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 627 software modules, in 7 categories, covering 99 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, 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, deep learning, graph computing, lib, linear algebra, machine learning, numerical analysis, numerical library, optimization, scientific computing, statistics, symbolic, technical computing, topic modelling

• physics astronomy, CFD, cliemate modeling, climate modeling, geophysics, geoscience, lib, magnetism, materials science, micromagnetics, particle, photonics, 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, hardware, job management, language, libs, media, performance, resource monitoring, scm, shell, testing, tools

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

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	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-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	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	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.
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	openmm	7.1.1	Website	A high performance toolkit for molecular simulation.
molecular dynamics	plumed	2.3.2	Website	PLUMED is an open source library for free energy calculations in molecular systems.
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	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	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	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	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-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	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	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	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	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	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	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-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	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.
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-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	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