Software list#

The full list of software centrally installed and managed on Sherlock is in the tables below.

Categories#

Software modules on Sherlock are organized in categories, by scientific field or functional class. It means that you will have to first load a category module before getting access to individual modules. The math and devel categories are loaded by default. See the Modules page for further details and examples.

We currently provide 663 software modules, in 7 categories, covering 106 fields of science:

• biology clinical science, computational biology, cryo-em, genomics, molecular biology, neurology, neurosciences, pathology, phylogenetics, population genetics, radiology, workflow management

• chemistry cheminformatics, computational chemistry, crystallography, docking, electrostatics, modelling, molecular dynamics, molecular dynamicx, quantum chemistry, tools, x-ray spectroscopy

• devel analytics, build, compiler, data, data analytics, debug, engine, framework, IDE, language, lib, mpi, networking, package management, parser, profiling, runtime

• math computational geometry, data science, deep learning, graph computing, lib, libs, linear algebra, machine learning, numerical analysis, numerical library, optimization, scientific computing, speech analysis, statistics, symbolic, technical computing, topic modelling

• physics astronomy, CFD, climate modeling, geophysics, geoscience, lib, magnetism, materials science, micromagnetics, particle, photonics, physics-ml, quantum information science, quantum mechanics

• system assembler, backup, benchmark, checkpointing, cloud interface, compiler, compression, containers, database, document management, document processing, file management, file transfer, framework, graphics, hardware, job management, language, libs, media, performance, resource monitoring, scm, shell, testing, tools

• viz data, gis, graphs, image processing, imaging, molecular visualization, plotting, remote display, toolkit

biology#

Field	Module name	Version(s)	URL	Description
clinical science	simvascular	20180704	Website	Simvascular is a blood flow simulation and analysis toolkit. This module provides the svFSI (Fluid Solid Interaction) solver.
computational biology	py-biopython	1.70_py27 1.79_py36 1.79_py39 1.84_py312	Website	Biopython is a set of freely available tools for biological computation written in Python.
computational biology	rosetta	3.8  3.14	Website	Rosetta is the premier software suite for modeling macromolecular structures. As a flexible, multi-purpose application, it includes tools for structure prediction, design, and remodeling of proteins and nucleic acids.
cryo-em	ctffind	4.1.13	Website	ctffind is a program for finding CTFs of electron micrographs.
cryo-em	eman2	2.2   2.91	Website	EMAN2 is a broadly based greyscale scientific image processing suite with a primary focus on processing data from transmission electron microscopes.
cryo-em	imod	4.9.12  4.11.5	Website	IMOD is a set of image processing, modeling and display programs used for tomographic reconstruction and for 3D reconstruction of EM serial sections and optical sections.
cryo-em	motioncor2	1.3.1   1.5.0  1.6.4	Website	MotionCor2 is a multi-GPU accelerated program which corrects anisotropic image motion at the single pixel level.
cryo-em	py-topaz	0.2.4_py36  0.2.5_py39	Website	A pipeline for particle detection in cryo-electron microscopy images using convolutional neural networks trained from positive and unlabeled examples.
cryo-em	relion	2.0.3   2.1   4.0.1	Website	RELION (for REgularised LIkelihood OptimisatioN, pronounce rely-on) 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).
genomics	angsd	0.919 0.931	Website	ANGSD is a software for analyzing next generation sequencing data.
genomics	augustus	3.3.2	Website	AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences.
genomics	bamtools	2.5.1	Website	BamTools is a project that provides both a C++ API and a command-line toolkit for reading, writing, and manipulating BAM (genome alignment) files.
genomics	bases2fastq	2.0.0	Website	The Bases2Fastq Software demultiplexess sequencing data from Element instruments and converts base calls into FASTQ files for secondary analysis with the FASTQ-compatible software of your choice.
genomics	bcftools	1.6 1.8 1.16	Website	BCFtools is a program for variant calling and manipulating files in the Variant Call Format (VCF) and its binary counterpart BCF.
genomics	bcl-convert	4.2.7 4.3.6	Website	The BCL Convert App generates demultiplexed FASTQ files from a run as input.
genomics	bcl2fastq	2.20	Website	The bcl2fastq2 conversion software can be used to convert BCL files from MiniSeq, MiSeq, NextSeq, HiSeq, iSeq and NovaSeq sequening systems.
genomics	bedops	2.4.40	Website	BEDOPS is an open-source command-line toolkit that performs highly efficient and scalable Boolean and other set operations, statistical calculations, archiving, conversion and other management of genomic data of arbitrary scale.
genomics	bedtools	2.27.1 2.30.0	Website	The bedtools utilities are a swiss-army knife of tools for a wide-range of genomics analysis tasks.
genomics	bgen	1.1.4	Website	bgen is the reference implementation of the BGEN format, a binary file format for imputed genotype and haplotype data.
genomics	bowtie	1.2.2	Website	Bowtie is an ultrafast, memory-efficient short read aligner.
genomics	bowtie2	2.3.4.1	Website	Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences.
genomics	breseq	0.38.1	Website	breseq is a computational pipeline for finding mutations relative to a reference sequence in short-read DNA resequencing data.
genomics	bwa	0.7.17	Website	BWA (Burrows-Wheeler Aligner) is a software package for mapping low-divergent sequences against a large reference genome, such as the human genome.
genomics	canu	1.8	Website	A single molecule sequence assembler for genomes large and small.
genomics	cellranger	7.1.0	Website	Cell Ranger is a set of analysis pipelines that process Chromium single-cell RNA-seq output to align reads, generate gene-cell matrices and perform clustering and gene expression analysis.
genomics	cellranger-atac	2.1.0	Website	Cell Ranger ATAC is a set of analysis pipelines that process Chromium Single Cell ATAC data.
genomics	cufflinks	2.2.1	Website	Cufflinks assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples.
genomics	dorado	0.3.4 0.5.3 0.7.3	Website	Dorado is a high-performance, easy-to-use, open source basecaller for Oxford Nanopore reads.
genomics	fastqc	0.11.8	Website	FastQC aims to provide a simple way to do some quality control checks on raw sequence data coming from high throughput sequencing pipelines.
genomics	fastx_toolkit	0.0.14	Website	The FASTX-Toolkit is a collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing.
genomics	freebayes	1.2.0	Website	FreeBayes is a Bayesian genetic variant detector designed to find small polymorphisms.
genomics	gatk	4.1.0.0 4.1.4.1 4.6.0.0	Website	GATK (Genome Analysis Toolkit) offers a wide variety of tools with a primary focus on variant discovery and genotyping.
genomics	gemma	0.98.5	Website	GEMMA is a software toolkit for fast application of linear mixed models (LMMs) and related models to genome-wide association studies (GWAS) and other large-scale data sets.
genomics	hic-pro	2.10.0	Website	HiC-Pro: An optimized and flexible pipeline for Hi-C data processing.
genomics	hisat2	2.1.0	Website	HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes (as well as to a single reference genome).
genomics	hmmer	3.4	Website	HMMER is used for searching sequence databases for sequence homologs, and for making sequence alignments.
genomics	htslib	1.6 1.8 1.10.2 1.14 1.16	Website	C library for high-throughput sequencing data formats.
genomics	jellyfish	2.2.10	Website	A fast multi-threaded k-mer counter.
genomics	kallisto	0.44.0  0.46.1 0.50.1	Website	kallisto is a program for quantifying abundances of transcripts from RNA-Seq data using high-throughput sequencing reads.
genomics	longshot	1.0.0	Website	Longshot is a variant calling tool for diploid genomes using long error prone reads.
genomics	metal	20110325	Website	The METAL software is designed to facilitate meta-analysis of large datasets (such as several whole genome scans) in a convenient, rapid and memory efficient manner.
genomics	mixcr	2.1.12 4.6.0	Website	MiXCR is a universal framework that processes big immunome data from raw sequences to quantitated clonotypes.
genomics	ncbi-blast+	2.6.0 2.7.1 2.11.0 2.16.0	Website	NCBI BLAST+ is a suite of command-line tools to run BLAST (Basic Local Alignment Search Tool), an algorithm for comparing primary biological sequence information.
genomics	ncbi-vdb	3.0.7	Website	NCBI VDB is the database engine used by NCBI SRA tools.
genomics	plink	1.07 1.90b5.3 2.0a1 2.0a2	Website	PLINK is a free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner.
genomics	popscle	0.1	Website	popscle is a suite of population scale analysis tools for single-cell genomics data.
genomics	py-busco	3.0.2_py27	Website	Assessing genome assembly and annotation completeness with Benchmarking Universal Single-Copy Orthologs (BUSCO).
genomics	py-bx-python	0.8.1_py27 0.8.13_py39	Website	Tools for manipulating biological data, particularly multiple sequence alignments.
genomics	py-crested	1.2.1_py312	Website	CREsted (Cis-Regulatory Element Sequence Training, Explanation, and Design) is an easy-to-use deep learning package for training enhancer models on single-cell ATAC sequencing (scATAC-seq) data.
genomics	py-cutadapt	1.18_py27  1.18_py36	Website	Cutadapt finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads.
genomics	py-deeplabcut	2.2.3_py39  2.3.10_py39	Website	A software package for animal pose estimation.
genomics	py-deeptools	3.3.1_py36	Website	Tools to process and analyze deep sequencing data.
genomics	py-demuxalot	0.4.2_py312	Website	Reliable, scalable, efficient demultiplexing for single-cell RNA sequencing.
genomics	py-fithic	1.1.3_py27	Website	Fit-Hi-C is a tool for assigning statistical confidence estimates to chromosomal contact maps produced by genome architecture assays.
genomics	py-htseq	2.0.1_py39	Website	HTSeq is a Python library to facilitate processing and analysis of data from high-throughput sequencing (HTS) experiments.
genomics	py-macs2	2.1.1_py27 2.2.9.1_py39	Website	MACS (Model-based Analysis of ChIP-Seq) implements a novel ChIP-Seq analysis method.
genomics	py-mageck	0.5.9.4_py36	Website	Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout (MAGeCK) is a computational tool to identify important genes from the recent genome-scale CRISPR-Cas9 knockout screens technology.
genomics	py-mapdamage	2.2.1_py36	Website	mapDamage2 is a computational framework which tracks and quantifies DNA damage patterns among ancient DNA sequencing reads generated by Next-Generation Sequencing platforms.
genomics	py-multiqc	1.6_py27  1.6_py36	Website	MultiQC is a reporting tool that parses summary statistics from results and log files generated by other bioinformatics tools.
genomics	py-obitools	1.2.13_py27	Website	OBITools is a set of programs designed for analyzing NGS data in a DNA metabarcoding context.
genomics	py-orthofinder	2.5.4_py39	Website	OrthoFinder is a fast, accurate and comprehensive platform for comparative genomics.
genomics	py-pybedtools	0.8.0_py27 0.8.2_py36 0.9.0_py39	Website	Pybedtools wraps and extends BEDTools and offers feature-level manipulations from within Python.
genomics	py-pysam	0.14.1_py27 0.15.3_py36 0.18.0_py39 0.22.1_py312	Website	Pysam is a python module for reading, manipulating and writing genomic data sets.
genomics	py-scanpy	1.8.2_py39 1.10.2_py312	Website	Scanpy is a scalable toolkit for analyzing single-cell gene expression data.
genomics	py-scenicplus	1.0.0_py39	Website	SCENIC+ is a python package to build enhancer driven gene regulatory networks (GRNs) using combined or separate single-cell gene expression (scRNA-seq) and single-cell chromatin accessibility (scATAC-seq) data.
genomics	py-scvi-tools	1.2.1_py312	Website	scvi-tools (single-cell variational inference tools) is a package for probabilistic modeling of single-cell omics data.
genomics	py-vcf2gwas	0.8.9_py39	Website	Python API for comprehensive GWAS analysis using GEMMA.
genomics	py-vispr	0.4.17_py36	Website	A visualization framework for CRISPR/Cas9 knockout screens, analyzed with MAGeCK.
genomics	regenie	2.2.4	Website	regenie is a C++ program for whole genome regression modelling of large genome-wide association studies.
genomics	rsem	1.3.3	Website	RSEM is a software package for estimating gene and isoform expression levels from RNA-Seq data.
genomics	salmon	0.12.0 1.10.0	Website	Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using lightweight alignments.
genomics	samtools	1.6 1.8 1.16.1	Website	Tools (written in C using htslib) for manipulating next-generation sequencing data.
genomics	sentieon	201808.01  202112.01	Website	Sentieon Genomics software is a set of software tools that perform analysis of genomic data obtained from DNA sequencing.
genomics	shapeit	4.0.0  4.2.2	Website	SHAPEIT4 is a fast and accurate method for estimation of haplotypes (aka phasing) for SNP array and high coverage sequencing data.
genomics	sra-tools	2.11.0 3.0.7	Website	The SRA Toolkit and SDK from NCBI is a collection of tools and libraries for using data in the INSDC Sequence Read Archives.
genomics	star	2.5.4b 2.7.10b	Website	STAR: ultrafast universal RNA-seq aligner.
genomics	stringtie	2.2.1	Website	StringTie is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts.
genomics	tophat	2.1.1	Website	TopHat is a fast splice junction mapper for RNA-Seq reads.
genomics	trim_galore	0.5.0	Website	Trim Galore! is a wrapper script to automate quality and adapter trimming as well as quality control, with some added functionality to remove biased methylation positions for RRBS sequence files.
genomics	trinity	2.8.4 2.13.1	Website	Trinity RNA-Seq de novo transcriptome assembly.
genomics	vcflib	1.0.0	Website	A C++ library for parsing and manipulating VCF files.
genomics	vcftools	0.1.15	Website	VCFtools is a program package designed for working with VCF files, such as those generated by the 1000 Genomes Project.
genomics	viennarna	2.5.1	Website	A C code library and several stand-alone programs for the prediction and comparison of RNA secondary structures.
molecular biology	dssp	4.0.3	Website	DSSP is an application to assign secondary structure to proteins.
molecular biology	libcifpp	3.0.0	Website	Library to work with mmCIF and PDB files.
neurology	afni	17.2.07 18.2.04 21.3.00	Website	AFNI (Analysis of Functional NeuroImages) is a set of C programs for processing, analyzing, and displaying functional MRI (FMRI) data - a technique for mapping human brain activity.
neurology	freesurfer	6.0.1 7.1.1 7.2.0 7.3.2 7.4.1	Website	An open source software suite for processing and analyzing (human) brain MRI images.
neurosciences	ants	2.1.0 2.3.1 2.4.0	Website	ANTs computes high-dimensional mappings to capture the statistics of brain structure and function.
neurosciences	bart	0.7.00	Website	BART is a toolbox for Computational Magnetic Resonance Imaging.
neurosciences	dcm2niix	1.0.20171215 1.0.20211006	Website	dcm2niix is a program esigned to convert neuroimaging data from the DICOM format to the NIfTI format.
neurosciences	fsl	5.0.10   6.0.7.10	Website	FSL is a comprehensive library of analysis tools for FMRI, MRI and DTI brain imaging data.
neurosciences	mricron	20160502	Website	MRIcron is a cross-platform NIfTI format image viewer.
neurosciences	mrtrix	0.3.16 3.0.3	Website	MRtrix3 provides a set of tools to perform various types of diffusion MRI analyses, from various forms of tractography through to next-generation group-level analyses.
neurosciences	py-mdt	0.10.9_py36	Website	The Maastricht Diffusion Toolbox, MDT, is a framework and library for parallelized (GPU and multi-core CPU) diffusion Magnetic Resonance Imaging (MRI) modeling.
neurosciences	py-nipype	1.1.3_py27 1.1.3_py36	Website	Nipype is a Python project that provides a uniform interface to existing neuroimaging software and facilitates interaction between these packages within a single workflow.
neurosciences	py-sleap	1.3.4_py39	Website	SLEAP is an open source deep-learning based framework for multi-animal pose tracking.
neurosciences	spm	12	Website	The SPM software package has been designed for the analysis of brain imaging data sequences. The sequences can be a series of images from different cohorts, or time-series from the same subject.
neurosciences	workbench	1.3.1	Website	Connectome Workbench is an open source, freely available visualization and discovery tool used to map neuroimaging data, especially data generated by the Human Connectome Project.
pathology	openslide	3.4.1	Website	OpenSlide is a C library that provides a simple interface to read whole-slide images (also known as virtual slides).
pathology	py-openslide-python	1.1.1_py27  1.1.1_py36	Website	OpenSlide Python is a Python interface to the OpenSlide library.
phylogenetics	py-ete	3.0.0_py27	Website	A Python framework for the analysis and visualization of trees.
population genetics	py-admixfrog	0.6.1_py36	Website	Admixfrog is a HMM to infer ancestry frogments (fragments) from low-coverage, contaminated data.
radiology	nbia-data-retriever	4.2	Website	The NBIA Data Retriever is an application to download radiology images from the TCIA Radiology Portal.
workflow management	nextflow	23.04.3 24.10.4	Website	Nextflow is a bioinformatics workflow manager that enables the development of portable and reproducible workflows.

