations, providing tools for energy minimization, molecular dynamics, and Monte Carlo simulations. | Molecular Modeling, Computational Chemistry, Simulations | Chemistry, Chemical Sciences | Simulation Software | Documentation, Uses, and more |
| tk | Anvil ACES Delta |
Tkinter is a standard GUI toolkit for Python. It is included with most Python installations and is widely used for building desktop applications in Python. | Gui, Python, Toolkit, Desktop Applications | Software Engineering, Computer & Information Sciences, Computer Science, Systems & Development | Library | Documentation, Uses, and more |
| tkinter | ACES | Tkinter is the standard GUI (Graphical User Interface) toolkit for Python. It provides a fast and easy way to create desktop applications with a collection of standard GUI elements. | Gui, Toolkit, Python Library | Software Engineering, Computer & Information Sciences | Gui Toolkit | Documentation, Uses, and more |
| tlparse | ACES | Documentation, Uses, and more | ||||
| tmux | ACES | tmux is a terminal multiplexer that allows users to access multiple separate terminal sessions inside a single terminal window or remote shell. It enables users to switch easily between several programs in one terminal, detach them (leave them running in the background), and reattach them to a different terminal. | Terminal, Multiplexer, Session Management, Productivity | Systems, and Development, Computer & Information Sciences | Text-Based | Documentation, Uses, and more |
| tokenizers | ACES | Tokenizers is a library for training and using tokenizers in natural language processing tasks. It provides a fast and efficient way to preprocess text data for machine learning models. | NLP, Tokenization, Machine Learning, Natural Language Processing | Artificial Intelligence, Natural Language Processing | Library | Documentation, Uses, and more |
| toml-fortran | ACES | Documentation, Uses, and more | ||||
| topaz | ACES | Documentation, Uses, and more | ||||
| tophat | Anvil | Tophat is a fast splice junction mapper for RNA-Seq reads. It aligns RNA-Seq reads to the genome using the Bowtie aligner and then analyzes the mapping results to identify splice junctions between exons. | RNA-Seq, Splice Junction Mapper, Genomics | Bioinformatics, Biological Sciences | Genomic Analysis Tool | Documentation, Uses, and more |
| torchani | Anvil | TorchANI is a PyTorch implementation of the ANI (Anisotropic Network Model) neural network potential for predicting molecular interactions and properties in chemical systems. | Computational Chemistry, Machine Learning, Python Library, Chemical Modeling | Physical Chemistry, Chemical Sciences | Python Library | Documentation, Uses, and more |
| torchsampler | ACES | torchsampler is a library for data sampling in PyTorch, designed to efficiently handle various sampling strategies and techniques to improve data processing and training of deep learning models. | Data Sampling, Pytorch, Deep Learning | Artificial Intelligence & Intelligent Systems, Computer & Information Sciences | Data Sampling | Documentation, Uses, and more |
| torchtext | ACES | torchtext is a library used for natural language processing (NLP) tasks in PyTorch. It provides utilities and datasets for processing text data, such as tokenization, vocabulary building, word embeddings, and data loading for NLP models. | Nlp, Natural Language Processing, Pytorch, Text Processing | Computer Science, Computer & Information Sciences | Library | Documentation, Uses, and more |
| torchvision | ACES | Torchvision is a package in the PyTorch deep learning framework that consists of popular datasets, model architectures, and common image transformations for computer vision tasks. | Deep Learning, Computer Vision, Image Processing | Artificial Intelligence & Intelligent Systems, Computer & Information Sciences | Deep Learning | Documentation, Uses, and more |
| tornado | ACES | Tornado is a Python web framework and asynchronous networking library. It is designed for handling asynchronous processes and is commonly used for building web applications. | Python, Web Framework, Asynchronous, Networking | Software Engineering, Computer & Information Sciences | Application Development | Documentation, Uses, and more |
| totalview | Anvil | TotalView is a comprehensive parallel debugging and performance analysis solution. It provides developers with advanced tools to effectively find and fix bugs, optimize code, and improve application performance for HPC, big data, and machine learning applications. | Debugging, Performance Analysis, Hpc, Big Data, Machine Learning | Computer Science | Development & Optimization Tools | Documentation, Uses, and more |
| tqdm | ACES | tqdm is a fast, extensible progress bar for loops and pipelines in Python. It provides a visual and text-based progress bar to indicate the progress of iterations. | Progress Bar, Python, Data Visualization, Productivity Tool | Computer Science, Computer & Information Sciences | Package | Documentation, Uses, and more |
| transdecoder | ACES | TransDecoder identifies candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity, or other full-length RNA-Seq datasets. It combines homology searches with open reading frame (ORF) detection to predict likely coding regions. | Bioinformatics, Computational Biology, Transcriptomics, Protein Prediction | Genetics, Biological Sciences | Tool | Documentation, Uses, and more |
| transformers | ACES | Transformers is a state-of-the-art natural language processing library, which provides thousands of pre-trained models for various NLP tasks. It offers an easy-to-use API for training and fine-tuning models on custom datasets. | Nlp, Deep Learning, Machine Learning | Artificial Intelligence & Intelligent Systems, Computer & Information Sciences | Machine Learning | Documentation, Uses, and more |
