Explore software available on ACCESS Resources.
Reporting providers: Anvil, Bridges-2, Delta, DeltaAI, Expanse, Jetstream2, KyRIC, Stampede3
| Software | Installed on | AI Description | AI Tags | AI Research Discipline | AI Software Type | Documentation, Uses, and more |
|---|---|---|---|---|---|---|
| abaqus | 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 |
| abinit | Bridges-2 | Abinit is a first-principles simulation software for materials science, condensed matter physics, and related fields. It performs electronic structure calculations based on density functional theory (DFT) and many-body perturbation theory. | Materials Science, Condensed Matter Physics, Electronic Structure Calculations | Condensed Matter Physics, Physical Sciences | Electronic Structure Calculation | Documentation, Uses, and more |
| abyss | Bridges-2 | 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 |
| adios2 | 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 | Stampede3 KyRIC |
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 |
| alphafold 3 | DeltaAI Delta |
Documentation, Uses, and more | ||||
| alps | Stampede3 | Documentation, Uses, and more | ||||
| alsa-lib | 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 | 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 | Bridges-2 Anvil |
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 |
| anaconda2 | Bridges-2 | Anaconda2 is a free and open-source distribution of the Python and R programming languages for scientific computing, that aims to simplify package management and deployment. It includes over 720 open-source packages and is widely used for data science, machine learning, and scientific computing. | Python Libraries, Conda Packages, Data Science, Scientific Computing, Machine Learning, Computational Software | Computational Science, Computer & Information Sciences, Artificial Intelligence & Intelligent Systems | Distribution | Documentation, Uses, and more |
| anaconda3 | Bridges-2 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 |
| ansys | Stampede3 Bridges-2 |
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 |
| anvi'o | Bridges-2 | Anvi'o is an open-source platform designed for the analysis and visualization of microbial genomes and metagenomes. It provides tools for comparative genomics, functional annotation, and interactive visualization of genomic data. | bioinformatics, genomics, metagenomics, data visualization | Bioinformatics, Genomics | Open-source | Documentation, Uses, and more |
| aocc | Bridges-2 Expanse Anvil 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 | Bridges-2 | AOCL is a set of numerical libraries optimized for AMD processors based on the AMD “Zen” core architecture and generations. The tuned implementations of industry-standard math libraries enable rapid development of scientific and high-performance computing applications. \r Description Source: https://www.amd.com/en/developer/aocl.html |
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 |
| aria2 | Expanse DeltaAI Delta |
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 |
| 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 | 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 |
| arriba | Bridges-2 | Arriba is a fast and accurate tool for gene fusion detection in RNA-Seq data. It can identify gene fusions, transcript fusions, and fusion transcript isoforms, providing detailed information on their structure. | Software, Gene Fusion Detection, RNA-Seq, Transcriptome Analysis | Genomics, Biological Sciences | Tool | Documentation, Uses, and more |
| asciinema | Bridges-2 | asciinema is a free and open-source solution for recording terminal sessions and sharing them on the web. It allows users to record their terminal sessions and playback the recordings directly in a terminal emulator. | Terminal Recording, Web Sharing, Cli Tool | Software Engineering, Computer & Information Sciences | Terminal Recorder | Documentation, Uses, and more |
| aspera connect | Bridges-2 | Aspera Connect is a high-speed file transfer application that enables users to send and receive large files over the internet quickly and securely. | file transfer, high-speed, secure, data transfer, cloud integration | Information Technology, Computer Science | Application | 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 | ||
| augustus | Bridges-2 | 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 | Stampede3 KyRIC DeltaAI |
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 |
| automake | Stampede3 KyRIC DeltaAI |
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 | 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 |
| 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 | ||||
| bamtools | Bridges-2 Anvil 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 | ||||
| bat | Bridges-2 | BAT (Bioinformatics Analysis Tool) is a bioinformatics software suite designed for the analysis of biological sequence data. | Bioinformatics, Computational Biology | Genetics, Biological Sciences | Analysis Tool | Documentation, Uses, and more |
| bazel | Bridges-2 | 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 |
| bbmap | Bridges-2 | 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 | Bridges-2 | 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 |
| 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 | ||||
| bedops | Bridges-2 | 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 | Bridges-2 | 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 |
| berkeley-db | KyRIC Anvil DeltaAI |
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 |
| berkeleygw | Stampede3 | Documentation, Uses, and more | ||||
| biocontainers | Stampede3 Anvil |
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 |
| bioformats | Bridges-2 | Bioformats is a software library that provides reading and writing support for a wide range of biological data formats. It aims to simplify the access and integration of diverse image data types in scientific research. | Bioinformatics, Imaging, Biological Data, Data Formats | Biology, Biological Sciences | Library | Documentation, Uses, and more |
| bismark | Bridges-2 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 | Stampede3 DeltaAI |
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 |
| 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+ | Bridges-2 | 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 | Bridges-2 | 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 |
| blis | Stampede3 Anvil |
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 |
| 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 | Stampede3 Bridges-2 Expanse Anvil Delta |
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 |
| bowtie | 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 | Bridges-2 Anvil 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 |
| 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 |
| busco | Bridges-2 | 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 | Bridges-2 Anvil |
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 |
| 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 | KyRIC Expanse Anvil DeltaAI |
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 | DeltaAI | 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 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 |
| 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 |
| canu | Bridges-2 | Canu is a software tool that is used for assembling genomes using nanopore sequencing data. It is designed to be efficient and scalable, making it suitable for large and complex genomes. | Genome Assembly, Nanopore Sequencing, Long-Read Sequencing, Bioinformatics | Genomics, Bioinformatics, Biological Sciences | Bioinformatics Tool | Documentation, Uses, and more |