chemistry#

Field	Module name	Version(s)	URL	Description
cheminformatics	py-rdkit	2018.09.1_py27  2018.09.1_py36 2022.09.1_py39 2024.3.2_py312	Website	RDKit is a collection of cheminformatics and machine-learning software written in C++ and Python.
computational chemistry	gaussian	g16.A03   g16.B01	Website	Gaussian is a general purpose computational chemistry software package.
computational chemistry	libint	1.1.4 2.0.3 2.6.0	Website	Libint computes molecular integrals.
computational chemistry	libxc	3.0.0 5.2.2	Website	Libxc is a library of exchange-correlation functionals for density-functional theory.
computational chemistry	nwchem	6.8   7.0.2	Website	NWChem is an ab initio computational chemistry software package which also includes quantum chemical and molecular dynamics functionality.
computational chemistry	py-ase	3.14.1_py27 3.22.1_py39	Website	The Atomic Simulation Environment (ASE) is a set of tools and Python modules for setting up, manipulating, running, visualizing and analyzing atomistic simulations.
computational chemistry	schrodinger	2021-1     2017-3    2018-1    2018-2    2019-2    2020-2    2022-3    2024-1	Website	Schrödinger Suites (Small-molecule Drug Discovery Suite, Material Science Suite, Biologics Suite) provide a set of molecular modelling software.
computational chemistry	vasp	5.4.1     6.1.1    6.3.2    6.4.1    6.4.3	Website	The Vienna Ab initio Simulation Package (VASP) is a computer program for atomic scale materials modelling, e.g. electronic structure calculations and quantum-mechanical molecular dynamics, from first principles.
crystallography	clipper	2.1.20180802	Website	Crystallographic automation and complex data manipulation libraries.
crystallography	mmdb2	2.0.20	Website	A C++ toolkit for working with macromolecular coordinate files.
crystallography	ssm	1.4	Website	A macromolecular superposition library.
crystallography	vesta	3.4.4	Website	VESTA is a 3D visualization program for structural models, volumetric data such as electron/nuclear densities, and crystal morphologies.
docking	gnina	1.0.2	Website	A deep learning framework for molecular docking
electrostatics	apbs	1.5	Website	APBS solves the equations of continuum electrostatics for large biomolecular assemblages.
modelling	py-boltz	0.3.2_py312	Website	Boltz-1 is the state-of-the-art open-source model that predicts the 3D structure of proteins, RNA, DNA, and small molecules.
molecular dynamics	gromacs	2016.3   2018   2021.3   2023.1	Website	GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.
molecular dynamics	lammps	20180316  20200303   20230802	Website	LAMMPS is a classical molecular dynamics code that models an ensemble of particles in a liquid, solid, or gaseous state.
molecular dynamics	mosaics	1.0.0	Website	A collection of tools for characterizing membrane structure and dynamics within simulated trajectories of molecular systems.
molecular dynamics	plumed	2.3.2	Website	PLUMED is an open source library for free energy calculations in molecular systems.
molecular dynamics	py-openmm	7.1.1_py27  8.1.1_py312	Website	A high performance toolkit for molecular simulation.
molecular dynamics	py-raspa2	2.0.3_py27	Website	RASPA2 is a general purpose classical simulation package that can be used for the simulation of molecules in gases, fluids, zeolites, aluminosilicates, metal-organic frameworks, carbon nanotubes and external fields.
molecular dynamics	qbox	1.65.0	Website	Qbox is a First-Principles Molecular Dynamics code.
molecular dynamics	quip	20170901  20220426	Website	The QUIP package is a collection of software tools to carry out molecular dynamics simulations.
molecular dynamicx	py-fatslim	0.2.2_py39	Website	FATSLiM stands for “Fast Analysis Toolbox for Simulations of Lipid Membranes” and its goal is to provide an efficient, yet robust, tool to extract physical parameters from MD trajectories.
quantum chemistry	cp2k	4.1    9.1	Website	CP2K is a quantum chemistry and solid state physics software package that can perform atomistic simulations of solid state, liquid, molecular, periodic, material, crystal, and biological systems.
quantum chemistry	ocean	2.9.7	Website	OCEAN is a versatile and user-friendly package for calculating core edge spectroscopy including excitonic effects.
quantum chemistry	orca	4.2.1  5.0.0  5.0.3  6.0.0	Website	ORCA is a flexible, efficient and easy-to-use general purpose tool for quantum chemistry.
quantum chemistry	quantum-espresso	6.2.1  6.6  7.0  7.1	Website	Quantum ESPRESSO is an integrated suite of Open-Source computer codes for electronic-structure calculations and materials modeling at the nanoscale. It is based on density-functional theory, plane waves, and pseudopotentials.
quantum chemistry	quantum-espresso_gpu	1.1   7.0   7.1	Website	Quantum ESPRESSO is an integrated suite of Open-Source computer codes for electronic-structure calculations and materials modeling at the nanoscale. It is based on density-functional theory, plane waves, and pseudopotentials.
quantum chemistry	terachem	1.95A    1.96H-beta	Website	TeraChem is general purpose quantum chemistry software designed to run on NVIDIA GPU architectures.
tools	openbabel	3.1.1	Website	Open Babel is a chemical toolbox designed to speak the many languages of chemical data.
tools	py-openbabel	3.1.1.1_py39	Website	Python bindings for Open Babel.
x-ray spectroscopy	py-xraylarch	0.9.80_py312	Website	Larch is a open-source library and set of applications for processing and analyzing X-ray absorption and fluorescence spectroscopy data and X-ray fluorescence and diffraction image data from synchrotron beamlines.