| transrate | ACES | Transrate is a software tool for de novo transcriptome assembly quality analysis. It assesses the quality of de novo transcriptome assemblies, identifies problem areas, and suggests improvements. Transrate helps in evaluating the accuracy and completeness of transcriptome assemblies. | Transcriptome Assembly, Quality Assessment, Bioinformatics | Genetics, Biological Sciences | Bioinformatics Tool | Documentation, Uses, and more |
| trilinos | ACES Stampede3 |
Trilinos is an open-source collection of solvers and libraries for the solution of large-scale, complex multi-physics engineering and scientific problems. It provides a framework for the development of parallel linear and nonlinear algebraic solvers, preconditioners, and other scientific computing capabilities. | Scientific Computing, Numerical Analysis, Parallel Computing, Computational Physics | Biology, Engineering & Technology | Library | Documentation, Uses, and more |
| trim_galore | ACES | Trim Galore! is a wrapper tool around Cutadapt and FastQC to consistently apply quality and adapter trimming to FastQ files. | bioinformatics, sequence analysis, data preprocessing | Biology, Biochemistry and Molecular Biology | Command-line tool | Documentation, Uses, and more |
| trimmomatic | Anvil ACES Delta |
Trimmomatic is a flexible and efficient tool for trimming raw next-generation sequencing data. It provides several trimming modes and options to cater to different sequencing platforms and quality control requirements. | Ngs Data Processing, Quality Control, Bioinformatics | Biology, Biological Sciences | Tool | Documentation, Uses, and more |
| trinity | ACES | Trinity is a de novo RNA-Seq assembly software that reconstructs transcriptomes from short RNA-Seq reads using a novel method for de novo transcriptome assembly from RNA-Seq data. It combines efficient full-length transcript assembly and full-length isoform reconstruction to result in high-sensitivity and high-accuracy transcriptomes. | Bioinformatics, Computational Biology, Transcriptomics, RNA-Seq, De Novo Assembly | Biological Sciences | Bioinformatics Tool | Documentation, Uses, and more |
| trinotate | ACES | Trinotate is a comprehensive annotation suite designed for functional annotation of de novo assembled transcriptomes, particularly for non-model organisms. It provides tools for sequence homology searches, protein domain predictions, functional annotation, and visualization of annotation results. | Bioinformatics, Computational Biology, Transcriptomics, Functional Annotation | Bioinformatics, Biological Sciences | Functional Annotation Tool | Documentation, Uses, and more |
| triton | ACES | Triton is a programming language and compiler designed to facilitate the development of high-performance deep learning applications on GPUs. | GPU Computing, Deep Learning, High Performance Computing, Compiler Technology | Artificial Intelligence and Intelligent Systems, Computer Science | Programming Language | Documentation, Uses, and more |
| tuning analysis utilities | Stampede3 | Documentation, Uses, and more | ||||
| turm | ACES | Documentation, Uses, and more | ||||
| twisted | ACES | Twisted is an event-driven networking engine written in Python. It supports multiple network protocols, including TCP, UDP, SSL/TLS, HTTP, IMAP, SSH, and more. Twisted is designed for scalability and to easily build networked applications. | Networking, Event-Driven, Python | Computer Science, Computer & Information Sciences | Library | Documentation, Uses, and more |
| typing-extensions | ACES | The typing-extensions module in Python provides additional type hinting support for Python 3.7 and later. It includes type hinting classes that were proposed for inclusion in the main 'typing' module but are specifically intended for external use. | Python, Type Hinting, Typing Module, Type Annotations | Software Engineering, Computer & Information Sciences | Python Library | Documentation, Uses, and more |
| ucc | ACES Stampede3 |
UCC (Universal Chemistry Converter) is a versatile software tool designed to convert chemical structures from one format to another. It supports a wide range of chemical structure file formats, making it an essential utility for chemists and researchers working with molecular structures. | Chemical Software, Chemical Structure Converter, Chemistry | Chemical Sciences, Natural Sciences | Conversion Tool | Documentation, Uses, and more |
| ucc-cuda | ACES | ucc-cuda is an open-source compiler that integrates Unified Code Coverage Analysis (UCC) with the CUDA programming model used for parallel computing on NVIDIA GPUs. It allows developers to perform code coverage analysis on CUDA programs to identify unexecuted code paths and improve code quality. | Compiler, Cuda, Code Coverage Analysis, Parallel Computing | Computer & Information Sciences, Engineering & Technology | Development Tool | Documentation, Uses, and more |
| ucx | ACES Expanse Anvil KyRIC Stampede3 |
Unified Communication X (UCX) is a flexible and high-performance communication library for applications and libraries. | Communication Library, High-Performance Computing, Distributed Computing | Computer Science | Communication Library | Documentation, Uses, and more |
| ucx-cuda | ACES | ucx-cuda is a CUDA-enabled version of the Unified Communication X (UCX) framework, designed to provide high-performance communication primitives for parallel programming models on NVIDIA GPUs. | Ucx, Cuda, Gpu-Accelerated Computing, Communication Primitives | Computer & Information Sciences | Communication Framework | Documentation, Uses, and more |