| catch2 | 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 |
| 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 | ||
| cdo | Stampede3 Anvil |
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 |
| cdtools | Stampede3 | Documentation, Uses, and more | ||||
| cfitsio | 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 |
| 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 |
| checklist | Stampede3 | Documentation, Uses, and more | ||||
| checkm | Bridges-2 | 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 |
| circos | Bridges-2 | Circos is a software package for visualizing data in a circular layout. It is widely used in genomics and other biological sciences to create visual representations of complex datasets. | Data Visualization, Genomics, Biological Sciences, Circular Layout | Bioinformatics, Biological Sciences | Visualization Tool | Documentation, Uses, and more |
| clck | KyRIC | 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 | Stampede3 KyRIC Expanse Anvil DeltaAI Delta |
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 | ||||
| code-server | Stampede3 | Code-server is a tool that allows you to run a Visual Studio Code instance in the browser, making it convenient for remote development, collaboration, and accessing your coding environment from anywhere. | Remote Development, Visual Studio Code, Browser-Based Coding, Collaboration, Coding Environment | Computer Science, Computer & Information Sciences | Development Tool | Documentation, Uses, and more |
| colabfold | 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 |
| 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 |
| comsol | Bridges-2 | COMSOL is a platform for modeling and simulating physics-based systems. It offers a wide range of tools for multiphysics simulations, allowing users to analyze and optimize designs in various scientific and engineering fields. | Simulation, Modeling, Physics, Engineering, Optimization | Mechanical Engineering, Engineering & Technology | Simulation Software | 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 |
| cp2k | Stampede3 Bridges-2 Anvil |
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 |
| 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 | ||||
| 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 |
| 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 | |
| cuda | Bridges-2 Anvil DeltaAI 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-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 |
| 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 | ||||
| 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 |
| cudnn | Bridges-2 Anvil DeltaAI |
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 | Expanse Anvil 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 |
| cuquantum-appliance | Anvil | Documentation, Uses, and more | ||||
| curl | KyRIC Expanse Anvil DeltaAI |
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 |
| cutadapt | Bridges-2 | 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 |
| 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 |
| dal | KyRIC | DAL is a library for collision avoidance in robotics applications. | Robotics, Collision Avoidance | Engineering & Technology | Collision Avoidance Software | Documentation, Uses, and more |
| ddt | Stampede3 Bridges-2 |
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 |
| dealii | Bridges-2 | deal.II is a C++ library targeted at adaptive finite element methods and is designed for solving partial differential equations (PDEs) in scientific computing. | Finite Element Analysis, Scientific Computing, C++, Parallel Computing | Numerical Methods, Finite Element Analysis | Library | 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 |
| default-orig | DeltaAI | Documentation, Uses, and more | ||||
| default-rh96 | Delta | 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 | ||||
| desmond | Bridges-2 | 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 |
| 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 |
| 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 | Bridges-2 | 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 |
| doxygen | 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 | ||
| 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 |
| 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 | 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 |
| eigen | Stampede3 Anvil |
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 |
| elfutils | 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 |
| emacs | Anvil 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 |
| entrezdirect | 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 |
| expat | KyRIC Anvil DeltaAI |
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 |
| fastani | Bridges-2 | 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 |
| fastq-tools | Bridges-2 | fastq-tools is a collection of simple and efficient command-line tools for processing FASTQ files commonly used in bioinformatics. It provides various utilities for quality control, filtering, and manipulation of raw sequencing data in FASTQ format. | Bioinformatics, Ngs, Genome Sequencing, Sequence Analysis | Bioinformatics, Biological Sciences | Data Processing Tool | Documentation, Uses, and more |
| fastqc | Bridges-2 Anvil 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 |
| fasttree | Anvil | 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 | Bridges-2 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 |
| ffmpeg | Stampede3 Bridges-2 Anvil DeltaAI Delta |
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 |
| 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 | KyRIC Bridges-2 Anvil DeltaAI Delta |
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 |
| 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 |
| filtlong | Bridges-2 | filtlong is a tool for filtering long reads generated by third-generation sequencing technologies such as PacBio or Oxford Nanopore. It allows for the removal of reads based on user-defined length or quality thresholds. | Bioinformatics, Long Read Sequencing, Sequence Data Processing | Biological Sciences | Data Filtering Tool | 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 |
| flash | Bridges-2 | 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 |
| flex | 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 |
| 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 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 | ||||
| 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 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 |
| fribidi | 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 |
| funannotate | Bridges-2 | funannotate is a pipeline for genome prediction and annotation of fungi. It automates the process of predicting gene models, functional annotation, and comparative genomics analysis for fungal genomes. | Genome Prediction, Genome Annotation, Fungi, Bioinformatics | Biological Sciences | Bioinformatics Tool | Documentation, Uses, and more |
| gamess | Stampede3 Bridges-2 |
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 |
| gatk | Bridges-2 Anvil |
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 Bridges-2 |
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 |
| gcc | KyRIC Bridges-2 Expanse Anvil DeltaAI |
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 |
| gdal | Stampede3 Anvil DeltaAI |
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 | Expanse Anvil DeltaAI |
