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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.


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 448 software modules, in 7 categories, covering 78 fields of science:

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

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

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

  • math computational geometry, deep learning, linear algebra, machine learning, numerical analysis, numerical library, optimization, scientific computing, statistics, symbolic

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

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


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
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
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
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
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
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
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
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
Website BCFtools is a program for variant calling and manipulating files in the Variant Call Format (VCF) and its binary counterpart BCF.
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
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
Website Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences.
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 cufflinks 2.2.1
Website Cufflinks assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples.
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
Website GATK (Genome Analysis Toolkit) offers a wide variety of tools with a primary focus on variant discovery and genotyping.
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
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
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
Website MiXCR is a universal framework that processes big immunome data from raw sequences to quantitated clonotypes.
genomics ncbi-blast+ 2.6.0
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 plink 1.07
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 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
Website Tools for manipulating biological data, particularly multiple sequence alignments.
genomics py-cutadapt 1.18_py27
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-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-macs2 2.1.1_py27
Website MACS (Model-based Analysis of ChIP-Seq) implements a novel ChIP-Seq analysis method.
genomics py-mageck
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
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-pybedtools 0.8.0_py27
Website Pybedtools wraps and extends BEDTools and offers feature-level manipulations from within Python.
genomics py-pysam 0.14.1_py27
Website Pysam is a python module for reading, manipulating and writing genomic data sets.
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
Website Tools (written in C using htslib) for manipulating next-generation sequencing data.
genomics sentieon 201808.01
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
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
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
Website STAR: ultrafast universal RNA-seq aligner.
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
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.
molecular biology coot 0.9.6
Website unixODBC is an open-source project that implements the ODBC API.
neurology afni 17.2.07
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
Website ANTs computes high-dimensional mappings to capture the statistics of brain structure and function.
neurology dcm2niix 1.0.20171215
Website dcm2niix is a program esigned to convert neuroimaging data from the DICOM format to the NIfTI format.
neurology freesurfer 6.0.0
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
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
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
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.


Field Module name Version(s) URL Description
cheminformatics py-rdkit 2018.09.1_py27
Website RDKit is a collection of cheminformatics and machine-learning software written in C++ and Python.
computational chemistry gaussian g16.A03
Website Gaussian is a general purpose computational chemistry software package.
computational chemistry libint 1.1.4
Website Libint computes molecular integrals.
computational chemistry libxc 3.0.0
Website Libxc is a library of exchange-correlation functionals for density-functional theory.
computational chemistry nwchem 6.8
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
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 2017-3
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
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.
electrostatics apbs 1.5
Website APBS solves the equations of continuum electrostatics for large biomolecular assemblages.
molecular dynamics gromacs 2016.3
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
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
Website The QUIP package is a collection of software tools to carry out molecular dynamics simulations.
quantum chemistry cp2k 4.1
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 orca 4.2.1
Website ORCA is a flexible, efficient and easy-to-use general purpose tool for quantum chemistry.
quantum chemistry quantum-espresso 6.2.1
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
Website GPU-accelerated Quantum ESPRESSO using CUDA FORTRAN


Field Module name Version(s) URL Description
build bazel 0.16.1
Website Bazel is a fast, scalable, multi-language and extensible build system.
build bazelisk 1.3.0
Website Bazelisk is a wrapper for Bazel written in Go.
build cmake 3.8.1
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 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
Website SCons is an Open Source software construction tool.
compiler aocc 2.1.0
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
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
Website Intel C++ Compiler, also known as icc or icl, is a group of C and C++ compilers from Intel
compiler ifort 2017.u2
Website Intel Fortran Compiler, also known as ifort, is a group of Fortran compilers from Intel
compiler llvm 3.8.1
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 nagfor npl6a70na
Website The NAG Fortran Compiler is a full standard implementation of the ISO Fortran 95 language with the addition of all of Fortran 2003, most of Fortran 2008 and OpenMP 3.0 and 3.1.
compiler nvhpc 21.5
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
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
Website NCL is a free interpreted language designed specifically for scientific data processing and visualization.
data nco 4.8.0
Website The NCO toolkit manipulates and analyzes data stored in netCDF-accessible formats.
data netcdf
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 pnetcdf 1.8.1
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
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
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
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 analytics hadoop 3.1.0
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
Website Launching and controlling spark on HPC clusters
data analytics spark 2.3.0
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
Website .NET is a free, cross-platform, open source developer platform for building many different types of applications.
language cuda 9.0.176
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 go 1.9
Website Go is an open source programming language that makes it easy to build simple, reliable, and efficient software.
language guile 2.0.11
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
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 1.0.0
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
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
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
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
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
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
Website Python is an interpreted, interactive, object-oriented programming language.
language ruby 2.4.1
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
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
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 cnmem 1.0.0
Website CNMeM is a simple library to help the Deep Learning frameworks manage CUDA memory.
lib cub 1.7.3
Website CUB is a flexible library of cooperative threadblock primitives and other utilities for CUDA kernel programming.
lib cutlass 0.1.0
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 eigen 3.3.3
Website Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms.
lib libctl 3.2.2
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 nccl 1.3.4
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 opencv 3.3.0
Website OpenCV (Open Source Computer Vision Library) is an open source computer vision and machine learning software library.
lib petsc 3.10.3
Website PETSc is a suite of data structures and routines for the scalable (parallel) solution of scientific applications modeled by partial differential equations.
lib py-h5py 2.7.1_py27
Website The h5py package is a Pythonic interface to the HDF5 binary data format.
lib py-netcdf4 1.3.1_py27
Website netcdf4-python is a Python interface to the netCDF C library.
lib py-numba 0.35.0_py27
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-pycuda 2017.1.1_py27
Website PyCUDA lets you access Nvidia‘s CUDA parallel computation API from Python.
lib py-schwimmbad 0.3.1_py36
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
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 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
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 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
Website Mellanox HPC-X toolkit is a comprehensive software package that includes MPI and SHMEM/PGAS communications libraries.
mpi impi 2017.u2
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
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
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
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 ucx 1.3.1
Website UCX is a communication library implementing high-performance messaging for MPI/PGAS frameworks.
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.
runtime starpu 1.3.2
Website StarPU is a unified runtime system that offers support for heterogeneous multicore architectures