| udunits | Anvil ACES Stampede3 |
UDUNITS supports conversion of unit specifications between formatted, human-readable strings and machine-friendly structures. In addition, UDUNITS defines functions that can be used to identify whether pairs of units are conformable for mathematical operations, to convert numerical values from one unit to another, and to generate strings representing the units of quantities. | Units, Unit Conversion, Udunits | Computer and Information Sciences | Conversion Tool | Documentation, Uses, and more |
| umap-learn | ACES | UMAP (Uniform Manifold Approximation and Projection) is a dimensionality reduction technique that is particularly well-suited for visualizing high-dimensional data. | Dimensionality Reduction, Machine Learning, Data Visualization, Unsupervised Learning | Machine Learning, Artificial Intelligence and Intelligent Systems | Library | Documentation, Uses, and more |
| umoci | ACES | umoci is a tool for managing Open Container Initiative (OCI) images. It allows users to create, modify, and unpack OCI container images. | Containerization, OCI, Image Management | Computer Science, Software Engineering | Command Line Tool | Documentation, Uses, and more |
| uni-core | ACES | Documentation, Uses, and more | ||||
| unicycler | ACES | Unicycler is a hybrid assembly pipeline for bacterial genomes. It can assemble both short and long reads using a combination of de novo assembly and polishing steps. | Bioinformatics, Genomics, Assembly, Bacteria | Genetics, Biological Sciences | Sequence Assembly | Documentation, Uses, and more |
| unifrac | ACES | UniFrac is a bioinformatics tool used to compare the phylogenetic diversity of microbial communities based on their DNA sequences. | bioinformatics, microbial ecology, phylogenetics | Bioinformatics, Ecology | Analysis Tool | Documentation, Uses, and more |
| unzip | ACES | Unzip is a popular open-source file extraction utility for extracting compressed files in various formats. It is commonly used to extract files from ZIP archives, but it also supports other archive formats. | File Extraction, Compression, Utility | Computer Science, Computer & Information Sciences | File Extraction | Documentation, Uses, and more |
| utf8proc | ACES | utf8proc is a small, clean C library that provides Unicode normalization, case-folding, and other operations for data in the UTF-8 encoding. It is written with performance and robustness in mind. | Unicode, Utf-8, Normalization, Case Folding, Character Manipulation | Software Engineering, Computer & Information Sciences | Data Processing | Documentation, Uses, and more |
| util-linux | ACES KyRIC |
Util-linux is a suite of essential utilities for any Linux system. It contains various programs for handling basic system functionalities, such as mounting drives, managing partitions, controlling system processes, monitoring system performance, and more. | Linux, System Utilities, Command Line Tools | Operating Systems, Computer & Information Sciences | Operating System Tools | Documentation, Uses, and more |
| util-linux-uuid | Anvil DeltaAI Delta KyRIC |
util-linux-uuid is a command-line utility that allows users to generate universally unique identifiers (UUIDs) in various formats. UUIDs are 128-bit numbers used as identifiers for entities in computer systems with a high probability of being unique. | Uuid Generator, Command-Line Utility, Unique Identifier, Data Management | Computer Science, Computer & Information Sciences | Command-Line Tool | Documentation, Uses, and more |
| util-macros | DeltaAI KyRIC |
util-macros is a collection of utility macros for C programmers to aid in simplifying common tasks and improving code readability. These macros are designed to enhance the efficiency and maintainability of C code by providing useful functions and utilities. | Programming, Development, C Programming, Utility Macros | Computer Science, Computer & Information Sciences | Utility | Documentation, Uses, and more |
| uv | ACES | uv is a high-performance Python package manager, project manager, and virtual environment tool designed as a fast, drop-in replacement for pip, pipx, venv, and virtualenv. | Python, Package Management | Documentation, Uses, and more | ||
| valgrind | Anvil ACES |
Valgrind is a programming tool for memory debugging, memory leak detection, and profiling. It can also be used for cache and thread error detection. | Debugging, Profiling, Development Tool | Computer Science, Computer & Information Sciences | Programming Tool | Documentation, Uses, and more |
| valgrind memory debugger | KyRIC | Valgrind is an instrumentation framework for building dynamic analysis tools. It is primarily used for memory debugging, memory leak detection, and profiling programs in a variety of programming languages. | Memory Debugging, Profiling, Performance Analysis, Dynamic Analysis | Software Engineering, Computer Science | Debugging Tool | Documentation, Uses, and more |
| valgrind4hpc | DeltaAI Delta |
Valgrind4HPC is a performance analysis tool suite specifically designed for high-performance computing (HPC) environments. It provides a comprehensive set of tools for profiling, memory debugging, and thread analysis to help optimize and improve the performance of parallel and distributed applications on HPC systems. | Performance Analysis, Hpc Environments, Profiling, Memory Debugging, Thread Analysis, Parallel Programming | Computer & Information Sciences, Engineering & Technology | Tool | Documentation, Uses, and more |
| vasp | Anvil ACES Stampede3 |