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 | KyRIC Anvil DeltaAI |
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 | ||||
| genemark-es | Bridges-2 | GeneMark-ES (Eukaryotic) is a eukaryotic gene prediction software that accurately predicts the location and structure of protein-coding genes in eukaryotic genomes. It is based on an unsupervised ab initio approach using hidden Markov model algorithms. | Gene Prediction, Bioinformatics, Eukaryotic Genomes, Hidden Markov Model | Biological Sciences | Gene Prediction Software | Documentation, Uses, and more |
| gent | Bridges-2 | Gent is a graph-based DNA comparison tool that enables the identification of structural variants, inversions, deletions, insertions, duplications, and translocations in the human genome. | DNA Comparison, Structural Variants, Genomics | Bioinformatics, Biological Sciences | Bioinformatics Tool | Documentation, Uses, and more |
| geos | Anvil 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 | KyRIC Bridges-2 Anvil DeltaAI |
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 |
| 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 | 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 |
| git | 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 | 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 |
| gklib | 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 |
| glib | Anvil 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 |
| 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 |
| 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 |
| gmp | Stampede3 KyRIC Expanse Anvil DeltaAI |
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 |
| 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 | Stampede3 Expanse Anvil DeltaAI Delta |
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 | 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 | KyRIC Expanse |
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 | 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 |
| gperf | 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 |
| 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 |
| 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 |
| gromacs | Stampede3 KyRIC Bridges-2 Anvil DeltaAI Delta |
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 |
| gsl | Stampede3 Anvil DeltaAI Delta |
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 |
| gstreamer | Anvil | 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 |
| guppy | Bridges-2 | Guppy is a basecaller developed by Oxford Nanopore Technologies for processing raw electrical signal data generated by their nanopore sequencing devices. It is designed to convert the raw signal data into nucleotide sequences, providing a platform for downstream analysis in genomics research. | Bioinformatics, Sequencing, Nanopore Sequencing, Genomics, DNA Sequencing | Genomics, Biological Sciences | Basecaller | Documentation, Uses, and more |
| guppy-gpu | Bridges-2 | Guppy is a basecaller software for Oxford Nanopore sequencing data. The GPU version utilizes the power of graphics processing units to accelerate the basecalling process for faster and more efficient analysis of sequencing data. | Basecaller, Oxford Nanopore, Sequencing, Gpu Acceleration | Bioinformatics, Biological Sciences | Bioinformatics Tool | Documentation, Uses, and more |
| gurobi | Bridges-2 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 |
| gzip | 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 |
| hadoop | Expanse Anvil |
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 | 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 |
| hashdeep | Bridges-2 | hashdeep is a cross-platform hashing utility that calculates and verifies hash signatures for files and directories. | Hashing, Data Integrity, Security | Computer Science, Computer & Information Sciences | Hashing | Documentation, Uses, and more |
| hdf | Anvil | 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 |
| hdf5 | Stampede3 Bridges-2 Expanse Anvil DeltaAI Delta |
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 | Computer Science | 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 |
| highfive | Stampede3 | Documentation, Uses, and more | ||||
| hisat2 | Bridges-2 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 | Stampede3 Bridges-2 |
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 |
| homer | Bridges-2 | HOMER (Hypergeometric Optimization of Motif EnRichment) is a suite of tools for motif discovery and next-gen sequencing analysis. It is widely used for identifying transcription factor binding sites and novel motifs in DNA sequences. | Bioinformatics, Next-Generation Sequencing, Motif Discovery, Transcription Factor Binding Sites | Genetics, Biological Sciences | Tool | Documentation, Uses, and more |
| hpc-gpt opencode | Delta | 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 |
| 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 |
| htslib | Bridges-2 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 |
| hwloc | KyRIC Bridges-2 Expanse Anvil |
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 |
| 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 |
| hypershell | Anvil | Documentation, Uses, and more | ||||
| hypre | 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 |
| icu4c | KyRIC DeltaAI |
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 | Stampede3 Expanse |
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 |
| imagemagick | 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 | Delta | Documentation, Uses, and more | ||||
| impi | Bridges-2 Anvil |
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 | Bridges-2 | 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 | KyRIC Bridges-2 Expanse 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-advisor | Bridges-2 | Intel Advisor is a performance profiling tool that helps developers optimize their applications for Intel architectures. It provides insights into vectorization, threading, and memory usage to improve performance. | Performance Analysis, Profiling, Optimization, Intel, HPC | Computer Science, Computer and Information Sciences | Profiling Tool | Documentation, Uses, and more |
| intel-ccl | Bridges-2 | Intel CCL (Cluster Communication Library) is a high-performance communication library designed for distributed computing environments, providing efficient data exchange and synchronization mechanisms for parallel applications. | HPC, Parallel Computing, Communication Library, Distributed Systems | Computer Science | Library | Documentation, Uses, and more |
| intel-compiler | Bridges-2 | The Intel Compiler suite is a set of optimizing compilers with support for C, C++, and Fortran languages. It provides advanced optimizations and performance tuning for applications running on Intel architecture-based platforms. | Compiler, Optimization, Performance, Parallelization | Computer Science, Computer & Information Sciences | Development Tools | Documentation, Uses, and more |
| intel-compiler-rt | Bridges-2 | The Intel Compiler Runtime Library (Intel Compiler RT) is a collection of runtime libraries for the Intel software development tools, designed to provide support for various runtime components in software applications compiled with Intel compilers. | Compiler, Runtime Library, Performance Optimization | Computer & Information Sciences | Compiler Runtime Library | Documentation, Uses, and more |
| intel-compiler-rt32 | Bridges-2 | Documentation, Uses, and more | ||||
| intel-compiler32 | Bridges-2 | Documentation, Uses, and more | ||||
