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Software list#

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

Permanent work in progress

Software installations on Sherlock are an ever ongoing process. We're continuously adding new software to the list. If you're looking for something that is not in the list, there may be other options.

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Never want to miss a software update again? Stay up-to-date with new software updates by following the Sherlock software update RSS feed.

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 570 software modules, in 7 categories, covering 93 fields of science:

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

  • chemistry cheminformatics, computational chemistry, crystallography, docking, electrostatics, molecular dynamics, quantum chemistry, tools

  • devel build, compiler, data, data analytics, debug, engine, framework, IDE, language, lib, mpi, networking, 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 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

Licensed software

Access to software modules marked with in the tables below is restricted to properly licensed user groups.

SRCC is not funded to provide commercial software on Sherlock and researchers are responsible for the costs of purchasing and renewing commercial software licenses. For more information, please feel free to contact us and see the Stanford Software Licensing page for purchasing information.

Additional flags and features

Some of the modules listed below have been built to support specific architectures or parallel execution modes:

  • versions marked with support GPU acceleration
  • versions marked with support MPI parallel execution
  • versions marked with are the default version for the module

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
Website Biopython is a set of freely available tools for biological computation written in Python.
computational biology rosetta 3.8 
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 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
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 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
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
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 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
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 
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-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
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
Website Pysam is a python module for reading, manipulating and writing genomic data sets.
genomics py-scanpy 1.8.2_py39
Website Scanpy is a scalable toolkit for analyzing single-cell gene expression 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
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 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.
neurology bart 0.7.00 
Website BART is a toolbox for Computational Magnetic Resonance Imaging.
neurology 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.
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.
neurology fsl 5.0.10 
Website FSL is a comprehensive library of analysis tools for FMRI, MRI and DTI brain imaging data.
neurology mricron 20160502
Website MRIcron is a cross-platform NIfTI format image viewer.
neurology 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.
neurology 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.
neurology 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.
neurology 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.
neurology 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   
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   
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  
Website LAMMPS is a classical molecular dynamics code that models an ensemble of particles in a liquid, solid, or gaseous state.
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.
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 
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.

devel#

Field Module name Version(s) URL Description
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
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
12.1.0
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
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  
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 
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
Website Protocol Buffers (a.k.a., protobuf) are Google's language-neutral, platform-neutral, extensible mechanism for serializing structured data.
data py-pandas 0.23.0_py27
0.23.0_py36
1.0.3_py36
1.3.1_py39
2.0.1_py39
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 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-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.
IDE code-server 4.16.1
Website Run VS Code on any machine anywhere and access it in the browser.
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 
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
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 1.3.1
1.4.0
1.5.1
1.6.2
1.7.2
1.8.4
1.9.0
1.10.0
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
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
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
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
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 
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
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
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-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
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 2.0.2 
2.1.1 
3.1.2  
4.0.3  
4.0.5  
4.1.0  
4.1.2  
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 
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 ucx 1.3.1
1.8.1 
1.9.0 
1.10.0 
1.12.1 
Website UCX is a communication library implementing high-performance messaging for MPI/PGAS frameworks.
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
Website Darshan is a scalable HPC I/O characterization tool.
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 
Website NVIDIA cuDNN is a GPU-accelerated library of primitives for deep neural networks.
deep learning cutensor 1.2.0 
1.5.0.3 
Website GPU-accelerated tensor linear algebra library.
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 
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 
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  
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 
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 
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-torchvision 0.15.1_py39
Website Datasets, model architectures, and common image transformations for computer vision for PyTorch.
deep learning py-triton 1.0.0_py39 
Website Triton is a language and compiler for writing highly efficient custom Deep-Learning primitives.
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 
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 
Website OpenCV (Open Source Computer Vision Library) is an open source computer vision and machine learning software 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 cusparselt 0.2.0.1 
Website NVIDIA cuSPARSELt is a high-performance CUDA library for sparse matrix-matrix multiplication.
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
Website Scikit-learn is a free software machine learning library for the Python programming language.
numerical analysis matlab R2017a 
R2017b 
R2018a 
R2019a 
R2020a 
R2022b 
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.
n