VASP (Vienna Ab-initio Simulation Package) is a computer program for atomic scale materials modelling, e.g. electronic structure calculations and quantum-mechanical molecular dynamics, from first principles. | Materials Modelling, Electronic Structure Calculations, Quantum-Mechanical Simulations, Dft Calculations, Molecular Dynamics | Chemistry, Physical Sciences, Engineering & Technology | Package | Documentation, Uses, and more |
| vcflib | ACES | vcflib is a C++ library for parsing and manipulating Variant Call Format (VCF) files, which are commonly used in bioinformatics for storing gene sequence variations. | bioinformatics, genomics, VCF, C++ | Bioinformatics, Genomics | Library | Documentation, Uses, and more |
| vcftools | Anvil ACES Delta |
VCFtools is a software package for manipulating and analyzing genetic variation data stored in Variant Call Format (VCF) files. It provides a wide range of tools for quality control, filtering, summarization, and other analyses of genetic variants. | Genetic Variation Analysis, Variant Call Format (Vcf), Population Genetics, Bioinformatics | Bioinformatics, Biological Sciences | Data Analysis Tool | Documentation, Uses, and more |
| velvet | ACES | Velvet is a de novo genomic assembler specially designed for short read sequencing technologies, such as those produced by the Illumina platform. It is efficient in handling large volumes of data and is widely used for assembling genomes, transcriptomes, and metagenomes. | Genomics, Bioinformatics, Sequencing, Assembly | Bioinformatics, Biological Sciences | Bioinformatics Tool | Documentation, Uses, and more |
| vesta | ACES | VESTA is a 3D visualization software for structural models, volumetric data, and crystal structures. It allows users to manipulate and analyze complex molecular and crystal structures with a range of visualization options. | 3D Visualization, Crystallography, Molecular Modeling, Structural Analysis | Chemical Sciences | Scientific Software | Documentation, Uses, and more |
| virtualenv | ACES | virtualenv is a tool used to create isolated Python environments. These environments can have their own installation directories and can be configured with different versions of Python and packages without affecting the global Python installation on the system. | Python, Virtual Environment, Package Management | Informatics, Analytics & Information Science, Computer & Information Sciences | Environment/Setup Tool | Documentation, Uses, and more |
| virtualgl | ACES | VirtualGL is an open-source toolkit that enables the 3D acceleration of applications that are running on a remote server. It redirects the 3D rendering commands from a Unix/Linux OpenGL application onto a server-side GPU and converts the rendered 3D images into a video stream that is sent to the client-side for display using a high-speed network connection. | Remote Rendering, Gpu Acceleration, Opengl Applications, Network Streaming | Computer Science, Computer & Information Sciences | Graphics Software | Documentation, Uses, and more |
| visit | Anvil ACES Delta Stampede3 |
Visit is an open-source interactive parallel visualization and graphical analysis tool. It is designed to handle very large data set visualization and enable users to visualize and analyze data from a variety of sources. | Visualization, Data Analysis, Scientific Computing | Informatics, Analytics & Information Science, Computer & Information Sciences | Visualization Software | Documentation, Uses, and more |
| visual studio code | Anvil | Visual Studio Code is a source-code editor developed by Microsoft. It includes support for debugging, syntax highlighting, intelligent code completion, snippets, code refactoring, and embedded Git. | Code Editor, IDE, Open Source, Cross-Platform | Computer Science | Code Editor | Documentation, Uses, and more |
| vlc player | Anvil | VLC media player is a free and open-source multimedia player and framework that plays most multimedia files, as well as DVDs, audio CDs, VCDs, and various streaming protocols. | Media Player, Open Source, Cross-Platform, Streaming | Computer Science | Multimedia Player | Documentation, Uses, and more |
| vmd | Anvil ACES Expanse |
Visual Molecular Dynamics (VMD) is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting. | Molecular Visualization, Molecular Dynamics, Structural Biology | Biophysics, Biochemistry & Molecular Biology, Biological Sciences | Molecular Visualization Tool | Documentation, Uses, and more |
| vmtouch | DeltaAI | vmtouch is a tool for controlling the file system cache in Linux. It allows users to lock files into memory, ensuring that they remain cached and accessible for faster access, which can be particularly useful for performance tuning in high-performance computing environments. | Linux, File System, Performance Tuning, Caching | Computer Science | Utility | Documentation, Uses, and more |
| voro++ | ACES | Voro++ is an open-source software library for the computation of the Voronoi diagram, a partitioning of space into a set of polygons based on the distance to a specified set of points. It provides a variety of algorithms for constructing Voronoi diagrams in both two and three dimensions. | Voronoi Diagram, Computational Geometry, Open-Source | Mathematics | Library | Documentation, Uses, and more |
| vpl | KyRIC | VPL (Visual Programming Language) is a software tool that allows users to create programs by manipulating graphical elements rather than by specifying them textually. It provides a visual interface for programming tasks, making it easier for beginners to understand programming concepts and create functioning code. | Visual Programming, Beginner-Friendly, Graphical Interface | Computer & Information Sciences | Language Programming | Documentation, Uses, and more |