| intel-dal | Bridges-2 | Intel Dynamic Application Loader (DAL) is a framework that enables applications to dynamically load and execute small code modules. It provides a secure environment for executing trusted applications on Intel platforms. | Security, Intel Platform, Dynamic Code Loading, Trusted Applications | Documentation, Uses, and more | ||
| intel-debugger | Bridges-2 | Intel Debugger is a powerful tool for debugging applications written in C, C++, and Fortran, specifically optimized for Intel architectures. | Debugging, Performance Analysis, Intel, C/C++, Fortran | Computer Science, Software Engineering | Debugging Tool | Documentation, Uses, and more |
| intel-dev-utilities | Bridges-2 | Documentation, Uses, and more | ||||
| intel-dnnl | Bridges-2 | Intel oneAPI Deep Neural Network Library (oneDNN) is a performance library for deep learning applications, providing highly optimized building blocks for deep learning frameworks. | Deep Learning, Performance Optimization, Machine Learning, Library | Machine Learning, Deep Learning | Library | Documentation, Uses, and more |
| intel-dnnl-cpu-gomp | Bridges-2 | Intel oneAPI Deep Neural Network Library (oneDNN) optimized for CPU with OpenMP support. | Deep Learning, High Performance Computing, Machine Learning, Intel | Computer Science, Artificial Intelligence and Intelligent Systems | Library | Documentation, Uses, and more |
| intel-dnnl-cpu-iomp | Bridges-2 | The Intel oneAPI Deep Neural Network Library (DNNL) for CPU with Intel oneAPI Math Kernel Library (iomp) is a high-performance library for deep learning applications optimized for Intel CPUs. It provides highly optimized functions for deep learning frameworks and applications to accelerate training and inference tasks. | Deep Learning, Cpu Optimization, Neural Networks | Artificial Intelligence, Computer & Information Sciences | Tool | Documentation, Uses, and more |
| intel-dnnl-cpu-tbb | Bridges-2 | Intel oneAPI Deep Neural Network Library (DNNL) for CPU with Threading Building Blocks (TBB) support is a high-performance library for deep learning applications. It provides optimized building blocks for implementing deep neural networks on Intel CPUs. | Deep Learning, Neural Networks, Cpu Optimization, Threading Building Blocks | Artificial Intelligence & Intelligent Systems, Computer & Information Sciences | Deep Learning Library | Documentation, Uses, and more |
| intel-dpct | Bridges-2 | Intel Data Parallel C++ (DPC++) Compatibility Tool (dpct) is a tool developed by Intel to facilitate migration of CUDA kernels to Data Parallel C++ (DPC++) for seamless porting to heterogeneous platforms. | Intel, Data Migration, Cuda, Dpc++, Heterogeneous Computing | Computer Science, Computer & Information Sciences | Compiler | Documentation, Uses, and more |
| intel-dpl | Bridges-2 | Intel-DPL (Data Parallel Library) is a software library that enables developers to write parallel programs in a natural and expressive way, without needing to have expertise in parallel programming. It helps in achieving high performance in parallel computing tasks by utilizing task parallelism and data parallelism. | Parallel Programming, High Performance Computing, Intel Architecture | Computer Science, Computer & Information Sciences | Development Tool | Documentation, Uses, and more |
| intel-icc | Bridges-2 | Intel C++ Compiler (icc) is a proprietary optimizing compiler for the C and C++ programming languages, developed by Intel. It is designed to take advantage of Intel's architecture and provides high performance for applications in scientific computing, engineering, and other performance-critical domains. | compiler, performance, C++, scientific computing, optimization | Computer Science, Software Engineering | Compiler | Documentation, Uses, and more |
| intel-icc32 | Bridges-2 | The intel-icc32 compiler is a part of the Intel Compiler Suite specifically designed for 32-bit architectures. It provides a set of tools and libraries for optimizing and building applications for Intel processors. | Compiler, Software Development, Optimization | Computer & Information Sciences | Development Tools | Documentation, Uses, and more |
| intel-inspector | Bridges-2 | The Intel Inspector is a dynamic memory and threading error checking tool for users developing serial and multithreaded applications on Windows or Linux operating systems. It helps developers find memory and threading errors early in the code development cycle to eliminate costly and time-consuming issues that might otherwise arise later in the development phase or in the field. | Software, Development, Debugging, Memory Management, Multithreading | Software Engineering, Engineering & Technology | Memory & Threading Error Checker | Documentation, Uses, and more |
| intel-ipp-ia32 | Bridges-2 | Intel Integrated Performance Primitives (Intel IPP) for IA-32 architecture is a software library that provides a comprehensive set of high-performance functions for building advanced applications in various domains. It offers optimized routines for signal and data processing, image processing, cryptography, and more. | Software Library, Performance Optimization, Signal Processing, Image Processing, Cryptography | Computer Science, Computer & Information Sciences | Shared Library | Documentation, Uses, and more |
| intel-ipp-intel64 | Bridges-2 | Intel Integrated Performance Primitives (IPP) is a software library for multimedia processing, data processing, and communications applications. It provides a set of highly optimized functions for various data types and operations, leveraging Intel architecture for performance improvements. | Performance, Optimization, Multimedia, Data Processing | Computer Science, Applied Computer Science | Library | Documentation, Uses, and more |
| intel-ippcp-ia32 | Bridges-2 | Intel Integrated Performance Primitives (IPP) Cryptography (IPP-Crypto) is a library of high-performance cryptographic and security functions optimized for Intel processors. It provides developers with a broad range of encryption, digital signature, and authentication functionality to secure data and communications. | Software Library, Cryptography, Security | Cryptography, Computer & Information Sciences | Program Library | Documentation, Uses, and more |
| intel-ippcp-intel64 | Bridges-2 | Intel Integrated Performance Primitives Cryptography (IPP Crypto) is a library that provides a comprehensive set of cryptographic functions for high-performance applications. | Cryptography, Performance, Intel, Library | Applied Computer Science, Software Engineering | Library | Documentation, Uses, and more |
| intel-itac | Bridges-2 | Intel ITAC (Intel Threading Analysis Console) is a performance analysis tool that helps developers optimize their multi-threaded applications by providing insights into threading behavior and performance bottlenecks. | Performance Analysis, Multi-threading, Optimization, Intel Tools | Computer Science | Analysis Tool | Documentation, Uses, and more |
| intel-mkl | Bridges-2 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-mkl32 | Bridges-2 | Documentation, Uses, and more | ||||
| intel-oclfpga | Bridges-2 | The Intel OneAPI Base Toolkit for OpenCL FPGA is a comprehensive suite of development tools for accelerating workloads on Intel FPGA devices. It provides a unified programming model for CPU, GPU, and FPGA to simplify application development and deployment across diverse hardware architectures. | Development Tools, Accelerating Workloads, Fpga Programming, Hardware Acceleration | Computer Science, Computer & Information Sciences | Compiler | Documentation, Uses, and more |