devel#

Field	Module name	Version(s)	URL	Description
analytics	py-pyarrow	18.1.0_py312	Website	Python library for Apache Arrow, a development platform for in-memory analytics.
build	bazel	0.16.1 0.26.1 0.29.1	Website	Bazel is a fast, scalable, multi-language and extensible build system.
build	bazelisk	1.3.0 1.8.0	Website	Bazelisk is a wrapper for Bazel written in Go.
build	binutils	2.38	Website	The GNU Binutils are a collection of binary tools.
build	cmake	3.8.1 3.11.1 3.13.1 3.20.3 3.24.2 3.31.4	Website	CMake is an extensible, open-source system that manages the build process in an operating system and in a compiler-independent manner.
build	kerl	1.8.5	Website	Kerl is a tool to easily build and install Erlang/OTP instances.
build	libconfig	1.7.3	Website	C/C++ library for processing structured configuration files.
build	make	4.4	Website	GNU Make is a tool which controls the generation of executables and other non-source files of a program from the program's source files.
build	ninja	1.9.0	Website	Ninja is a small build system with a focus on speed.
build	py-meson	0.51.1_py36 1.6.1_py312	Website	Meson is an open source build system meant to be both extremely fast, and, even more importantly, as user friendly as possible.
build	py-scons	3.0.5_py27 3.0.5_py36 4.7.0_py312	Website	SCons is an Open Source software construction tool.
compiler	aocc	2.1.0 2.2.0	Website	AMD Optimizing C/C++ Compiler - AOCC is a highly optimized C, C++ and Fortran compiler for x86 targets especially for Zen based AMD processors.
compiler	gcc	6.3.0  7.1.0 7.3.0 8.1.0 9.1.0 10.1.0 10.3.0 12.4.0 14.2.0	Website	The GNU Compiler Collection includes front ends for C, C++, Fortran, Java, and Go, as well as libraries for these languages (libstdc++, libgcj,...).
compiler	icc	2017.u2 2018.u1 2018 2019	Website	Intel C++ Compiler, also known as icc or icl, is a group of C and C++ compilers from Intel
compiler	ifort	2017.u2 2018.u1 2018 2019	Website	Intel Fortran Compiler, also known as ifort, is a group of Fortran compilers from Intel
compiler	ldc	1.26.0 1.40.0	Website	The LLVM-based D Compiler.
compiler	llvm	7.0.0  3.8.1 4.0.0 5.0.0 9.0.1 15.0.3 17.0.6	Website	The LLVM Project is a collection of modular and reusable compiler and toolchain technologies. Clang is an LLVM native C/C++/Objective-C compiler,
compiler	nvhpc	21.5  21.7   22.3   23.3   24.7	Website	NVIDIA HPC Software Development Kit (SDK) including C, C++, and Fortran compilers.
compiler	pgi	19.10	Website	PGI compilers and tools, including Open MPI (Community Edition).
compiler	smlnj	110.81	Website	Standard ML of New Jersey (abbreviated SML/NJ) is a compiler for the Standard ML '97 programming language.
data	h5utils	1.12.1	Website	h5utils is a set of utilities for visualization and conversion of scientific data in the free, portable HDF5 format.
data	hdf5	1.10.6   1.10.0p1 1.10.2  1.12.0 1.12.2  1.14.4	Website	HDF5 is a data model, library, and file format for storing and managing data. It supports an unlimited variety of datatypes, and is designed for flexible and efficient I/O and for high volume and complex data.
data	hiredis	0.13.3	Website	Hiredis is a minimalistic C client library for the Redis database.
data	ncl	6.4.0 6.6.2	Website	NCL is a free interpreted language designed specifically for scientific data processing and visualization.
data	nco	4.8.0  5.0.6	Website	The NCO toolkit manipulates and analyzes data stored in netCDF-accessible formats.
data	netcdf	4.4.1.1 4.8.1	Website	NetCDF is a set of software libraries and self-describing, machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data.
data	netcdf-c	4.9.0	Website	NetCDF is a set of software libraries and self-describing, machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data. This module provides C libraries.
data	netcdf-cxx	4.3.1	Website	NetCDF is a set of software libraries and self-describing, machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data. This module provides C++ libraries.
data	netcdf-fortran	4.5.4	Website	NetCDF is a set of software libraries and self-describing, machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data. This module provides Fortran libraries.
data	pnetcdf	1.8.1  1.12.3	Website	Parallel netCDF (PnetCDF) is a parallel I/O library for accessing NetCDF files in CDF-1, 2, and 5 formats.
data	protobuf	3.4.0  3.20.0 21.9 29.1	Website	Protocol Buffers (a.k.a., protobuf) are Google's language-neutral, platform-neutral, extensible mechanism for serializing structured data.
data	py-dali	1.44.0_py312	Website	The NVIDIA Data Loading Library (DALI) is a GPU-accelerated library for data loading and pre-processing to accelerate deep learning applications.
data	py-kaggle	1.6.3_py312	Website	Official API for https://www.kaggle.com, accessible using a command line tool implemented in Python 3.
data	py-pandas	0.23.0_py27 0.23.0_py36 1.0.3_py36 1.3.1_py39 2.0.1_py39 2.2.1_py312	Website	pandas is an open source, BSD-licensed library providing high-performance, easy-to-use data structures and data analysis tools for the Python programming language.
data	py-protobuf	3.4.0_py27  3.4.0_py36 3.6.1_py27 3.6.1_py36 3.15.8_py36 3.20.1_py39 4.21.9_py39 5.29.1_py312	Website	Python bindings for Google's Protocol Buffers data interchange format.
data	py-tables	3.10.1_py312	Website	A Python package to manage extremely large amounts of data.
data	redis	4.0.1	Website	Redis is an open source, in-memory data structure store, used as a database, cache and message broker.
data	zfp	1.0.0	Website	zfp is an open-source library for compressed floating-point and integer arrays that support high throughput read and write random access.
data analytics	hadoop	3.1.0  3.3.1	Website	The Apache Hadoop software library is a framework that allows for the distributed processing of large data sets across clusters of computers using simple programming models.
data analytics	py-pyspark	3.2.1_py39 3.2.1_py312	Website	Launching and controlling spark on HPC clusters
data analytics	py-sparkhpc	0.3_py27	Website	Launching and controlling spark on HPC clusters
data analytics	spark	2.3.0  3.2.1	Website	Apache Spark™ is a unified analytics engine for large-scale data processing.
debug	gdb	8.2.1	Website	GDB is the GNU Project debugger.
debug	valgrind	3.14.0	Website	Valgrind is an instrumentation framework for building dynamic analysis tools.
engine	v8	8.4.371.22	Website	V8 is Google’s open source high-performance JavaScript and WebAssembly engine, written in C++.
framework	dotnet	2.1.500 6.0.413	Website	.NET is a free, cross-platform, open source developer platform for building many different types of applications.
framework	ga	5.8.2	Website	Global Arrays (GA) is a Partitioned Global Address Space (PGAS) programming model.
framework	py-kedro	0.18.0_py39	Website	Kedro is an open-source Python framework for creating reproducible, maintainable and modular data science code.
framework	py-warp-lang	1.5.0_py312	Website	Warp is a Python framework for writing high-performance simulation and graphics code.
IDE	code-server	4.16.1 4.93.1	Website	Run VS Code on any machine anywhere and access it in the browser.
IDE	py-jupytext	1.16.1_py39	Website	Jupyter Notebooks as Markdown Documents, Julia, Python or R scripts.
language	cuda	9.0.176   8.0.61  9.1.85  9.2.88  9.2.148  10.0.130  10.1.105  10.1.168  10.2.89  11.0.3  11.1.1  11.2.0  11.3.1  11.4.1  11.5.0  11.7.1  12.0.0  12.1.1  12.2.0  12.4.0  12.6.1	Website	CUDA is a parallel computing platform and application programming interface (API) model created by Nvidia. It allows software developers and software engineers to use a CUDA-enabled graphics processing unit (GPU) for general purpose processing.
language	erlang	21.3	Website	Erlang is a programming language used to build massively scalable soft real-time systems with requirements on high availability.
language	gcl	2.6.14	Website	GCL is the official Common Lisp for the GNU project.
language	go	1.9 1.14 1.18.2 1.22.7	Website	Go is an open source programming language that makes it easy to build simple, reliable, and efficient software.
language	guile	2.0.11 2.2.2	Website	GNU Guile is the preferred extension system for the GNU Project, which features an implementation of the Scheme programming language.
language	haskell	8.6.5	Website	Haskell is a statically typed, purely functional programming language with type inference and lazy evaluation.
language	java	1.8.0_131  11.0.11 12.0.2 17.0.4 18.0.2 21.0.4	Website	Java is a general-purpose computer programming language that is concurrent, class-based, object-oriented,[14] and specifically designed to have as few implementation dependencies as possible.
language	julia	1.6.2 1.7.2 1.8.4 1.9.4 1.10.5 1.11.4	Website	Julia is a high-level, high-performance dynamic programming language for numerical computing.
language	lua	5.3.4	Website	Lua is a powerful, efficient, lightweight, embeddable scripting language. It supports procedural programming, object-oriented programming, functional programming, data-driven programming, and data description.
language	luarocks	2.4.3	Website	LuaRocks is the package manager for Lua modules.
language	manticore	20180301	Website	Manticore is a high-level parallel programming language aimed at general-purpose applications running on multi-core processors.
language	nodejs	8.9.4 9.5.0 16.13.0 18.15.0 20.18.0	Website	Node.js is a JavaScript runtime built on Chrome's V8 JavaScript engine. It provides the npm package manager.
language	perl	5.26.0 5.36.1	Website	Perl 5 is a highly capable, feature-rich programming language with over 29 years of development.
language	php	7.3.0	Website	PHP (recursive acronym for PHP: Hypertext Preprocessor) is an open source general-purpose scripting language that is especially suited for web development.
language	py-cython	0.27.3_py27 0.27.3_py36 0.29.21_py36 0.29.28_py39	Website	Cython is an optimising static compiler for both the Python programming language and the extended Cython programming language (based on Pyrex).