| vscode | ACES | Visual Studio Code (VSCode) is a source-code editor developed by Microsoft that includes support for debugging, syntax highlighting, intelligent code completion, snippets, code refactoring, and embedded Git. | Code Editor, Development, Open Source, Cross-Platform | Computer Science | Code Editor | Documentation, Uses, and more |
| vsearch | ACES | VSEARCH is a versatile open-source tool for metagenomics and sequence analysis. It supports DNA and RNA sequence analysis, clustering, dereplication, chimera detection, pairwise alignment, searching, and filtering. | Metagenomics, Sequence Analysis, Bioinformatics | Bioinformatics, Biological Sciences | Sequence Analysis Tool | Documentation, Uses, and more |
| vtk | Anvil ACES Stampede3 |
The Visualization Toolkit (VTK) is an open-source software system for 3D computer graphics, image processing, and visualization used by thousands of researchers and developers around the world. VTK offers a wide range of functionality for tasks such as scientific visualization, medical imaging, computational fluid dynamics, and more. | 3D Computer Graphics, Image Processing, Scientific Visualization, Medical Imaging, Computational Fluid Dynamics | Computer Graphics, Physical Sciences | Visualization | Documentation, Uses, and more |
| vtune | ACES KyRIC Stampede3 |
VTune Profiler is a performance profiling tool for optimizing application performance on Intel architecture. It provides deep insights to help you understand and improve performance and power characteristics of your application. | Performance Optimization, Profiling, Intel Architecture | Software Engineering, Computer & Information Sciences | Profiling Tool | Documentation, Uses, and more |
| vulkansdk | ACES | The Vulkan SDK provides a comprehensive set of tools, libraries, and documentation for developers to create high-performance graphics applications using the Vulkan API. | Graphics, API, High Performance, Cross-platform | Computer Science | SDK | Documentation, Uses, and more |
| wandb | ACES | Weights & Biases (wandb) is a tool for tracking machine learning experiments, visualizing results, and collaborating on projects. | Machine Learning, Experiment Tracking, Data Visualization, Collaboration | Machine Learning, Artificial Intelligence and Intelligent Systems | Library | Documentation, Uses, and more |
| wannier90 | Anvil | Wannier90 is a tool used for the computation of maximally-localized Wannier functions, which are spatially compact and localized functions that provide a natural description of the electronic structure of a solid. These functions are often used in condensed matter physics calculations to study the electronic properties of materials. | Computational Chemistry, Solid State Physics, Electronic Structure, Materials Science | Condensed Matter Physics, Physical Sciences | Library | Documentation, Uses, and more |
| wayland | ACES | Wayland is a communication protocol that specifies the communication between a display server and its clients, as well as a reference implementation of the protocol in the C programming language. | Display Server, Communication Protocol, Graphics Rendering | Software Engineering, Computer & Information Sciences | Communication Protocol Implementation | Documentation, Uses, and more |
| waylandpp | ACES | waylandpp is a C++ binding library for Wayland, which is a protocol for a compositor to talk to its clients. | Wayland, C++, Binding Library | Computer & Information Sciences | Programming Interface | Documentation, Uses, and more |
| webkitgtk+ | ACES | WebKitGTK+ is an open-source web browser engine. It is a GTK+ port of the WebKit engine. It offers a framework for rendering web content in applications built with GTK+. | Web Browser Engine, Gtk+ Port, Open-Source, Web Content Rendering | Software Engineering, Computer & Information Sciences | Rendering Engine | Documentation, Uses, and more |
| webproxy | ACES | WebProxy is a tool that allows users to access websites anonymously by hiding their IP address. It acts as an intermediary between the user's device and the internet, masking the user's IP address and encrypting their internet traffic for increased privacy and security. | Proxy Server, Internet Privacy, Security, Anonymity | Computer & Information Sciences | Tool | Documentation, Uses, and more |
| wfa2 | ACES | Documentation, Uses, and more | ||||
| wget | ACES | GNU Wget is a utility for non-interactive download of files from the Web. It supports HTTP, HTTPS, and FTP protocols, as well as retrieval through HTTP proxies. | Download Manager, Command-Line Tool | Computer Science, Computer & Information Sciences | System Tool | Documentation, Uses, and more |
| which | DeltaAI | Documentation, Uses, and more | ||||
| wpebackend-fdo | ACES | wpebackend-fdo is a software project that provides a backend implementation for WebKit's WPE WebKit using a Flatpak distributed runtime for sandboxing. | Software, Sandboxing, Integration, Performance Optimization | Computer Science, Computer & Information Sciences | Backend Implementation | Documentation, Uses, and more |
| wps | ACES | WPS Office is a comprehensive office suite that includes Writer, Presentation, and Spreadsheets. It provides a familiar interface and full compatibility with Microsoft Office file formats. | Office Suite, Word Processing, Presentation, Spreadsheets, Pdf Editing | Other | Office Suite | Documentation, Uses, and more |
| wrapt | ACES | wrapt is a Python module for decorators, wrappers, and monkey patching. It provides a way to create decorators that can be applied to functions and methods, allowing for enhanced functionality and behavior. | Python, Decorators, Wrapper, Monkey Patching | Software Engineering, Other Computer and Information Sciences | Library | Documentation, Uses, and more |