| intel-oneapi | Bridges-2 | Intel oneAPI is a unified programming model that simplifies development across diverse computing architectures, including CPUs, GPUs, FPGAs, and other accelerators. | HPC, parallel computing, data analytics, machine learning, deep learning | Computer Science | Development Toolkit | 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-tbb | Bridges-2 | Intel Threading Building Blocks (TBB) is a C++ library that helps developers create scalable parallel applications. | Parallel Computing, C++, Multithreading, Performance Optimization | Software Engineering, Computer and Information Sciences | Library | Documentation, Uses, and more |
| intel-tbb32 | Bridges-2 | Intel Threading Building Blocks (TBB) is a widely-used C++ library for parallelism. It provides a way to write parallel C++ programs that take full advantage of multi-core processors. | Parallelism, C++, Multi-Core, Library | Software Engineering, Computer & Information Sciences, Computer Science, Applied Computer Science | Library | Documentation, Uses, and more |
| intel-vtune | Bridges-2 | 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 |
| intelmpi | Bridges-2 | Intel MPI Library focuses on enabling applications to perform better on Intel architecture-based clusters. It enables applications to gain faster communication performance on Intel Xeon Phi coprocessors and Intel Xeon processors. | Hpc, Mpi Library, Intel Architecture | Computer Science, Engineering & Technology | Library | Documentation, Uses, and more |
| intermol | Bridges-2 | InterMol is a software package designed for molecular simulations and modeling, providing tools for the analysis and visualization of molecular dynamics and Monte Carlo simulations. | Molecular Dynamics, Monte Carlo, Simulation, Visualization, Bioinformatics | Molecular Simulation, Chemical Sciences | Simulation Software | 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 |
| 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 |
| irods-icommands | Bridges-2 | iRODS (integrated Rule-Oriented Data System) iCommands are command-line tools that allow users to interact with iRODS servers for data management, including data transfer, metadata management, and rule execution. | Data Management, Command Line Tools, Data Transfer, Metadata, Automation | Information Science, Data Science | Command Line Interface | Documentation, Uses, and more |
| itac | Stampede3 KyRIC |
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 |
| json-c | KyRIC DeltaAI |
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-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 | ||||
| julia | Bridges-2 Anvil 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 |
| 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 |
| 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 | 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 |
| knime | Bridges-2 | KNIME is an open-source data analytics, reporting, and integration platform. It allows users to visually design data flows, execute data processing, data cleansing, analysis, and reporting without needing to write any code. | Data Analytics, Data Integration, Data Visualization | Informatics, Analytics & Information Science, Computer & Information Sciences | Data Analysis Tool | 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 | Bridges-2 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 |
| lammps | Stampede3 Bridges-2 Anvil DeltaAI Delta |
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 |
| 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 | |
| lazygit | Bridges-2 | lazygit is a simple terminal UI for git commands, with the ability to easily view and manage changes in repositories. | Version Control, Git, Terminal Ui, Software Development | Computer Science, Engineering & Technology | Tools | Documentation, Uses, and more |
| learning | Anvil | Documentation, Uses, and more | ||||
| libaio | 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 |
| libbsd | KyRIC Anvil DeltaAI |
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 | 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 |
| 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 |
| libevent | 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 | KyRIC Anvil DeltaAI Delta |
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 |
| libffi | KyRIC Anvil DeltaAI |
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 |
| libgcrypt | DeltaAI | 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 | 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 | 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 |
| libgpg-error | KyRIC DeltaAI |
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 |
| libiconv | KyRIC Anvil |
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 |
| libidn2 | KyRIC DeltaAI |
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 |
| libjpeg-turbo | 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 |
| 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 | Stampede3 Anvil |
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 |
| libpciaccess | 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 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 |
| libpthread-stubs | Anvil DeltaAI |
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 | 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 |
| 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 |
| libssh2 | DeltaAI | libssh2 is a library implementing the SSH2 protocol, providing a way to securely connect to remote servers and execute commands or transfer files. | SSH, Networking, Security, Library | Computer Science | Library | 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 |
| libtiff | Anvil 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 | Expanse Anvil |
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 |
| libtool | KyRIC DeltaAI |
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 | KyRIC DeltaAI |
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 | 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 |
| 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 | 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 | KyRIC Anvil DeltaAI |
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 | 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 |
| llvm | 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 |
| lmod | Stampede3 Bridges-2 DeltaAI Delta |
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 |
| lowcharts | Bridges-2 | Lowcharts is a Python library for creating basic low-level charts with a simplistic and minimalistic interface. It aims to provide users with an easy-to-use tool for generating simple line charts, bar charts, and scatter plots. | Python Library, Data Visualization, Charting Library | Computer & Information Sciences | Library | Documentation, Uses, and more |
| lua | 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 |
| m4 | KyRIC DeltaAI |
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 |
| make | 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 |
| 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 |
| 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 |
| matlab | Stampede3 Bridges-2 Expanse Anvil Delta |
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 |
| mc | Bridges-2 | MC is a popular C compiler and interpreter that is widely used for developing efficient and portable software. | Compiler, Interpreter, C, Software Development | Computer & Information Sciences | Compiler | 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 |