language	py-ipython	5.4.1_py27  6.1.0_py36 8.3.0_py39 8.22.2_py312	Website	IPython is a command shell for interactive computing in multiple programming languages, originally developed for the Python programming language.
language	py-jupyter	1.0.0_py27  1.0.0_py36 1.0.0_py39	Website	Jupyter is a browser-based interactive notebook for programming, mathematics, and data science. It supports a number of languages via plugins.
language	py-jupyterlab	2.3.2_py36 4.0.8_py39 4.3.2_py312	Website	Jupyter is a browser-based interactive notebook for programming, mathematics, and data science. It supports a number of languages via plugins.
language	python	2.7.13  3.6.1 3.9.0 3.12.1	Website	Python is an interpreted, interactive, object-oriented programming language.
language	ruby	2.4.1 2.7.1 3.1.2	Website	A dynamic, open source programming language with a focus on simplicity and productivity. It has an elegant syntax that is natural to read and easy to write.
language	rust	1.35.0 1.56.1 1.63.0 1.72.0 1.81.0	Website	A language empowering everyone to build reliable and efficient software.
language	scala	2.12.6	Website	Scala combines object-oriented and functional programming in one concise, high-level language.
lib	ant	1.10.1	Website	Apache Ant is a Java library and command-line tool whose mission is to drive processes described in build files as targets and extension points dependent upon each other.
lib	boost	1.64.0 1.69.0  1.75.0  1.76.0  1.79.0  1.87.0	Website	Boost is a set of libraries for the C++ programming language that provide support for tasks and structures such as linear algebra, pseudorandom number generation, multithreading, image processing, regular expressions, and unit testing.
lib	chai	2.2.2	Website	Copy-hiding array abstraction to automatically migrate data between memory spaces.
lib	cnmem	1.0.0	Website	CNMeM is a simple library to help the Deep Learning frameworks manage CUDA memory.
lib	conduit	0.5.1	Website	Simplified Data Exchange for HPC Simulations.
lib	cub	1.7.3  1.10.0	Website	CUB is a flexible library of cooperative threadblock primitives and other utilities for CUDA kernel programming.
lib	cutlass	0.1.0 3.1.0	Website	CUTLASS is a collection of CUDA C++ template abstractions for implementing high-performance matrix-multiplication (GEMM) at all levels and scales within CUDA.
lib	cvcuda	0.13.0	Website	CV-CUDA is an open-source project that enables building efficient cloud-scale Artificial Intelligence (AI) imaging and computer vision (CV) applications.
lib	dtcmp	1.1.3	Website	Datatype Compare (DTCMP) Library for sorting and ranking distributed data using MPI.
lib	eigen	3.3.3 3.4.0	Website	Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms.
lib	libcircle	0.3.0	Website	libcircle is an API for distributing embarrassingly parallel workloads using self-stabilization.
lib	libctl	3.2.2 4.0.1 4.5.0	Website	libctl is a library for supporting flexible control files in scientific simulations.
lib	libevent	2.1.12	Website	The libevent API provides a mechanism to execute a callback function when a specific event occurs on a file descriptor or after a timeout has been reached.
lib	libgpuarray	0.7.5	Website	Library to manipulate tensors on the GPU.
lib	libtree	2.0.0	Website	libtree prints shared object dependencies as a tree.
lib	lwgrp	1.0.4	Website	The Light-weight Group Library provides methods for MPI codes to quickly create and destroy process groups.
lib	nccl	1.3.4  2.0.4  2.1.15  2.2.13  2.3.7  2.4.8  2.5.6  2.8.4  2.11.4  2.17.1  2.20.5  2.23.4	Website	NCCL (pronounced 'Nickel') is a stand-alone library of standard collective communication routines, such as all-gather, reduce, broadcast, etc., that have been optimized to achieve high bandwidth over PCIe.
lib	pio	2.6.2	Website	A high-level Parallel I/O Library for structured grid applications.
lib	pugixml	1.12.1	Website	Light-weight, simple and fast XML parser for C++ with XPath support.
lib	py-cutlass	3.1.0_py39	Website	Python interface for CUTLASS
lib	py-cvcuda	0.13.0_py312	Website	Python bindings for CV_CUDA.
lib	py-h5py	2.7.1_py27  2.8.0_py36 2.10.0_py36 3.1.0_py36 3.7.0_py39 3.10.0_py312	Website	The h5py package is a Pythonic interface to the HDF5 binary data format.
lib	py-netcdf4	1.3.1_py27  1.3.1_py36	Website	netcdf4-python is a Python interface to the netCDF C library.
lib	py-nose	1.3.7_py39	Website	nose is nicer testing for python.
lib	py-numba	0.35.0_py27  0.35.0_py36 0.53.1_py36 0.54.1_py39 0.59.1_py39 0.60.0_py312	Website	Numba is a compiler for Python array and numerical functions that gives you the power to speed up your applications with high performance functions written directly in Python..
lib	py-parsl	1.2.0_py39	Website	Parsl is a flexible and scalable parallel programming library for Python.
lib	py-pycuda	2017.1.1_py27  2021.1_py36	Website	PyCUDA lets you access Nvidia‘s CUDA parallel computation API from Python.
lib	py-regex	20247.24_py36 20247.24_py39 20247.24_py312	Website	Alternative regular expression module for Python, to replace re.
lib	py-rmm	23.04.00_py39	Website	Python interface for RMM
lib	py-schwimmbad	0.3.1_py36  0.3.2_py39	Website	schwimmbad provides a uniform interface to parallel processing pools and enables switching easily between local development (e.g., serial processing or with multiprocessing) and deployment on a cluster or supercomputer (via, e.g., MPI or JobLib).
lib	py-scikit-image	0.13.0_py27 0.14.0_py27 0.15.0_py27 0.15.0_py36 0.17.2_py36 0.19.3_py39 0.20.0_py39 0.24.0_py312	Website	scikit-image is a collection of algorithms for image processing.
lib	rabbitmq	3.7.13	Website	RabbitMQ is an open-source message broker.
lib	raja	0.12.1	Website	Collection of C++ software abstractions that enable architecture portability for HPC applications.
lib	rmm	23.04.00	Website	RAPIDS Memory Manager library
lib	swig	3.0.12	Website	SWIG is an interface compiler that connects programs written in C and C++ with scripting languages such as Perl, Python, Ruby, and Tcl.
lib	tbb	2017.u2 2018.u1 2018 2019	Website	Intel® Threading Building Blocks (Intel® TBB) is a widely used C++ library for shared-memory parallel programming and heterogeneous computing (intra-node distributed memory programming).
lib	trilinos	12.12.1	Website	Trilinos is a collection of open-source software libraries, called packages, intended to be used as building blocks for the development of scientific applications.
lib	xsimd	7.6.0 8.1.0	Website	C++ wrappers for SIMD intrinsics and parallelized, optimized mathematical functions (SSE, AVX, NEON, AVX512)
lib	zeromq	4.2.2	Website	ZeroMQ (also spelled ØMQ, 0MQ or ZMQ) is a high-performance asynchronous messaging library, aimed at use in distributed or concurrent applications.
mpi	hpcx	2.6.0   2.7.0   2.8.1	Website	Mellanox HPC-X toolkit is a comprehensive software package that includes MPI and SHMEM/PGAS communications libraries.
mpi	impi	2017.u2  2018.u1  2018  2019	Website	Intel® MPI Library is a multi-fabric message passing library that implements the Message Passing Interface, version 3.1 (MPI-3.1) specification.
mpi	openmpi	4.1.2    2.0.2  2.1.1  3.1.2   4.0.3   4.1.0   4.1.6   5.0.5	Website	The Open MPI Project is an open source Message Passing Interface implementation that is developed and maintained by a consortium of academic, research, and industry partners.
mpi	py-mpi4py	3.0.0_py27  3.0.3_py36  3.1.3_py39  3.1.5_py312	Website	MPI for Python provides Python bindings for the Message Passing Interface (MPI) standard. It is implemented on top of the MPI-½/3 specification and exposes an API which grounds on the standard MPI-2 C++ bindings.
networking	gasnet	1.30.0	Website	GASNet is a language-independent, low-level networking layer that provides network-independent, high-performance communication primitives tailored for implementing parallel global address space SPMD languages and libraries.
networking	libfabric	1.6.0 1.6.2 1.7.1 1.9.1 1.10.1 1.11.1 1.14.0	Website	The Open Fabrics Interfaces (OFI) is a framework focused on exporting fabric communication services to applications. Libfabric is the library that defines and exports the user-space API of OFI.
networking	py-ucx-py	0.24.0_py39	Website	Python bindinbgs for UCX.
networking	ucc	1.3.0	Website	UCC is a collective communication operations API and library that is flexible, complete, and feature-rich for current and emerging programming models and runtimes.
networking	ucx	1.3.1 1.8.1  1.9.0  1.10.0  1.12.1  1.15.0  1.17.0	Website	UCX is a communication library implementing high-performance messaging for MPI/PGAS frameworks.
package management	pixi	0.28.1	Website	Pixi is a package management tool for developers. It allows the developer to install libraries and applications in a reproducible way.
package management	uv	0.3.5	Website	An extremely fast Python package and project manager, written in Rust.
parser	antlr	2.7.7	Website	ANTLR (ANother Tool for Language Recognition) is a powerful parser generator for reading, processing, executing, or translating structured text or binary files.
parser	xerces-c	3.2.1	Website	Xerces-C++ is a validating XML parser written in a portable subset of C++.
profiling	amd-uprof	3.3.462	Website	AMD uProf is a performance analysis tool for applications.
profiling	darshan	3.4.4 3.4.6	Website	Darshan is a scalable HPC I/O characterization tool.
profiling	nsight-systems	2024.4	Website	NVIDIA Nsight™ Systems is a system-wide performance analysis tool designed to visualize an application’s algorithms, identify the largest opportunities to optimize, and tune to scale efficiently across any quantity or size of CPUs and GPUs, from large servers to our smallest systems-on-a-chip (SoCs).
profiling	py-scalene	1.55.4_py39  1.55.4_py312	Website	Scalene is a high-performance, high-precision CPU, GPU, and memory profiler for Python with AI-powered optimization proposals
runtime	starpu	1.3.2	Website	StarPU is a unified runtime system that offers support for heterogeneous multicore architectures