| wrf | ACES | The Weather Research and Forecasting (WRF) model is a next-generation mesoscale numerical weather prediction system designed to serve both atmospheric research and operational forecasting needs. It features multiple options for parameterizations, data assimilation techniques, and model domains, allowing for simulations at various spatial and temporal scales. | Weather Forecasting, Numerical Modeling, Atmospheric Science | Meteorology, Earth & Environmental Sciences | Meteorological Modeling Software | Documentation, Uses, and more |
| wxpython | ACES | wxPython is a cross-platform GUI toolkit for the Python programming language. It allows Python programmers to create functional and native-looking user interfaces for their applications. | Gui Toolkit, Cross-Platform, Python | Software Engineering, Computer & Information Sciences | Library | Documentation, Uses, and more |
| wxwidgets | ACES | wxWidgets is a C++ library that lets developers create applications for Windows, macOS, Linux and other platforms with a single code base. It is a mature and comprehensive framework that allows for native user interfaces with a wide range of widgets. | Gui Library, Cross-Platform Development, Native User Interfaces, Open-Source Software | Computer Science, Engineering & Technology | Library/Framework | Documentation, Uses, and more |
| x11 | ACES | X11 is a windowing system for bitmap displays, common on Unix-like operating systems and desktop environments. It provides the basic framework for building GUI applications on these systems, handling graphical elements such as windows, menus, and user input. | Windowing System, Gui Applications, Unix-Like Operating Systems | Human-Computer Interaction, Computer & Information Sciences | System Software | Documentation, Uses, and more |
| x264 | ACES | x264 is a free and open-source software library and a command-line utility for encoding video streams into the H.264/MPEG-4 AVC format. | Video Encoding, H.264/Mpeg-4 Avc, Open-Source | Software Engineering, Engineering & Technology | Video Encoding | Documentation, Uses, and more |
| x265 | ACES | x265 is a free and open-source software library and application for encoding video streams into the H.265/MPEG-H HEVC (High Efficiency Video Coding) format. It is widely used for efficient video compression and playback on various platforms. | Video Encoding, Compression, Hevc | Software Engineering, Computer & Information Sciences | Library & Application | Documentation, Uses, and more |
| xalt | Anvil Stampede3 Jetstream2 |
XALT (XALT Accounting for Loadable and Transient Objects) is a tool designed to track the detailed usage of HPC systems by monitoring library dependencies and executables during job executions. It captures information on modules, compilers, libraries, and executables used in each job, providing detailed insights into the software stack and usage patterns on the HPC system. | Hpc, Monitoring | Computer Science, Engineering & Technology | Performance Tracking | Documentation, Uses, and more |
| xarray | ACES | Xarray is an open source Python library that provides data structures and functions for working with labelled multidimensional arrays. It aims to bring the labeled data power of pandas to the physical sciences, by providing N-dimensional variants of the core pandas data structures. | Python Library, Data Analysis, Scientific Computing, Multidimensional Arrays | Computational Science, Other Natural Sciences | Library | Documentation, Uses, and more |
| xcb-proto | Anvil DeltaAI |
Documentation, Uses, and more | ||||
| xcb-util-cursor | Delta | xcb-util-cursor is a library that provides an interface for managing cursors in X11 applications using the XCB (X C Binding) protocol. | X11, Cursor Management, XCB | Software Engineering, Other Computer and Information Sciences | Library | Documentation, Uses, and more |
| xcb-util-image | Anvil | The xcb-util-image library provides a number of functions used for manipulating and creating XCB format images, including loading and saving images to disk in various formats. | Image Processing, Xcb, Library | Computer & Information Sciences | Library | Documentation, Uses, and more |
| xcb-util-keysyms | Anvil | The xcb-util-keysyms library provides utility functions for obtaining the keysyms keycode values, as used in the X Window System, as well as common XKB functions. It is part of the X C Bindings (XCB) utility libraries which provide a number of convenience functions and interfaces for usage with XCB. | X Window System, Utility Functions, Xcb | Computer Science, Computer & Information Sciences | Utility | Documentation, Uses, and more |
| xcb-util-renderutil | Anvil | A set of libraries which provide a convenient API for rendering text with XCB. | Xcb, Rendering, Text, Api | Computer & Information Sciences | Rendering | Documentation, Uses, and more |
| xcb-util-wm | Anvil | xcb-util-wm is a set of utility functions for interfacing with the X Window Manager (WM) extension of the XCB library. It provides a number of functions that are useful to XCB WM clients. | X Window System, Window Manager, Xcb Library, Utility Functions | Utility | Documentation, Uses, and more | |
| xcfun | ACES | Documentation, Uses, and more | ||||
| xclip | ACES | xclip is a command-line utility that provides an interface to X selections (the clipboard) in X11 environments. | Clipboard, X11, Command-line, Utilities | Software Engineering, Other Computer and Information Sciences | Command-line tool | Documentation, Uses, and more |