| 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 |
| meme suite | Bridges-2 | MEME Suite is a collection of tools for discovering and analyzing sequence motifs in biological sequences. | bioinformatics, motif discovery, sequence analysis | Bioinformatics, Computational Biology | Analysis Tool | Documentation, Uses, and more |
| mentorgraphics | Bridges-2 | Mentor Graphics provides electronic design automation (EDA) software and engineering services for the design, verification, and manufacturing of electronic systems. | EDA, PCB design, IC design, Simulation, Verification | Engineering, Electrical, Electronic, and Information Engineering | Commercial | Documentation, Uses, and more |
| mesa | 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 | 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 |
| methylpy | Bridges-2 | methylpy is a Python package designed for the analysis of DNA methylation data obtained from bisulfite sequencing. It provides various tools for processing, analyzing, visualizing, and interpreting DNA methylation data. | DNA Methylation, Bisulfite Sequencing, Epigenetics, Bioinformatics, Python Package | Genetics, Biological Sciences | Python Library | Documentation, Uses, and more |
| metis | 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 | 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 |
| minialign | Bridges-2 | minialign is an ultrafast, memory efficient, and highly accurate tool for multiple sequence alignment (MSA) of biological sequences. It is designed to handle very large datasets with high throughput. The software employs a k-mer based approach for rapid pairwise alignment followed by progressive alignment to generate the final MSA. | Bioinformatics, Hpc Tools | Bioinformatics, Biological Sciences | Tool | Documentation, Uses, and more |
| miniconda cuquantum | DeltaAI | Documentation, Uses, and more | ||||
| miniconda3 | 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-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 | ||||
| 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 | ||||
| mlflow | Bridges-2 | MLflow is an open-source platform for managing the end-to-end machine learning lifecycle. It enables tracking experimentation, packaging code into reproducible runs, and sharing and deploying models. | Machine Learning, Data Science, Model Management, Experimentation, Model Deployment | Computer Science, Computer & Information Sciences | Open-Source | Documentation, Uses, and more |
| mmseqs2 | Bridges-2 | 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 |
| 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 |
| 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 | |
| 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 | |
| mpc | KyRIC Anvil DeltaAI |
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 | Stampede3 KyRIC Expanse Anvil DeltaAI |
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 |
| mpich | DeltaAI Delta |
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 | ||||
| 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 |
| 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 | |
| mumps | 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 |
| must | Bridges-2 | MuST is software package designed for performing ab initio electornic structure calculations for metals, alloys, and nanostructures. It is an all-electron DFT code based on multiple scattering theory, also known as KKR method, and Green function techniques. | 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-cpu | Stampede3 | Documentation, Uses, and more | ||||
| mvapich-plus-pvc | Stampede3 | Documentation, Uses, and more | ||||
| mvapich2 | Bridges-2 Anvil |
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 |
| namd | Stampede3 Bridges-2 Anvil Delta |
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 |
| nano | 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 |
| nanoplot | Bridges-2 | NanoPlot is a plotting tool specifically designed for visualization of long read sequencing data generated by Nanopore sequencers like MinION. It can create quality control plots to help users assess the quality and characteristics of the sequencing data. | Bioinformatics, Genomics, Sequencing Data, Quality Control, Visualization | Bioinformatics, Biological Sciences | Bioinformatics Tool | Documentation, Uses, and more |
| nasm | 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 |
| 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 |
| nccl | Anvil DeltaAI |
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 | ||||
| ncdu | Bridges-2 | ncdu (NCurses Disk Usage) is a disk utility for analyzing disk usage in a terminal environment. It provides a fast way to see what directories are using the most space on a filesystem. | Disk Utility, Disk Usage Analyzer, Terminal Tool, Storage Management | Systems, and Development, Other Computer & Information Sciences | Command Line Tool | Documentation, Uses, and more |
| ncl | Anvil | 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 | Stampede3 Anvil |
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 | KyRIC Anvil DeltaAI |
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 | Stampede3 Bridges-2 Anvil |
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 |
| netcdf | Stampede3 Expanse |
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-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 | 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 |
| 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 | 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 |
| nextflow | Bridges-2 Anvil |
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 | 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 |
| ninja | Stampede3 DeltaAI |
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 |
| nltk | Anvil | 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 |
| 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 | ||||
| numactl | KyRIC Expanse Anvil |
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 |
| nvbandwidth | Delta | Documentation, Uses, and more | ||||
| nvhpc | Bridges-2 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 cuda toolkit | Bridges-2 | The NVIDIA CUDA Toolkit is a parallel computing platform and application programming interface (API) model created by NVIDIA. It allows developers to use a CUDA-enabled graphics processing unit (GPU) for general-purpose processing – an approach known as GPGPU (General-Purpose computing on Graphics Processing Units). | GPU Computing, Parallel Computing, High-Performance Computing, Machine Learning, Deep Learning | Computer Science | Development Toolkit | 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 | ||||
| nvtop | 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 | Stampede3 Bridges-2 Anvil Delta |
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 |
| 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 | Bridges-2 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 | 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 |
| openblas | KyRIC Bridges-2 Expanse Anvil DeltaAI Delta |
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 | Bridges-2 Anvil 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 |
| openfoam | Stampede3 Bridges-2 Anvil |
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 |
| openjdk | KyRIC Expanse Anvil |
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 |
| 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 |
| openmpi | KyRIC Bridges-2 Expanse Anvil |
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 |
| 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 |