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 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.
deep learning caffe2 0.8.1
Website Caffe2 is a deep learning framework that provides an easy and straightforward way to experiment with deep learning and leverage community contributions of new models and algorithms.
deep learning cudnn 6.0
Website NVIDIA cuDNN is a GPU-accelerated library of primitives for deep neural networks.
deep learning cutensor 1.2.0
Website GPU-accelerated tensor linear algebra library.
deep learning py-horovod 0.12.1_py27
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
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
Website ONNX is a open format to represent deep learning models.
deep learning py-pytorch 0.3.0_py27
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 1.12.0_py27
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-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-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
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.
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.
machine learning py-scikit-learn 0.19.1_py27
Website Scikit-learn is a free software machine learning library for the Python programming language.
numerical analysis matlab R2017a
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
Website Collection of Fortran77 subroutines designed to solve large scale eigenvalue problems.
numerical library blis 2.1
Website BLIS is a portable software framework for instantiating high-performance BLAS-like dense linear algebra libraries.
numerical library fftw 2.1.5
Website The Fastest Fourier Transform in the West (FFTW) is a software library for computing discrete Fourier transforms (DFTs).
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
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
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
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
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
Website libflame is a portable library for dense matrix computations, providing much of the functionality present in LAPACK
numerical library libxsmm 1.8.1
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
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 nagdc dcl6i34ngl
Website (Adjoint) Algorithmic Differentiation software tool for computing sensitivities of C++ codes.
numerical library nagfs fsl6i26dcl
Website The NAG Library for SMP & Multicore is based on, and includes, the full functionality of the NAG Fortran Library.
numerical library nagmb MBL6I25DNL
Website The NAG C Library is the largest and most comprehensive collection of mathematical and statistical algorithms for C and C++.
numerical library nagnl nll6i272nl
Website NAG library of numerical algorithms.
numerical library openblas 0.3.4
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 py-cupy 7.8.0_py36
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-numpy 1.14.3_py27
Website NumPy is the fundamental package for scientific computing with Python.
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-scipy 1.1.0_py27
Website The SciPy library provides many user-friendly and efficient numerical routines such as routines for numerical integration and optimization.
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
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 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
Website The Gurobi Optimizer is a commercial optimization solver for mathematical programming.
optimization knitro 10.3.0
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).
scientific computing py-scipystack 1.0_py27
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.
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
Website Just another Gibbs sampler (JAGS) is a program for simulation from Bayesian hierarchical models using Markov chain Monte Carlo (MCMC).
statistics py-rpy2 2.8.6_py27
Website rpy2 is an interface to R running embedded in a Python process.
statistics R 3.5.1
Website R is a free software environment for statistical computing and graphics.
statistics rstudio 1.3.1093
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 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
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 py-sympy 1.1.1_py27
Website SymPy is a Python library for symbolic mathematics.


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
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 1.2.1_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 su2 7.0.3
Website SU2: An Open-Source Suite for Multiphysics Simulation and Design
climate modeling cdo
Website CDO is a collection of command line Operators to manipulate and analyse Climate and NWP model Data.
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 2.2.1
Website GDAL is a translator library for raster and vector geospatial data formats.
geoscience geos 3.6.2
Website GEOS (Geometry Engine - Open Source) is a C++ port of Java Topology Suite (JTS).
geoscience proj 4.9.3
Website proj.4 is a standard UNIX filter function which converts geographic longitude and latitude coordinates into cartesian coordinates (and vice versa.
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
Website Python interface to PROJ4 library for cartographic transformations.
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.
materials science atat 3.36
Website Alloy Theoretic Automated Toolkit: a software toolkit for modeling coupled configurational and vibrational disorder in alloy systems.
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
Website Meep is a free finite-difference time-domain (FDTD) simulation software package to model electromagnetic systems.
photonics mpb 1.5
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.
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.


Field Module name Version(s) URL Description
backup restic 0.9.5
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
Website The OSU MicroBenchmarks carry out a variety of message passing performance tests using MPI.
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 240.0.0
Website Command-line interface for Google Cloud Platform products and services.
compression libarchive 3.3.2
Website The libarchive project develops a portable, efficient C library that can read and write streaming archives in a variety of formats.
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 is free general-purpose data compression software with a high compression ratio.
compression zlib 1.2.11
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.
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 5.1.0
Website PRoot is a user-space implementation of chroot, mount --bind, and binfmt_misc.
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 mariadb 10.2.11
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
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
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 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 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 fpart 0.9.3
Website fpart sorts files and packs them into partitions.
file management ncdu 1.15.1
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 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 gsutil 4.31
Website gsutil is a Python application that lets you access Cloud Storage 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
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
Website A command line wrapper over the Globus SDK for Python.
file transfer rclone 1.39
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
Website Mono is an open source implementation of Microsoft's .NET Framework based on the ECMA standards for C# and the Common Language Runtime.
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
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
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 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
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
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