math#

Field	Module name	Version(s)	URL	Description
computational geometry	cgal	4.10	Website	The Computational Geometry Algorithms Library (CGAL) is a C++ library that aims to provide easy access to efficient and reliable algorithms in computational geometry.
computational geometry	dealii	9.4.1	Website	deal.II is a C++ program library targeted at the computational solution of partial differential equations using adaptive finite elements.
computational geometry	gmsh	4.10.1	Website	Gmsh is an open source 3D finite element mesh generator with a built-in CAD engine and post-processor.
computational geometry	opencascade	7.6.2	Website	Open CASCADE Technology (OCCT) is an open-source full-scale 3D geometry library
computational geometry	polymake	4.10	Website	polymake is open source software for research in polyhedral geometry.
computational geometry	qhull	2015.2 2020.2	Website	Qhull computes the convex hull, Delaunay triangulation, Voronoi diagram, halfspace intersection about a point, furthest-site Delaunay triangulation, and furthest-site Voronoi diagram.
computational geometry	silo	4.11	Website	A mesh and field I/O library and scientific database.
data science	py-rapids	24.04_py39	Website	NVIDIA RAPIDS is an open-source suite of GPU-accelerated data science and AI libraries with APIs that match the most popular open-source data tools.
deep learning	cudnn	6.0  7.0.1  7.0.4  7.0.5  7.1.4  7.4.1.5  7.6.4  7.6.5  8.1.1.33  8.3.3.40  8.6.0.163  8.9.0.131  9.0.0.312  9.4.0	Website	NVIDIA cuDNN is a GPU-accelerated library of primitives for deep neural networks.
deep learning	cutensor	1.2.0  1.5.0.3  2.0.2.5	Website	GPU-accelerated tensor linear algebra library.
deep learning	py-deepsparse	1.8.0_py39	Website	Sparsity-aware deep learning inference runtime for CPUs.
deep learning	py-deepspeed	0.15.4_py312	Website	DeepSpeed is a deep learning optimization library that makes distributed training and inference easy, efficient, and effective.
deep learning	py-flash-attention	2.6.3_py312	Website	Fast and memory-efficient exact attention
deep learning	py-gym	0.21.0_py39	Website	Gym is a toolkit for developing and comparing reinforcement learning algorithms.
deep learning	py-horovod	0.12.1_py27    0.12.1_py36	Website	Horovod is a distributed training framework for TensorFlow. The goal of Horovod is to make distributed Deep Learning fast and easy to use.
deep learning	py-keras	2.1.5_py27   2.0.8_py27  2.1.5_py36  2.2.4_py27  2.2.4_py36  2.3.1_py36  3.7.0_py312	Website	Keras is a high-level neural networks API, written in Python and capable of running on top of TensorFlow, CNTK, or Theano.
deep learning	py-onnx	1.0.1_py27 1.8.1_py36 1.12.0_py39 1.17.0_py312	Website	ONNX is a open format to represent deep learning models.
deep learning	py-pytorch	0.3.0_py27   0.2.0_py27  0.2.0_py36  0.3.0_py36  1.0.0_py27  1.0.0_py36  1.4.0_py36  1.6.0_py36  1.8.1_py39  1.11.0_py39   2.0.0_py39   2.2.1_py312   2.4.1_py312	Website	PyTorch is a deep learning framework that puts Python first.
deep learning	py-tensorboardx	1.8_py27	Website	TensorboardX is TensorBoard™ for PyTorch (and Chainer, MXNet, NumPy...)
deep learning	py-tensorflow	2.1.0_py36   1.4.0_py27  1.5.0_py27  1.5.0_py36  1.9.0_py27  1.9.0_py36  2.4.1_py36  2.6.2_py36  2.9.1_py39  2.10.0_py39  2.18.0_py312	Website	TensorFlow™ is an open source software library for numerical computation using data flow graphs.
deep learning	py-tensorlayer	1.6.3_py27	Website	TensorLayer is a Deep Learning (DL) and Reinforcement Learning (RL) library extended from Google TensorFlow.
deep learning	py-tensorrt	8.5.1.7_py39  10.0.1_py312	Website	Python bindings for the TensorRT library.
deep learning	py-theano	1.0.1_py27	Website	Theano is a Python library that allows you to define, optimize, and evaluate mathematical expressions involving multi-dimensional arrays efficiently.
deep learning	py-torch-scatter	2.1.2_py312	Website	PyTorch Extension Library of Optimized Scatter Operations.
deep learning	py-torchvision	0.15.1_py39 0.17.1_py312 0.19.1_py312	Website	Datasets, model architectures, and common image transformations for computer vision for PyTorch.
deep learning	py-triton	1.0.0_py39  3.1.0_py312	Website	Triton is a language and compiler for writing highly efficient custom Deep-Learning primitives.
deep learning	py-ultralytics	8.3.14_py312	Website	Ultra YOLO11 is a cutting-edge, state-of-the-art (SOTA) model that builds upon the success of previous YOLO versions and introduces new features and improvements to further boost performance and flexibility.
deep learning	py-wandb	0.18.7_py312	Website	WandB (Weights and Biases) is a machine learning development platform that enables data scientists and machine learning engineers to track, visualize, and reproduce their experiments in real-time.
deep learning	tensorrt	3.0.1  3.0.4  4.0.1.6  5.0.2.6  6.0.1.8  7.0.0.11  7.2.3.4  8.5.1.7  10.0.1.6	Website	NVIDIA TensorRT™ is a high-performance deep learning inference optimizer and runtime that delivers low latency, high-throughput inference for deep learning applications.
deep learning	torch	20180202	Website	Torch is a scientific computing framework with wide support for machine learning algorithms that puts GPUs first.
graph computing	bliss	0.73	Website	A tool for computing automorphism groups and canonical forms of graphs.
lib	opencv	3.3.0   4.5.2  4.5.5  4.7.0  4.9.0  4.10.0	Website	OpenCV (Open Source Computer Vision Library) is an open source computer vision and machine learning software library.
libs	py-pynvjitlink	0.5.0_py312	Website	Python bindings for the nvJitLink library
linear algebra	armadillo	8.200.1	Website	Armadillo is a high quality linear algebra library (matrix maths) for the C++ language, aiming towards a good balance between speed and ease of use.
linear algebra	cudss	0.3.0.9	Website	NVIDIA cuDSS is an optimized, first-generation GPU-accelerated Direct Sparse Solver library for solving linear systems with very sparse matrices.
linear algebra	cusparselt	0.2.0.1  0.6.3.2	Website	NVIDIA cuSPARSELt is a high-performance CUDA library for sparse matrix-matrix multiplication.
machine learning	lightgbm	4.5.0	Website	LightGBM is a gradient boosting framework that uses tree based learning algorithms
machine learning	ollama	0.5.7	Website	Ollama is a free, open-source platform that allows users to run large language models (LLMs) locally.
machine learning	py-accelerate	0.29.3_py312	Website	Huggingface Accelerate is a library that enables the same PyTorch code to be run across any distributed configuration.
machine learning	py-datasets	2.18.0_py312	Website	Hugging Face Datasets is a library for easily accessing and sharing datasets for Audio, Computer Vision, and Natural Language Processing (NLP) tasks.
machine learning	py-evaluate	0.4.3_py312	Website	Hugging Face Evaluate is a library for easily evaluating machine learning models and datasets.
machine learning	py-huggingface-hub	0.22.1_py312	Website	The huggingface_hub library allows you to interact with the Hugging Face Hub, a machine learning platform for creators and collaborators.
machine learning	py-kaolin	0.15.0_py39 0.17.0_py312	Website	A PyTorch Library for Accelerating 3D Deep Learning Research.
machine learning	py-lightgbm	4.5.0_py312	Website	Python bindings for LIghtGBM
machine learning	py-safetensors	0.4.2_py312	Website	Simple, safe way to store and distribute tensors.
machine learning	py-scikit-learn	0.19.1_py27  0.19.1_py36 0.24.2_py36 1.0.2_py39 1.3.2_py39 1.5.1_py312	Website	Scikit-learn is a free software machine learning library for the Python programming language.
machine learning	py-timm	1.0.12_py312	Website	timm is a library containing SOTA computer vision models, layers, utilities, optimizers, schedulers, data-loaders, augmentations, and training/evaluation scripts.
machine learning	py-tinygrad	0.8.0_py312	Website	tinygrad is a deep learning framework that aims to provide a balance between simplicity and functionality.
machine learning	py-tokenizers	0.15.2_py312	Website	Hugging Face Tokenizers provides an implementation of today’s most used tokenizers, with a focus on performance and versatility.T
machine learning	py-torch-nvidia-apex	23.08_py312	Website	A PyTorch Extension: Tools for easy mixed precision and distributed training in Pytorch.
machine learning	py-torchtune	0.1.1_py312	Website	torchtune is a PyTorch-native library for easily authoring, fine-tuning and experimenting with LLMs.
machine learning	py-transformers	4.39.1_py312	Website	Hugging Face Transformers provides APIs and tools to easily download and train state-of-the-art pretrained models.
machine learning	py-vllm	0.7.0_py312	Website	vLLM is a fast and easy-to-use library for LLM inference and serving.
machine learning	py-xgrammar	0.1.8_py312	Website	XGrammar is open-source solution for flexible, portable, and fast structured generations, aiming at bring flexible zero-overhead structure generation everywhere.
numerical analysis	matlab	R2022b   R2017a  R2017b  R2018a  R2019a  R2020a  R2023b	Website	MATLAB is a multi-paradigm numerical computing environment and proprietary programming language developed by MathWorks.
numerical analysis	octave	4.2.1	Website	GNU Octave is a high-level language primarily intended for numerical computations.
numerical library	arpack	3.5.0 3.7.0  3.9.0	Website	Collection of Fortran77 subroutines designed to solve large scale eigenvalue problems.
numerical library	blis	2.1 2.2.4 3.1.0	Website	BLIS is a portable software framework for instantiating high-performance BLAS-like dense linear algebra libraries.
numerical library	fftw	2.1.5 3.3.6  3.3.8  3.3.9 3.3.10	Website	The Fastest Fourier Transform in the West (FFTW) is a software library for computing discrete Fourier transforms (DFTs).
numerical library	flexiblas	3.1.3	Website	FlexiBLAS is a BLAS and LAPACK wrapper library with runtime exchangeable backends.
numerical library	flint	2.9.0	Website	FLINT is a C library for doing number theory.
numerical library	glpk	4.63	Website	The GLPK (GNU Linear Programming Kit) package is intended for solving large-scale linear programming (LP), mixed integer programming (MIP), and other related problems.
numerical library	gmp	6.1.2 6.2.1	Website	GMP is a free library for arbitrary precision arithmetic, operating on signed integers, rational numbers, and floating-point numbers.
numerical library	gsl	1.16 2.3 2.7	Website	The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers. The library provides a wide range of mathematical routines such as random number generators, special functions and least-squares fitting.
numerical library	harminv	1.4.1	Website	harminv is a program designed to solve the problem of harmonic inversion: given a time series consisting of a sum of sinusoids (modes), extract their frequencies and amplitudes.
numerical library	hypre	2.20.0  2.32.0	Website	HYPRE is a library of high performance preconditioners and solvers featuring multigrid methods for the solution of large, sparse linear systems of equations on massively parallel computers.
numerical library	imkl	2017.u2 2018.u1 2018 2019	Website	Intel Math Kernel Library (Intel MKL) is a library of optimized math routines for science, engineering, and financial applications. Core math functions include BLAS, LAPACK, ScaLAPACK, sparse solvers, fast Fourier transforms, and vector math.[3] The routines in MKL are hand-optimized specifically for Intel processors
numerical library	libflame	2.1 2.2.4 3.1.0	Website	libflame is a portable library for dense matrix computations, providing much of the functionality present in LAPACK
numerical library	libxsmm	1.8.1 1.17	Website	LIBXSMM is a library for small dense and small sparse matrix-matrix multiplications as well as for deep learning primitives such as small convolutions
numerical library	metis	5.1.0	Website	METIS is a set of serial programs for partitioning graphs, partitioning finite element meshes, and producing fill reducing orderings for sparse matrices.
numerical library	mpc	1.2.1	Website	GNU MPC is a C library for the arithmetic of complex numbers with arbitrarily high precision and correct rounding of the result.
numerical library	mpfr	3.1.5 4.1.0	Website	The MPFR library is a C library for multiple-precision floating-point computations with correct rounding.
numerical library	mumps	5.1.2	Website	A parallel sparse direct solver.
numerical library	openblas	0.3.10  0.2.19 0.3.4 0.3.9 0.3.20 0.3.26 0.3.28	Website	OpenBLAS is an optimized BLAS library
numerical library	parmetis	4.0.3	Website	ParMETIS is an MPI-based parallel library that implements a variety of algorithms for partitioning unstructured graphs, meshes, and for computing fill-reducing orderings of sparse matrices.
numerical library	petsc	3.10.3  3.18.5	Website	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.
numerical library	py-autograd	1.0_py39	Website	Autograd can automatically differentiate native Python and Numpy code.
numerical library	py-cupy	7.8.0_py36  10.2.0_py39  12.1.0_py39  13.3.0_py312	Website	CuPy is an implementation of NumPy-compatible multi-dimensional array on CUDA.
numerical library	py-gmpy2	2.0.8_py36	Website	gmpy2 is a C-coded Python extension module that supports multiple-precision arithmetic.
numerical library	py-jax	0.4.7_py39 0.4.36_py312	Website	JAX is Autograd and XLA, brought together for high-performance numerical computing.
numerical library	py-jaxlib	0.4.7_py39 0.4.36_py312	Website	XLA library for Jax.
numerical library	py-numpy	1.14.3_py27  1.14.3_py36 1.17.2_py36 1.18.1_py36 1.19.2_py36 1.20.3_py39 1.24.2_py39 1.26.3_py312	Website	NumPy is the fundamental package for scientific computing with Python.
numerical library	py-nvmath-python	0.2.1_py312	Website	NVIDIA Math Libraries for the Python Ecosystem
numerical library	py-petsc4py	3.18.5_py39	Website	Python bindings for PETSc, the Portable, Extensible Toolkit for Scientific Computation.
numerical library	py-psbody-mesh	0.4_py39	Website	The MPI-IS Mesh Processing Library contains core functions for manipulating meshes and visualizing them.
numerical library	py-pyublas	2017.1_py27	Website	PyUblas provides a seamless glue layer between Numpy and Boost.Ublas for use with Boost.Python.
numerical library	py-pywavelets	1.6.0_py39 1.6.0_py312	Website	PyWavelets is a free Open Source library for wavelet transforms in Python.
numerical library	py-scipy	1.1.0_py27  1.1.0_py36 1.4.1_py36 1.6.3_py39 1.10.1_py39 1.12.0_py312	Website	The SciPy library provides many user-friendly and efficient numerical routines such as routines for numerical integration and optimization.
numerical library	py-slepc4py	3.18.2_py39	Website	Python bindings for SLEPc.
numerical library	py-tabmat	3.1.2_py39	Website	Efficient matrix representations for working with tabular data.
numerical library	qrupdate	1.1.2	Website	qrupdate is a Fortran library for fast updates of QR and Cholesky decompositions.
numerical library	scalapack	2.0.2  2.1  2.2.0	Website	ScaLAPACK is a library of high-performance linear algebra routines for parallel distributed memory machines.
numerical library	scotch	6.0.4	Website	Software package and libraries for sequential and parallel graph partitioning, static mapping and clustering, sequential mesh and hypergraph partitioning, and sequential and parallel sparse matrix block ordering.
numerical library	slepc	3.18.2	Website	SLEPc is a Scalable Library for Eigenvalue Problem Computations.
numerical library	suitesparse	7.4.0	Website	SuiteSparse is a suite of sparse matrix algorithms.
numerical library	superlu	5.2.1	Website	SuperLU is a general purpose library for the direct solution of large, sparse, nonsymmetric systems of linear equations.
numerical library	tetgen	1.6.0	Website	TetGen provides various features to generate good quality and adaptive tetrahedral meshes suitable for numerical methods, such as finite element or finite volume methods.
numerical library	xblas	1.0.248	Website	Extra precise basic linear algebra subroutines.
optimization	gurobi	7.5.1 8.0.1_py27 8.0.1_py36 9.0.3_py36 10.0.1_py39 11.0.2	Website	The Gurobi Optimizer is a commercial optimization solver for mathematical programming.
optimization	knitro	10.3.0  12.4.0	Website	Artelys Knitro is an optimization solver for difficult large-scale nonlinear problems.
optimization	nlopt	2.6.2	Website	NLopt is a free/open-source library for nonlinear optimization.
optimization	octeract	3.3.0	Website	Octeract Engine is a proprietary massively parallel deterministic global optimization solver for general Mixed-Integer Nonlinear Programs (MINLP).
optimization	py-optuna	2.10.0_py39	Website	Optuna is an automatic hyperparameter optimization software framework, particularly designed for machine learning.
optimization	sundials	6.4.1	Website	SUNDIALS is a family of software packages providing robust and efficient time integrators and nonlinear solvers that can easily be incorporated into existing simulation codes.
scientific computing	py-scipystack	1.0_py27  1.0_py36	Website	The SciPy Stack is a collection of open source software for scientific computing in Python. It provides the following packages: numpy, scipy, matplotlib, ipython, jupyter, pandas, sympy and nose.
speech analysis	praat	6.4.26	Website	Praat is a speech analysis tool used for doing phonetics by computer.
statistics	datamash	1.3	Website	GNU datamash is a command-line program which performs basic numeric, textual and statistical operations on input textual data files.
statistics	jags	4.3.0 4.3.1	Website	Just another Gibbs sampler (JAGS) is a program for simulation from Bayesian hierarchical models using Markov chain Monte Carlo (MCMC).
statistics	py-emcee	3.1.4_py39	Website	The Python ensemble sampling toolkit for affine-invariant MCMC
statistics	py-glum	2.1.2_py39	Website	glum is a fast, modern, Python-first GLM estimation library.
statistics	py-rpy2	2.8.6_py27 2.9.2_py36	Website	rpy2 is an interface to R running embedded in a Python process.
statistics	R	4.2.0  3.4.0 3.5.1 3.6.1 4.0.2 4.1.2 4.3.2 4.4.2	Website	R is a free software environment for statistical computing and graphics.
statistics	rstudio	1.3.1093  2023.09.1	Website	RStudio is an integrated development environment (IDE) for R. It includes a console, syntax-highlighting editor that supports direct code execution, as well as tools for plotting, history, debugging and workspace management.
statistics	rstudio-desktop	2022.02.2-485	Website	RStudio is an integrated development environment (IDE) for R. It includes a console, syntax-highlighting editor that supports direct code execution, as well as tools for plotting, history, debugging and workspace management. This is the X11/GUI version.
statistics	sas	9.4	Website	SAS is a software suite developed by SAS Institute for advanced analytics, multivariate analyses, business intelligence, data management, and predictive analytics.
statistics	stata	15   14  16  17  18	Website	Stata is a complete, integrated statistical software package that provides everything you need for data analysis, data management, and graphics.
symbolic	libmatheval	1.1.11	Website	GNU libmatheval is a library (callable from C and Fortran) to parse and evaluate symbolic expressions input as text.
symbolic	maxima	5.47.0	Website	Maxima is a system for the manipulation of symbolic and numerical expressions.
symbolic	py-pysr	0.12.3_py39	Website	High-Performance Symbolic Regression in Python and Julia.
symbolic	py-sympy	1.1.1_py27 1.1.1_py36 1.11.1_py39	Website	SymPy is a Python library for symbolic mathematics.
technical computing	mathematica	13.1.0	Website	A symbolic language and platform for modern technical computing.
topic modelling	py-gensim	4.2.0_py39	Website	Gensim is a Python library for topic modelling, document indexing and similarity retrieval with large corpora.