| openslide | Bridges-2 | OpenSlide is a C library that provides a simple interface to read whole slide images (WSIs) and their associated metadata. | bioinformatics, image processing, whole slide imaging | Pathology, Medical and Health Sciences | 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 | KyRIC Anvil DeltaAI |
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 |
| operating system provided modules | KyRIC | Documentation, Uses, and more | ||||
| orca | KyRIC Bridges-2 |
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 |
| osmesa | Delta | Documentation, Uses, and more | ||||
| osu-micro-benchmarks | 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 |
| 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 |
| 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 | 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 |
| pango | 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 | Stampede3 KyRIC Anvil DeltaAI Delta |
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 |
| 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 |
| parallel | Expanse Anvil DeltaAI 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 | Stampede3 Bridges-2 Anvil DeltaAI Delta |
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 |
| paraview | Anvil 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 | 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 |
| patch | KyRIC Delta |
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 |
| 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 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 | Stampede3 KyRIC DeltaAI |
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 |
| pelican | Anvil | 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 | KyRIC Anvil DeltaAI |
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 |
| petsc | Stampede3 Anvil DeltaAI Delta |
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 |
| phdf5 | Stampede3 Bridges-2 |
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-suite | Bridges-2 | PHYLIP (Phylogeny Inference Package) is a software package for inferring phylogenies (evolutionary trees) using various methods including distance, parsimony, and likelihood. | phylogenetics, evolution, bioinformatics | Computational Biology, Bioinformatics | Open Source | Documentation, Uses, and more |
| picard | Bridges-2 Anvil 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 | 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 |
| pilon | Bridges-2 | Pilon is a software package that automates the improvement of draft assemblies of microbial genomes, using information from multiple sources to correct draft assemblies. | Genome Assembly, Genomics, Bioinformatics, Computational Biology | Genomics, Biological Sciences | Tool | Documentation, Uses, and more |
| pixman | Anvil 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 |
| pkgconf | KyRIC DeltaAI |
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 |
| plumed | Bridges-2 Anvil 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 |
| 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 | 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 | 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 | 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 |
| 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 |
| porechop | Bridges-2 | Porechop is a tool designed for the trimming of Illumina sequencing data, specifically focusing on the removal of adapter sequences and low-quality reads. | bioinformatics, sequence analysis, data processing | Bioinformatics, Genomics | Command-line tool | 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 | Bridges-2 | 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 | Stampede3 Anvil DeltaAI |
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 | Bridges-2 | 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 | 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 |
| prun job launch utility | KyRIC | 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 | KyRIC DeltaAI |
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 | Bridges-2 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 | KyRIC DeltaAI |
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 | ||||
| pylauncher | Stampede3 | Documentation, Uses, and more | ||||
| python | KyRIC Bridges-2 Anvil DeltaAI Delta |
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-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 |
| python3 | Stampede3 Expanse |
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 | Bridges-2 Anvil |
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-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 |
| 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 |
| qemu | Anvil | 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 | 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 |
| 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 | 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 |
| 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-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 | Bridges-2 | 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 |
| qupath | Bridges-2 | QuPath is an open-source software for bioimage analysis, particularly designed for digital pathology and whole slide image analysis. | bioinformatics, image analysis, digital pathology, machine learning | Bioinformatics, Digital Pathology | Open-source | Documentation, Uses, and more |
| r | KyRIC Anvil DeltaAI Delta 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 |
| 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 |
| raxml | Bridges-2 | RAxML (Randomized Axelerated Maximum Likelihood) is a software for phylogenetic analysis and inference of evolutionary trees. It is widely used for maximum likelihood-based phylogenetic tree estimation. | Phylogenetics, Evolutionary Biology, Bioinformatics | Systematics & Population Biology, Biological Sciences | Bioinformatics Tool | Documentation, Uses, and more |
| rclone | Bridges-2 Expanse Anvil |
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 |
| re2c | 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 | KyRIC Anvil DeltaAI |
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 |
| relion | 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 | ||||
| rich-cli | Bridges-2 | Rich CLI is a command-line interface tool that provides rich text formatting and interactive features for terminal applications. | CLI, Terminal, Text Formatting, Interactive | Software Engineering | Command-Line Interface Tool | Documentation, Uses, and more |
| rnaview | Bridges-2 | RNAview is a software tool for visualizing RNA secondary structures. It provides an interactive graphical interface for users to explore and analyze RNA molecules' structural properties. | RNA Secondary Structure, Visualization Tool, Bioinformatics | Bioinformatics, Biological Sciences | Molecular Biology | Documentation, Uses, and more |
| rstudio | Expanse Anvil 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 |
| samtools | Bridges-2 Anvil 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 |
| scalapack | Bridges-2 | 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 |
| scotch | 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 |
| 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 | |
| settarg | Stampede3 Bridges-2 DeltaAI Delta |
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 | |
| 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 |
| 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 | Stampede3 Bridges-2 |
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 | ||||