| xdinfo | Expanse | xdinfo is a Python package which provides information about X-ray diffraction (XD) like functions, atomic scattering, Mueller matrix, XD profiles, and more. It is designed for the analysis and interpretation of X-ray diffraction data in various scientific applications. | Python Package, X-Ray Diffraction Analysis, Scientific Data Interpretation | Physical Sciences | Library | Documentation, Uses, and more |
| xerces-c++ | ACES | Xerces-C++ is a validating XML parser written in C++ and released by the Apache Software Foundation. It is a high-performance, feature-rich parser that is widely used for parsing and processing XML documents in a variety of applications. | Xml Parser, Data Processing, Software Development | Software Engineering, Computer & Information Sciences | Parser | Documentation, Uses, and more |
| xextproto | Anvil DeltaAI |
X11 Extension protocols and auxiliary headers | Linux, X11, X Window System | Computer & Information Sciences | Library | Documentation, Uses, and more |
| xgboost | ACES | XGBoost is an open-source software library which provides a gradient boosting framework for efficient and high-performance machine learning. | Machine Learning, Gradient Boosting, Ensemble Learning | Machine Learning, Computer & Information Sciences, Artificial Intelligence & Intelligent Systems | Library | Documentation, Uses, and more |
| xlsxwriter | ACES | XlsxWriter is a Python module for creating Excel XLSX files. It allows for the generation of complex Excel files with features such as formatting, charts, and formulas. | Excel, Python, Data Analysis, Spreadsheet | Computer Science, Applied Computer Science | Library | Documentation, Uses, and more |
| xml-libxml | ACES | xml-libxml is a software library for reading, writing, and manipulating XML files. It provides a robust set of tools for parsing and processing XML documents. | Xml, Parser, Library, Data Processing | Other Computer & Information Sciences, Computer & Information Sciences | Data Processing | Documentation, Uses, and more |
| xmlf90 | ACES | Documentation, Uses, and more | ||||
| xmltodict | ACES | xmltodict is a Python library that makes working with XML data as easy as working with JSON. It provides a simple way to convert XML to Python dictionaries and vice versa. | XML, JSON, Python, Data Processing, Libraries | Computer Science, Applied Computer Science | Library | Documentation, Uses, and more |
| xorg-macros | ACES | The xorg-macros package provides a set of autoconf macros used by X.org software packages for consistent and simplified build procedures across various Unix and Linux systems. | Build Tools, Autoconf Macros | Computer & Information Sciences | Library/Dependency | Documentation, Uses, and more |
| xpmem | ACES DeltaAI |
XPMEM is a kernel module that provides a kernel-level interface for sharing memory between processes. | Kernel Module, Inter-Process Communication, Memory Sharing | Computer Science, Computer & Information Sciences | System Software | Documentation, Uses, and more |
| xprop | ACES | xprop is a utility for retrieving the properties of a window in a X server system. It allows users to query and display properties of a given X server window, which can be useful for debugging and troubleshooting GUI-related issues. | X Server, Window Properties, Gui Debugging | Computer Science, Computer & Information Sciences | System Tool | Documentation, Uses, and more |
| xproto | Anvil ACES DeltaAI |
X Window System protocol development files. | Software Development, Protocol Development, X Window System | Computer & Information Sciences | Library | Documentation, Uses, and more |
| xtb | ACES | xtb (eXtended Tight Binding) is a quantum chemistry software package designed for efficient calculations of molecular properties and simulations, particularly for large molecular systems. | Quantum Chemistry, Molecular Modeling, Computational Chemistry | Chemistry, Chemical Sciences | Scientific Software | Documentation, Uses, and more |
| xterm | DeltaAI Delta |
xterm is a terminal emulator for the X Window System. It provides a command-line interface for users to interact with the system and run shell commands. | Terminal Emulator, X Window System, Open Source | Software Engineering, Other Computer and Information Sciences | Terminal Emulator | Documentation, Uses, and more |
| xtrans | DeltaAI | xtrans is a general-purpose transducer-based approach for defining translations between various formats and data representations. It provides a flexible framework for specifying bidirectional transformations between different data structures. | Data Transformation, Format Conversion, Transducer-Based Tool | Computer & Information Sciences | Tool | Documentation, Uses, and more |
| xvfb | ACES | Xvfb (X virtual framebuffer) is an in-memory display server for Unix-like systems that enable running graphical applications without a display. | Display Server, Headless, Virtual Display | Software Engineering, Computer & Information Sciences | Virtual Display Server | Documentation, Uses, and more |
| xxd | ACES | xxd is a command-line utility on Unix and Unix-like systems for creating a hex dump of a given file or standard input. | Hex Dump, Command-Line Utility, Data Conversion | Computer Science, Other Computer & Information Sciences | Command-Line Tool | Documentation, Uses, and more |
| xxhash | ACES | xxHash is an extremely fast non-cryptographic hash algorithm, providing high-speed hashing for data integrity checks. | hashing, performance, data integrity | Software Engineering, Other Computer and Information Sciences | Library | Documentation, Uses, and more |
| xz | Anvil ACES DeltaAI KyRIC |
xz is a free and open-source data compression tool that uses the LZMA compression algorithm. It is designed to be an efficient and high-performance compression utility. | Compression, Data Compression, Open-Source | Computer Science, Computer & Information Sciences | Utility | Documentation, Uses, and more |