physics#

Field	Module name	Version(s)	URL	Description
astronomy	cfitsio	4.0.0	Website	FITSIO is a library of C and Fortran subroutines for reading and writing data files in FITS (Flexible Image Transport System) data format.
astronomy	heasoft	6.22.1 6.26.1	Website	HEAsoft is a Unified Release of the FTOOLS (General and mission-specific tools to manipulate FITS files) and XANADU (High-level, multi-mission tasks for X-ray astronomical spectral, timing, and imaging data analysis) software packages.
astronomy	py-astropy	4.0.1_py36	Website	The Astropy Project is a community effort to develop a common core package for Astronomy in Python and foster an ecosystem of interoperable astronomy packages.
astronomy	py-lenstools	1.0_py36	Website	This python package collects together a suite of widely used analysis tools in Weak Gravitational Lensing.
astronomy	py-namaster	1.2.2_py36	Website	NaMaster is a C library, Python module and standalone program to compute full-sky angular cross-power spectra of masked fields with arbitrary spin and an arbitrary number of known contaminants using a pseudo-Cl (aka MASTER) approach.
CFD	amr-wind	3.1.5  3.2.0	Website	AMR-Wind is a massively parallel, block-structured adaptive-mesh, incompressible flow solver for wind turbine and wind farm simulations.
CFD	openfast	3.5.4	Website	OpenFAST is a multi-physics, multi-fidelity tool for simulating the coupled dynamic response of wind turbines.
CFD	su2	7.0.3	Website	SU2: An Open-Source Suite for Multiphysics Simulation and Design
climate modeling	cdo	1.9.7.1 2.1.1	Website	CDO is a collection of command line Operators to manipulate and analyse Climate and NWP model Data.
climate modeling	fre-nctools	2022.01	Website	FRE-NCtools is a collection of tools to help with the creation and manipulation of netCDF files used for climate modeling.
geophysics	opensees	2.5.0	Website	OpenSees is a software framework for developing applications to simulate the performance of structural and geotechnical systems subjected to earthquakes.
geoscience	gdal	3.4.1  2.2.1 3.5.2	Website	GDAL is a translator library for raster and vector geospatial data formats.
geoscience	geos	3.6.2  3.11.0 3.12.1 3.13.1	Website	GEOS (Geometry Engine - Open Source) is a C++ port of Java Topology Suite (JTS).
geoscience	geosx	0.2.0-20220523	Website	GEOSX is a simulation framework for modeling coupled flow, transport, and geomechanics in the subsurface.
geoscience	gmtsar	6.2.2	Website	An InSAR processing system based on GMT (Generic Mapping Tools).
geoscience	postgis	3.5.3	Website	PostGIS extends the capabilities of the PostgreSQL relational database by adding support for storing, indexing, and querying geospatial data.
geoscience	proj	8.2.1  4.9.3 9.1.0 9.5.1	Website	PROJ is a generic coordinate transformation software that transforms geospatial coordinates from one coordinate reference system (CRS) to another.
geoscience	py-gdal-utils	3.4.1_py39	Website	gdal-utils is the GDAL Python Utilities distribution.
geoscience	py-opendrift	1.0.3_py27	Website	OpenDrift is a software for modeling the trajectories and fate of objects or substances drifting in the ocean, or even in the atmosphere.
geoscience	py-pyproj	1.9.5.1_py27  1.9.5.1_py36 3.4.0_py39	Website	Python interface to PROJ4 library for cartographic transformations.
geoscience	swash	9.01a	Website	SWASH (an acronym of Simulating WAves till SHore) is a non-hydrostatic wave-flow model.
geoscience	udunits	2.2.26	Website	The UDUNITS package from Unidata is a C-based package for the programatic handling of units of physical quantities.
lib	libgdsii	0.21	Website	libGDSII C++ is a library and command-line utility for reading GDSII geometry files.
magnetism	mumax	3.10	Website	mumax3 is a GPU-accelerated micromagnetic simulation program.
materials science	atat	3.36	Website	Alloy Theoretic Automated Toolkit: a software toolkit for modeling coupled configurational and vibrational disorder in alloy systems.
materials science	py-megnet	1.3.0_py39	Website	The MatErials Graph Network (MEGNet) is an implementation of DeepMind's graph networks[1] for universal machine learning in materials science.
materials science	py-pymatgen	2022.5.26_py39	Website	Pymatgen (Python Materials Genomics) is a robust, open-source Python library for materials analysis.
micromagnetics	oommf	1.2b4	Website	OOMMF is a set of portable, extensible public domain micromagnetic program and associated tools.
particle	openmc	0.10.0	Website	OpenMC is a Monte Carlo particle transport simulation code focused on neutron criticality calculations.
photonics	meep	1.3  1.4.3  1.24.0	Website	Meep is a free finite-difference time-domain (FDTD) simulation software package to model electromagnetic systems.
photonics	mpb	1.5  1.6.2  1.11.1	Website	MPB is a free software package for computing the band structures, or dispersion relations, and electromagnetic modes of periodic dielectric structures, on both serial and parallel computers.
physics-ml	py-nvidia-modulus	0.9.0_py312	Website	NVIDIA Modulus is an open-source framework for building, training, and fine-tuning Physics-ML models with a simple Python interface.
quantum information science	cuquantum	22.03.0.40	Website	NVIDIA cuQuantum is an SDK of optimized libraries and tools for accelerating quantum computing workflows.
quantum information science	py-cuquantum-python	22.3.0_py39	Website	NVIDIA cuQuantum Python provides Python bindings and high-level object-oriented models for accessing the full functionalities of NVIDIA cuQuantum SDK from Python.
quantum mechanics	py-quspin	0.3.5_py36	Website	QuSpin is an open-source Python package for exact diagonalization and quantum dynamics of arbitrary boson, fermion and spin many-body systems.
quantum mechanics	py-qutip	4.5.2_py36	Website	QuTiP is open-source software for simulating the dynamics of closed and open quantum systems.