| 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 |
| 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 |
| spack | 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 |
| spades | Bridges-2 | 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 | Bridges-2 Expanse Anvil |
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 |
| spice-server | Anvil | Documentation, Uses, and more | ||||
| sqlite | Stampede3 KyRIC Anvil DeltaAI |
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 | Bridges-2 | The SRA Toolkit is a collection of tools for working with the Sequence Read Archive (SRA), allowing users to download, convert, and manipulate sequencing data from the SRA database. | bioinformatics, data analysis, genomics, sequencing | Bioinformatics, Genomics | Command-line tools | Documentation, Uses, and more |
| sratoolkit | Expanse Anvil |
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 |
| star | Bridges-2 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 |
| star-fusion | Bridges-2 | Star-Fusion is a computational tool developed to identify fusion transcripts from RNA-Seq data. It utilizes the STAR aligner to map reads and searches for evidence of chimeric transcripts, providing insight into gene fusions in cancer and other diseases. | RNA-Seq, Fusion Transcripts, Gene Fusions, Computational Tool | Bioinformatics, Biological Sciences | Computational Software | 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 |
| subversion | 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 | 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 | 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 |
| swig | Stampede3 Anvil DeltaAI |
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 |
| sz | Stampede3 | 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 | ||||
| tar | KyRIC Anvil Delta |
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 |
| tbb | 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 |
| tcl | Expanse Anvil 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 |
| tensorflow | Bridges-2 Anvil |
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 |
| texlive | Stampede3 Anvil |
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 |
| tiger | Bridges-2 | TIGER (Topical Information in Genomic Experiments) is a software suite designed for the analysis and interpretation of genomics and transcriptomics data. It offers a range of tools for processing and visualizing genomic data to facilitate research in molecular biology and genetics. | Genomics, Transcriptomics, Data Analysis, Molecular Biology, Genetics | Genomics, Biological Sciences | Tool | Documentation, Uses, and more |
| tinker | Stampede3 Delta |
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 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 |
| 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 |
| 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 |
| trilinos | 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 |
| trimmomatic | Bridges-2 Anvil 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 | Bridges-2 | 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 |
| trnascan-se | Bridges-2 | tRNAscan-SE is a program for the identification of transfer RNA (tRNA) genes in genomic sequence. It combines search techniques for computational RNA gene detection and a homology search for analyzing secondary structure features of candidate genes. tRNAscan-SE is widely used for the prediction of tRNA genes in both prokaryotic and eukaryotic genomes. | Bioinformatics, Genomics, Computational Biology, Sequence Analysis | Genomics, Biological Sciences | Bioinformatics Tool | Documentation, Uses, and more |
| tuning analysis utilities | Stampede3 | Documentation, Uses, and more | ||||
| ucc | 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 |
| ucx | Stampede3 KyRIC Bridges-2 Expanse Anvil |
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 |
| udunits | Stampede3 Anvil |
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 |
| util-linux | 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 | KyRIC Anvil DeltaAI Delta |
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 | KyRIC DeltaAI |
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 |
| valgrind | Anvil | 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 | Stampede3 Bridges-2 Anvil |
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 |
| vcf2maf | Bridges-2 | vcf2maf is a tool that annotates variants in VCF files with Variant Effect Predictor (VEP) and converts them to Mutation Annotation Format (MAF). It helps in interpreting and analyzing genetic variants in the context of known genomic annotations. | Bioinformatics, Variant Annotation, Genetic Variants, Annotation Tool | Biological Sciences | Bioinformatics Tool | Documentation, Uses, and more |
| vcftools | Bridges-2 Anvil 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 |
| visidata | Bridges-2 | VisiData is a fast, interactive multitool for tabular data. It combines the clarity of a spreadsheet, the efficiency of the terminal, and the power of Python, into a lightweight utility which can handle millions of rows with ease. | Data Manipulation, Visualization, Python, Data Analysis | Data Analysis, Computer & Information Sciences | Utility Software | Documentation, Uses, and more |
| visit | Stampede3 Bridges-2 Anvil Delta |
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 | Bridges-2 Expanse Anvil |
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 |
| 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 |
| vtk | Stampede3 Anvil |
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 | Stampede3 KyRIC |
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 |
| 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 |
| which | DeltaAI | Documentation, Uses, and more | ||||
| xalt | Stampede3 Anvil 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 |
| 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 | |
| xdinfo | Bridges-2 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 |
| xdresourceid | Bridges-2 | xdResourceID is a tool used for identifying and managing unique resource identifiers within a digital environment. It provides a systematic approach to assigning and tracking identifiers for various digital resources. | Resource Management, Digital Environment, Identifier Tracking | Engineering & Technology | Documentation, Uses, and more | |
| xdusage | Bridges-2 | xdusage is a tool used for monitoring and analyzing batch job resource utilization on High Performance Computing (HPC) systems. It allows users to track resource usage, such as CPU time, memory, and disk space, for individual jobs or users. | Hpc, Resource Monitoring, Batch Job Management, Performance Analysis | Infrastructure & Instrumentation, Engineering & Technology | Command Line Tool | 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 |
| xpmem | 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 |
| xproto | Anvil DeltaAI |
X Window System protocol development files. | Software Development, Protocol Development, X Window System | Computer & Information Sciences | Library | 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 |
| xz | KyRIC Anvil DeltaAI |
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 |
| 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 | 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 |
| zlib | Stampede3 KyRIC Anvil DeltaAI |
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 | Bridges-2 | 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 | KyRIC Expanse DeltaAI |
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 |