| yacs | ACES | YACS (Yet Another Constraint Solver) is a Python-based constraint satisfaction problem (CSP) solver that allows for the modeling and solving of constraint problems using a high-level interface. | Constraint Satisfaction Problem, Csp Solver, Python-Based, Constraint Modeling | Computer & Information Sciences | Optimization Tool | Documentation, Uses, and more |
| yamlcpp | Stampede3 | yaml-cpp is a YAML parser and emitter in C++. | C++, YAML, Parser, Emitter | Software Engineering, Other Computer and Information Sciences | Library | Documentation, Uses, and more |
| yasm | ACES DeltaAI |
Yasm is a complete rewrite of the NASM assembler under the new BSD License. It is designed to have NASM compatibility for NASM's source code usage. Yasm currently supports the x86 and AMD64 instruction sets, accepts NASM and GAS assembler syntaxes, outputs binary, ELF32, ELF64, COFF, Mach-O (32 and 64), RDOFF2, SREC, and Hex formats, and generates source debugging information in STABS, DWARF 2, and CodeView 8 formats. | Assembler, Assembly, Development, Programming | Software Engineering, Engineering & Technology | Assembler | Documentation, Uses, and more |
| yaxt | ACES | YAXT (Yet Another XTabulator) is a Python library for creating publication-ready quantitative tables with an emphasis on simplicity and customization. It provides a straightforward interface for generating tables directly from pandas DataFrames. | Python Library, Data Analysis, Table Generation | Computer & Information Sciences | Library | Documentation, Uses, and more |
| yell | ACES | Documentation, Uses, and more | ||||
| z3 | ACES | Z3 is a high-performance theorem prover being developed at Microsoft Research. Z3 is a state-of-the-art SMT (Satisfiability Modulo Theories) solver used in various applications including software and hardware verification, security, AI and ML, and more. It provides a programming interface for both C and Python. | Theorem Prover, Satisfiability Modulo Theories (Smt) Solver, Software Verification, Hardware Verification, Security, Ai, Machine Learning | Artificial Intelligence, Computer & Information Sciences | Theorem Prover | Documentation, Uses, and more |
| zarr | ACES | Zarr is a Python package providing an implementation of chunked, compressed, N-dimensional arrays which can be stored in memory, on disk, or on cloud storage. It is designed to efficiently store and retrieve large arrays of data while minimizing the use of computational resources. | Python Library, Data Storage, Data Management | Computational Science, Computer & Information Sciences | Library | Documentation, Uses, and more |
| zeromq | ACES | ZeroMQ is a high-performance asynchronous messaging library that is designed for building distributed and concurrent applications. It provides messaging patterns like pub-sub, request-reply, push-pull, etc., along with sockets and transports for communication between nodes. | Messaging, Distributed Computing, Async | Distributed Systems, Computer & Information Sciences | Communication | Documentation, Uses, and more |
| zfp | ACES | zfp is a compressed numerical array library providing high-throughput, low-overhead fixed-rate, fixed-precision encoding and compression of 1D and 2D scientific data. | Numerical Array, Compression, Scientific Data | Computer Science, Computer & Information Sciences | Library | Documentation, Uses, and more |
| zip | ACES | zip is a compression and file packaging utility for Unix, VMS, DOS, OS/2, Windows 9x/NT/XP, Minix, Atari, Macintosh, Amiga, and Acorn RISC OS. | Compression, File Packaging, Utility | Computer Science, Other Computer & Information Sciences | Utility | Documentation, Uses, and more |
| zlib | Anvil ACES DeltaAI KyRIC Stampede3 |
zlib is a software library for data compression that provides functions for file compression and decompression using the DEFLATE compression algorithm. It is widely used in various applications for reducing file size and conserving storage space. | Compression, Data Compression, File Compression, Deflate Algorithm | Software Engineering, Computer & Information Sciences | Data Compression | Documentation, Uses, and more |
| zlib-ng | DeltaAI Delta |
zlib-ng is a fast, efficient, and portable data compression library that is a drop-in replacement for zlib. It is designed to be compatible with zlib while providing improved performance and additional features. | compression, data processing, library, performance | Computer Science, Software Engineering | Library | Documentation, Uses, and more |
| zmqnet | DeltaAI Delta |
Documentation, Uses, and more | ||||
| zoltan | ACES | Zoltan is a toolkit for managing parallel memory for dynamic applications in high-performance computing environments. It provides scalable parallel dynamic load-balancing, graph partitioning, and dynamic data restructuring services. | Parallel Computing, High-Performance Computing, Dynamic Applications | High-Performance Computing, Engineering & Technology | Hpc Tools | Documentation, Uses, and more |
| zstd | ACES DeltaAI Expanse KyRIC |
Zstandard (or zstd) is a fast data compression algorithm developed by Facebook. It is designed to provide high compression ratios with very low latency, making it suitable for real-time compression/decompression scenarios. Zstandard offers a wide range of compression levels, from very fast to very strong, allowing users to balance between speed and compression ratio based on their requirements. | Compression, Data Compression, Algorithm | Computer Science, Computer & Information Sciences | Compression Algorithm | Documentation, Uses, and more |