system#

Field	Module name	Version(s)	URL	Description
assembler	nasm	2.16.03	Website	A cross-platform x86 assembler with an Intel-like syntax.
backup	restic	0.9.5 0.12.1 0.16.3 0.17.0	Website	Fast, secure, efficient backup program.
benchmark	hp2p	3.2	Website	Heavy Peer To Peer: a MPI based benchmark for network diagnostic.
benchmark	mpibench	20190729	Website	Times MPI collectives over a series of message sizes.
benchmark	mprime	29.4	Website	mprime is used by GIMPS, a distributed computing project dedicated to finding new Mersenne prime numbers, and which is commonly used as a stability testing utility.
benchmark	osu-micro-benchmarks	5.6.1  5.7   5.9	Website	The OSU MicroBenchmarks carry out a variety of message passing performance tests using MPI.
benchmark	py-linktest	2.1.19_py39	Website	LinkTest is a communication API benchmarking tool that tests point-to-point connections.
checkpointing	dmtcp	2.6.0	Website	DMTCP (Distributed MultiThreaded Checkpointing) transparently checkpoints a single-host or distributed computation in user-space -- with no modifications to user code or to the O/S.
cloud interface	aws-cli	2.0.50	Website	This package provides a unified command line interface to Amazon Web Services.
cloud interface	google-cloud-sdk	400.0.0 448.0.0	Website	Command-line interface for Google Cloud Platform products and services.
cloud interface	s5cmd	2.0.0	Website	Parallel S3 and local filesystem execution tool.
cloud interface	steampipe	0.14.6	Website	Steampipe is an open source tool for querying cloud APIs in a universal way and reasoning about the data in SQL.
compiler	mrc	1.3.3	Website	MRC is a resource compiler that can create self-contained applications, by including all the required data inside executable files.
compression	c-blosc	1.21.6	Website	A blocking, shuffling and loss-less compression library that can be faster than memcpy().
compression	c-blosc2	2.15.2	Website	A fast, compressed, persistent binary data store library for C.
compression	libarchive	3.3.2 3.4.2 3.5.2	Website	The libarchive project develops a portable, efficient C library that can read and write streaming archives in a variety of formats.
compression	libtar	1.2.20	Website	C library for manipulating tar files.
compression	libzip	1.5.1	Website	libzip is a C library for reading, creating, and modifying zip archives.
compression	lz4	1.8.0	Website	LZ4 is lossless compression algorithm.
compression	lzo	2.10	Website	LZO is a portable lossless data compression library written in ANSI C.
compression	mpibzip2	0.6	Website	MPIBZIP2 is a parallel implementation of the bzip2 block-sorting file compressor that uses MPI and achieves significant speedup on cluster machines.
compression	p7zip	16.02	Website	p7zip is a Linux port of 7zip, a file archiver with high compression ratio.
compression	pbzip2	1.1.12	Website	PBZIP2 is a parallel implementation of the bzip2 block-sorting file compressor that uses pthreads and achieves near-linear speedup on SMP machines.
compression	pigz	2.4	Website	A parallel implementation of gzip for modern multi-processor, multi-core machines.
compression	szip	2.1.1	Website	Szip compression software, providing lossless compression of scientific data, is an implementation of the extended-Rice lossless compression algorithm.
compression	xz	5.2.3	Website	XZ Utils, the successor to LZMA Utils, is free general-purpose data compression software with a high compression ratio.
compression	zlib	1.2.11  1.3.1	Website	zlib is designed to be a free, general-purpose, legally unencumbered -- that is, not covered by any patents -- lossless data-compression library for use on virtually any computer hardware and operating system.
compression	zstd	1.5.2	Website	Zstandard, or zstd, is a fast lossless compression algorithm, targeting real-time compression scenarios at zlib-level and better compression ratios.
containers	libnvidia-container	1.0.0rc2	Website	libnvidia-container is a library and a simple CLI utility to automatically configure GNU/Linux containers leveraging NVIDIA hardware.
containers	proot	5.2.0  5.1.0	Website	PRoot is a user-space implementation of chroot, mount --bind, and binfmt_misc.
containers	py-spython	0.3.13_py39 0.3.13_py312	Website	Singularity Python (spython) is the Python API for working with Singularity containers.
database	bdb	6.2.32	Website	Berkeley DB (BDB) is a software library intended to provide a high-performance embedded database for key/value data.
database	duckdb	1.1.3	Website	DuckDB is an analytical in-process SQL database management system.
database	mariadb	10.2.11  10.6.9	Website	MariaDB is a community-developed fork of the MySQL relational database management system intended to remain free under the GNU GPL.
database	postgresql	10.5 14.5	Website	PostgreSQL is a powerful, open source object-relational database system with a strong focus on reliability, feature robustness, and performance.
database	sqlite	3.18.0 3.37.2 3.44.2	Website	SQLite is a self-contained, high-reliability, embedded, full-featured, public-domain, SQL database engine.
database	sqliteodbc	0.9998	Website	ODBC driver for SQLite
database	unixodbc	2.3.9	Website	unixODBC is an open-source project that implements the ODBC API.
document management	pandoc	2.7.3	Website	Pandoc is a universal document converter.
document processing	ghostscript	9.53.2	Website	Ghostscript is an interpreter for the PostScript language and PDF files.
document processing	groff	1.23.0	Website	groff (GNU roff) is a typesetting system that reads plain text input files that include formatting commands to produce output in PostScript, PDF, HTML, or DVI formats or for display to a terminal.
document processing	lyx	2.3.2	Website	LyX is a document processor.
document processing	poppler	0.47.0	Website	Poppler is a PDF rendering library.
document processing	texinfo	6.6	Website	Texinfo is the official documentation format of the GNU project.
document processing	texlive	2019	Website	TeX Live is an easy way to get up and running with the TeX document production system.
file management	dua-cli	2.20.1	Website	dua (-> Disk Usage Analyzer) is a tool to conveniently learn about the usage of disk space of a given directory.
file management	duc	1.4.4	Website	Duc is a collection of tools for indexing, inspecting and visualizing disk usage.
file management	exa	0.8.0	Website	exa is a replacement for ls written in Rust.
file management	fdupes	2.2.1	Website	FDUPES is a program for identifying or deleting duplicate files residing within specified directories.
file management	fpart	0.9.3	Website	fpart sorts files and packs them into partitions.
file management	midnight-commander	4.8.29	Website	GNU Midnight Commander is a visual file manager.
file management	ncdu	1.18.1  1.15.1 2.2.1	Website	Ncdu is a disk usage analyzer with an ncurses interface.
file management	py-pcircle	0.17_py27	Website	pcircle contains a suite of file system tools developed at OLCF to take advantage of highly scalable parallel file system such as Lustre.
file management	rmlint	2.8.0	Website	rmlint finds space waste and other broken things on your filesystem and offers to remove it.
file management	tdu	1.36	Website	tdu estimates the disk space occupied by all files in a given path.
file transfer	aria2	1.35.0	Website	aria2 is a lightweight multi-protocol & multi-source command-line download utility.
file transfer	aspera-cli	3.9.6	Website	The IBM Aspera Command-Line Interface (the Aspera CLI) is a collection of Aspera tools for performing high-speed, secure data transfers from the command line.
file transfer	lftp	4.8.1	Website	LFTP is a sophisticated file transfer program supporting a number of network protocols (ftp, http, sftp, fish, torrent).
file transfer	mpifileutils	0.10.1  0.11  0.11.1	Website	mpiFileUtils is a suite of MPI-based tools to manage large datasets, which may vary from large directory trees to large files.
file transfer	py-globus-cli	1.2.0 1.9.0_py27 1.9.0_py36 3.2.0_py39 3.8.0_py39 3.19.0_py39	Website	A command line wrapper over the Globus SDK for Python.
file transfer	py-httpie	3.2.1_py39	Website	HTTPie is a command-line HTTP client designed for testing, debugging, and generally interacting with APIs and HTTP servers.
file transfer	rclone	1.55.1 1.59.1 1.65.0	Website	Rclone is a command line program to sync files and directories to and from: Google Drive, Amazon S3, Dropbox, Google Cloud Storage, Amazon Drive, Microsoft One Drive, Hubic, Backblaze B2, Yandex Disk, or the local filesystem.
framework	mono	5.12.0.301 5.20.1.19	Website	Mono is an open source implementation of Microsoft's .NET Framework based on the ECMA standards for C# and the Common Language Runtime.
graphics	lcms2	2.16	Website	Little CMS is an open-source, small-footprint color management engine, with special focus on accuracy and performance.
hardware	hwloc	2.7.0 2.9.3	Website	The Portable Hardware Locality (hwloc) software package provides a portable abstraction of the hierarchical topology of modern architectures.
hardware	libpciaccess	0.16	Website	Generic PCI access library.
job management	slurm-drmaa	1.1.2	Website	DRMAA for Slurm Workload Manager (Slurm) is an implementation of Open Grid Forum Distributed Resource Management Application API (DRMAA) version 1 for submission and control of jobs to Slurm.
language	tcltk	8.6.6	Website	Tcl (Tool Command Language) is a dynamic programming language, suitable for web and desktop applications, networking, administration, testing. Tk is a graphical user interface toolkit.
libs	apr	1.6.3	Website	The Apache Portable Runtime is a supporting library for the Apache web server. It provides a set of APIs that map to the underlying operating system.
libs	apr-util	1.6.1	Website	The Apache Portable Runtime is a supporting library for the Apache web server. It provides a set of APIs that map to the underlying operating system.
libs	atk	2.24.0	Website	ATK is the Accessibility Toolkit. It provides a set of generic interfaces allowing accessibility technologies such as screen readers to interact with a graphical user interface.
libs	benchmark	1.2.0	Website	A microbenchmark support library
libs	cairo	1.14.10	Website	Cairo is a 2D graphics library with support for multiple output devices.
libs	cups	2.2.4	Website	CUPS is the standards-based, open source printing system.
libs	dbus	1.10.22	Website	D-Bus is a message bus system, a simple way for applications to talk to one another.
libs	enchant	1.6.1 2.2.3	Website	Enchant is a library (and command-line program) that wraps a number of different spelling libraries and programs with a consistent interface.
libs	fltk	1.3.4	Website	FLTK (pronounced 'fulltick') is a cross-platform C++ GUI toolkit.
libs	fontconfig	2.12.4	Website	Fontconfig is a library for configuring and customizing font access.
libs	freeglut	3.0.0	Website	FreeGLUT is a free-software/open-source alternative to the OpenGL Utility Toolkit (GLUT) library.
libs	freetype	2.8.1 2.9.1	Website	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).
libs	fribidi	1.0.12	Website	The Free Implementation of the Unicode Bidirectional Algorithm.
libs	ftgl	2.1.2	Website	FTGL is a free cross-platform Open Source C++ library that uses Freetype2 to simplify rendering fonts in OpenGL applications.
libs	gc	7.6.0	Website	The Boehm-Demers-Weiser conservative garbage collector can be used as a garbage collecting replacement for C malloc or C++ new.
libs	gconf	2.9.91	Website	GConf is a system for storing application preferences.
libs	gdk-pixbuf	2.36.8	Website	The GdkPixbuf library provides facilities for loading images in a variety of file formats.
libs	gflags	2.2.1 2.2.2	Website	The gflags package contains a C++ library that implements commandline flags processing.
libs	giflib	5.1.4	Website	GIFLIB is a package of portable tools and library routines for working with GIF images.
libs	glib	2.52.3	Website	The GLib library provides core non-graphical functionality such as high level data types, Unicode manipulation, and an object and type system to C programs.
libs	glog	0.3.5	Website	C++ implementation of the Google logging module.
libs	gnutls	3.5.9	Website	GnuTLS is a secure communications library implementing the SSL, TLS and DTLS protocols and technologies around them.
libs	gobject-introspection	1.52.1	Website	GObject introspection is a middleware layer between C libraries (using GObject) and language bindings.
libs	googletest	1.8.0	Website	Google Test is Google's C++ test framework.
libs	gstreamer	1.12.0	Website	GStreamer is a library for constructing graphs of media-handling components.
libs	gtk+	2.24.30 3.22.18	Website	GTK+, or the GIMP Toolkit, is a multi-platform toolkit for creating graphical user interfaces.
libs	harfbuzz	1.4.8	Website	HarfBuzz is an OpenType text shaping engine.
libs	hunspell	1.6.2	Website	Hunspell is a spell checker.
libs	hyphen	2.8.8	Website	Hyphen is a hyphenation library to use converted TeX hyphenation patterns.
libs	icu	59.1	Website	ICU is a set of C/C++ and Java libraries providing Unicode and Globalization support for software applications.
libs	jansson	2.13.1	Website	C library for encoding, decoding and manipulating JSON data.
libs	jemalloc	5.3.0	Website	jemalloc is a general purpose malloc(3) implementation that emphasizes fragmentation avoidance and scalable concurrency support.
libs	json-glib	1.4.4	Website	JSON-GLib is a library providing serialization and deserialization support for the JavaScript Object Notation (JSON) format described by RFC 4627.
libs	leptonica	1.82.0	Website	Leptonica is an open source library containing software that is broadly useful for image processing and image analysis applications.
libs	libaio	0.3.111	Website	libaio provides the Linux-native API for async I/O.
libs	libart_lgpl	2.3.21	Website	Libart is a library for high-performance 2D graphics.
libs	libcroco	0.6.13	Website	Libcroco is a standalone css2 parsing and manipulation library.
libs	libepoxy	1.4.1	Website	Epoxy is a library for handling OpenGL function pointer management for you.
libs	libexif	0.6.21	Website	A library for parsing, editing, and saving EXIF data.
libs	libffi	3.2.1	Website	libffi is a portable Foreign Function Interface library.
libs	libgcrypt	1.8.2	Website	Libgcrypt is a general purpose cryptographic library originally based on code from GnuPG.
libs	libgd	2.2.5	Website	GD is an open source code library for the dynamic creation of images by programmers.
libs	libgdiplus	5.6	Website	C-based implementation of the GDI+ API
libs	libglvnd	1.2.0	Website	libglvnd is a vendor-neutral dispatch layer for arbitrating OpenGL API calls between multiple vendors.
libs	libgnomecanvas	2.30.3	Website	Library for the GNOME canvas, an engine for structured graphics that offers a rich imaging model, high performance rendering, and a powerful, high-level API.
libs	libgpg-error	1.27	Website	Libgpg-error is a small library that originally defined common error values for all GnuPG components.
libs	libiconv	1.16	Website	libiconv is a conversion library for string encoding.
libs	libidl	0.8.14	Website	The libIDL package contains libraries for Interface Definition Language files. This is a specification for defining portable interfaces.
libs	libidn	2.3.7	Website	GNU Libidn is a fully documented implementation of the Stringprep, Punycode and IDNA 2003 specifications.
libs	libjpeg-turbo	1.5.1  2.1.4	Website	libjpeg-turbo is a JPEG image codec that uses SIMD instructions (MMX, SSE2, AVX2, NEON, AltiVec) to accelerate baseline JPEG compression and decompression on x86, x86-64, ARM, and PowerPC systems
libs	libmetalink	0.1.3	Website	Libmetalink is a library to read Metalink XML download description format.
libs	libmng	2.0.3	Website	THE reference library for reading, displaying, writing and examining Multiple-Image Network Graphics. MNG is the animation extension to the popular PNG image-format.
libs	libpng	1.2.57 1.6.29 1.6.44	Website	libpng is the official PNG reference library. It supports almost all PNG features, is extensible, and has been extensively tested for over 20 years.
libs	libproxy	0.4.15	Website	libproxy is a library that provides automatic proxy configuration management.
libs	libressl	2.5.3 3.2.1	Website	LibreSSL is a version of the TLS/crypto stack forked from OpenSSL in 2014, with goals of modernizing the codebase, improving security, and applying best practice development processes.
libs	librsvg	2.36.4	Website	Librsvg is a library to render SVG files using cairo as a rendering engine.
libs	libseccomp	2.3.3	Website	The libseccomp library provides an easy to use, platform independent, interface to the Linux Kernel's syscall filtering mechanism..
libs	libsodium	1.0.18	Website	Sodium is a modern, easy-to-use software library for encryption, decryption, signatures, password hashing and more.
libs	libsoup	2.61.2	Website	libsoup is an HTTP client/server library for GNOME.
libs	libtasn1	4.13	Website	Libtasn1 is the ASN.1 library used by GnuTLS, p11-kit and some other packages.
libs	libtiff	4.0.8  4.4.0 4.5.0	Website	libtiff provides support for the Tag Image File Format (TIFF), a widely used format for storing image data.
libs	libtool	2.4.7	Website	GNU Libtool is a generic library support script that hides the complexity of using shared libraries behind a consistent, portable interface.
libs	libunistring	0.9.7	Website	Libunistring provides functions for manipulating Unicode strings and for manipulating C strings according to the Unicode standard.
libs	libuuid	1.0.3	Website	Portable uuid C library.
libs	libuv	1.38.1	Website	libuv is a multi-platform support library with a focus on asynchronous I/O.
libs	libwebp	0.6.1	Website	WebP is a modern image format that provides superior lossless and lossy compression for images on the web.
libs	libxkbcommon	0.9.1	Website	libxkbcommon is a keyboard keymap compiler and support library which processes a reduced subset of keymaps as defined by the XKB (X Keyboard Extension) specification.
libs	libxml2	2.9.4	Website	Libxml2 is a XML C parser and toolkit.
libs	libxslt	1.1.32	Website	Libxslt is the XSLT C library developed for the GNOME project. XSLT itself is a an XML language to define transformation for XML.
libs	mesa	17.1.6	Website	Mesa is an open-source implementation of the OpenGL, Vulkan and other specifications.
libs	minipmi	1.0	Website	Implementation of a minimal subset of the PMI1 and PMI2 specifications.
libs	ncurses	6.0 6.4	Website	The ncurses (new curses) library is a free software emulation of curses in System V Release 4.0 (SVr4), and more.
libs	nettle	3.3	Website	Nettle is a cryptographic library that is designed to fit easily in more or less any context.
libs	openjpeg	2.3.1 2.5.3	Website	OpenJPEG is an open-source JPEG 2000 codec written in C language.
libs	openssl	3.0.7	Website	OpenSSL is a full-featured toolkit for general-purpose cryptography and secure communication.
libs	orbit	2.14.19	Website	ORBit2 is a CORBA 2.4-compliant Object Request Broker (ORB) featuring mature C, C++ and Python bindings.
libs	pango	1.40.10	Website	Pango is a library for laying out and rendering of text, with an emphasis on internationalization.
libs	pcre	8.40	Website	The PCRE library is a set of functions that implement regular expression pattern matching using the same syntax and semantics as Perl 5.
libs	pcre2	10.35 10.40	Website	The PCRE22 library is a set of functions that implement regular expression pattern matching using the same syntax and semantics as Perl 5.
libs	popt	1.16	Website	Library for parsing command line options.
libs	py-lmdb	0.93	Website	Universal Python binding for the LMDB 'Lightning' Database.
libs	py-mako	1.0.7_py27  1.0.7_py36	Website	Mako is a template library written in Python. It provides a familiar, non-XML syntax which compiles into Python modules for maximum performance.
libs	py-pygobject	3.32.2_py36	Website	PyGObject is a Python package which provides bindings for GObject based libraries such as GTK, GStreamer, WebKitGTK, GLib, GIO and many more.
libs	py-pyopengl	3.1.5_py39	Website	Standard OpenGL bindings for Python.
libs	py-pyqt5	5.9.1_py36	Website	PyQt5 is a comprehensive set of Python bindings for Qt v5.
libs	readline	7.0 8.2	Website	The GNU Readline library provides a set of functions for use by applications that allow users to edit command lines as they are typed in.
libs	serf	1.3.9	Website	The serf library is a high performance C-based HTTP client library built upon the Apache Portable Runtime (APR) library.
libs	sionlib	1.7.7	Website	Scalable I/O library for parallel access to task-local files.
libs	snappy	1.1.7	Website	A fast compressor/decompressor.
libs	talloc	2.1.14	Website	talloc is a hierarchical, reference counted memory pool system with destructors.
libs	tesseract	5.1.0	Website	Tesseract is an open source text recognition (OCR) Engine.
libs	utf8proc	2.4.0	Website	iutf8proc is a small, clean C library that provides Unicode normalization, case-folding, and other operations for data in the UTF-8 encoding.
libs	webkitgtk	2.28.4	Website	WebKitGTK is a full-featured port of the WebKit rendering engine, suitable for projects requiring any kind of web integration, from hybrid HTML/CSS applications to full-fledged web browsers.
libs	wxwidgets	3.0.4	Website	wxWidgets is a C++ library that lets developers create applications for Windows, macOS, Linux and other platforms with a single code base.
libs	yaml-cpp	0.7.0	Website	yaml-cpp is a YAML parser and emitter in C++ matching the YAML 1.2 spec.
media	ffmpeg	4.0 4.2.1 5.0 7.1	Website	FFmpeg is the leading multimedia framework, able to decode, encode, transcode, mux, demux, stream, filter and play pretty much anything that humans and machines have created.
media	flac	1.4.3	Website	FLAC is the Free Lossless Audio Codec
media	lame	3.100	Website	LAME is a high quality MPEG Audio Layer III (MP3) encoder licensed under the LGPL.
media	libogg	1.3.5	Website	OGG media container.
media	libsndfile	1.0.28	Website	Libsndfile is a C library for reading and writing files containing sampled sound (such as MS Windows WAV and the Apple/SGI AIFF format) through one standard library interface.
media	libvorbis	1.3.7	Website	Ogg Vorbis is a fully open, non-proprietary, patent-and-royalty-free, general-purpose compressed audio format.
media	portaudio	19.7.0	Website	PortAudio is a free, cross-platform, open-source, audio I/O library.
media	sox	14.4.2	Website	SoX, Swiss Army knife of sound processing.
media	wavpack	5.7.0	Website	WavPack is a completely open audio compression format providing lossless, high-quality lossy, and a unique hybrid compression mode.
performance	likwid	4.3.2 5.2.1	Website	Likwid is a simple toolsuite of command line applications for performance oriented programmers.
resource monitoring	nvtop	1.1.0  2.0.3  3.0.2	Website	Nvtop stands for NVidia TOP, a (h)top like task monitor for NVIDIA GPUs.
resource monitoring	py-nvitop	1.3.2_py39   1.3.2_py312	Website	An interactive NVIDIA-GPU process viewer and beyond.
resource monitoring	remora	1.8.5	Website	Remora is a tool to monitor runtime resource utilization.
resource monitoring	ruse	2.0	Website	A command line tool to measure process resource usage.
scm	gh	2.49.2	Website	gh is GitHub on the command line. It brings pull requests, issues, and other GitHub concepts to the terminal next to where you are already working with git and your code.
scm	git	2.45.1	Website	Git is a free and open source distributed version control system designed to handle everything from small to very large projects with speed and efficiency.
scm	git-annex	8.20210622	Website	git-annex allows managing files with git, without checking the file contents into git.
scm	git-credential-manager	2.0.696	Website	Secure, cross-platform Git credential storage with authentication to GitHub, Azure Repos, and other popular Git hosting services.
scm	git-lfs	2.4.0	Website	Git Large File Storage (LFS) replaces large files such as audio samples, videos, datasets, and graphics with text pointers inside Git, while storing the file contents on a remote server.
scm	libgit2	1.1.0	Website	libgit2 is a portable, pure C implementation of the Git core methods provided as a re-entrant linkable library with a solid API
scm	mercurial	4.5.3	Website	Mercurial is a free, distributed source control management tool.
scm	py-dvc	0.91.1_py36	Website	Data Version Control or DVC is an open-source tool for data science and machine learning projects.
scm	subversion	1.9.7 1.12.2	Website	Subversion is an open source version control system.
shell	powershell	7.1.5	Website	PowerShell Core is a cross-platform automation and configuration tool/framework.
testing	py-pytest	7.1.3_py39	Website	pytest is a full-featured Python testing framework
tools	clinfo	2.2.18.04.06	Website	clinfo is a simple command-line application that enumerates all possible (known) properties of the OpenCL platform and devices available on the system.
tools	curl	8.4.0	Website	curl is an open source command line tool and library for transferring data with URL syntax.
tools	depot_tools	20200731	Website	Tools for working with Chromium development.
tools	expat	2.2.3	Website	Expat is a stream-oriented XML parser library written in C.
tools	graphicsmagick	1.3.26	Website	GraphicsMagick is the swiss army knife of image processing.
tools	imagemagick	7.0.7-2 7.1.1-43	Website	ImageMagick is a free and open-source software suite for displaying, converting, and editing raster image and vector image files.
tools	jq	1.6	Website	jq is a lightweight and flexible command-line JSON processor.
tools	leveldb	1.20	Website	LevelDB is a fast key-value storage library written at Google that provides an ordered mapping from string keys to string values.
tools	libxcb	1.17.0	Website	The X protocol C-language Binding (XCB) is a replacement for Xlib featuring a small footprint, latency hiding, direct access to the protocol, improved threading support, and extensibility.
tools	lmdb	0.9.21	Website	Symas LMDB is an extraordinarily fast, memory-efficient database we developed for the Symas OpenLDAP Project.
tools	motif	2.3.7	Website	Motif is the toolkit for the Common Desktop Environment.
tools	munge	0.5.16	Website	MUNGE (MUNGE Uid 'N' Gid Emporium) is an authentication service for creating and validating user credentials.
tools	parallel	20180122 20200822	Website	GNU parallel is a shell tool for executing jobs in parallel using one or more computers.
tools	password-store	1.7.4	Website	Simple password manager using gpg and ordinary unix directories.
tools	patchelf	0.17.2 0.18	Website	A small utility to modify the dynamic linker and RPATH of ELF executables.
tools	py-clustershell	1.9.0_py39	Website	ClusterShell is an event-driven open source Python library, designed to run local or distant commands in parallel on server farms or on large Linux clusters.
tools	py-matlab-proxy	0.9.1_py39 0.10.0_py39	Website	matlab-proxy is a Python package which enables you to launch MATLAB and access it from a web browser.
tools	py-nvidia-ml-py	12.550.52_py39  12.550.52_py312  12.560.30_py39  12.560.30_py312	Website	Python bindings to the NVIDIA Management Library.
tools	py-pyside	5.15.2.1_py39	Website	PySide is the official Python module from the Qt for Python project, which provides access to the complete Qt framework.
tools	py-wxpython	4.0.7_py39 4.2.0_py39 4.2.1_py312	Website	wxPython is the cross-platform GUI toolkit for the Python language,
tools	qt	5.9.1  6.4.0	Website	QT is a cross-platform application framework that is used for developing application software that can be run on various software and hardware platforms.
tools	ripgrep	11.0.1	Website	ripgrep recursively searches directories for a regex pattern.
tools	rocksdb	5.7.3	Website	A library that provides an embeddable, persistent key-value store for fast storage.
tools	unifdef	2.12	Website	The unifdef utility selectively processes conditional C preprocessor #if and #ifdef directives.
tools	wget	1.25.0	Website	GNU Wget is a free software package for retrieving files using HTTP, HTTPS, FTP and FTPS, the most widely used Internet protocols.
tools	x11	7.7	Website	The X.Org project provides an open source implementation of the X Window System.
tools	xcb-proto	1.17.0	Website	xcb-proto provides the XML-XCB protocol descriptions that libxcb uses to generate the majority of its code and API.
tools	xcb-util-cursor	0.1.5	Website	The XCB util modules provides a number of libraries which sit on top of libxcb, the core X protocol library, and some of the extension libraries.
tools	xkeyboard-config	2.21	Website	The non-arch keyboard configuration database for X Window.