Software list#

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

Software modules on Sherlock are organized in categories, by scientific field. 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.

Categories#

As of Thursday, January 16 2020, we provide 580 software packages, in 7 categories, covering 68 fields of science:

• viz data, gis, graphs, imaging, molecular visualization, plotting, remote display
• system backup, benchmark, benchmarks, compression, containers, database, doc, document management, document processing, file management, file transfer, framework, language, libs, media, performance, resource monitoring, scm, tools
• math computational geometry, deep learning, linear algebra, machine learning, numerical analysis, numerical library, optimization, scientific computing, statistics, symbolic
• physics astronomy, climate modeling, geophysics, geoscience, materials science, photonics
• biology clinical science, computational biology, cryo-em, genomics, neurology, pathology, phylogenetics
• chemistry cheminformatics, computational chemistry, cristallography, electrostatics, molecular dynamics, quantum chemistry
• devel build, compiler, data, data analytics, debug, framework, language, lib, mpi, networking, parser, runtime, sdk

Viz#

Field	Module name	Version(s)	URL	Description
data	ncview	2.1.7	Website	Ncview is a visual browser for netCDF format files.
gis	panoply	4.10.8	Website	Panoply plots geo-referenced and other arrays from netCDF, HDF, GRIB, and other datasets.
graphs	graphviz	2.40.1	Website	Graphviz is open source graph visualization software.
imaging	py-pillow	5.1.0_py36 5.1.0_py27	Website	Pillow is a friendly PIL (Python Imaging Library) fork.
molecular visualization	pymol	1.8.6.2	Website	PyMOL is a Python-enhanced molecular graphics tool.
plotting	gnuplot	5.2.0	Website	Gnuplot is a portable command-line driven graphing utility for Linux, OS/2, MS Windows, OSX, VMS, and many other platforms.
plotting	grace	5.1.25	Website	Grace is a WYSIWYG tool to make two-dimensional plots of numerical data.
plotting	py-basemap	1.1.0_py36 1.1.0_py27	Website	The matplotlib basemap toolkit is a library for plotting 2D data on maps in Python.
plotting	py-matplotlib	2.1.2_py27 2.1.2_py36 2.2.2_py36 3.1.1_py36 2.2.2_py27	Website	Matplotlib is a Python 2D plotting library which produces publication quality figures in a variety of hardcopy formats and interactive environments across platforms.
plotting	py-plotly	2.4.1_py27	Website	Plotly's Python graphing library makes interactive, publication-quality graphs online.
remote display	virtualgl	2.5.2	Website	VirtualGL is an open source toolkit that gives any Unix or Linux remote display software the ability to run OpenGL applications with full 3D hardware acceleration.

System#

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	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.
benchmarks	mpibench	20190729	Website	Times MPI collectives over a series of message sizes.
benchmarks	osu-micro-benchmarks	5.6.1	Website	The OSU MicroBenchmarks carry out a variety of message passing performance tests using MPI.
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. Usage on Sherlock
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. Usage on Sherlock
database	sqlite	3.18.0	Website	SQLite is a self-contained, high-reliability, embedded, full-featured, public-domain, SQL database engine.
doc	texinfo	6.6	Website	Texinfo is the official documentation format of the GNU project.
document management	pandoc	2.7.3	Website	Pandoc is a universal document converter.
document processing	lyx	2.3.2	Website	LyX is a document processor.
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	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	gdrive	2.1.0	Website	gdrive is a command line utility for interacting with Google Drive.
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	0.9.1 20170210	Website	mpiFileUtils is a suite of MPI-based tools to manage large datasets, which may vary from large directory trees to large files.
file transfer	py-globus-cli	1.2.0 1.9.0_py27 1.9.0_py36	Website	A command line wrapper over the Globus SDK for Python.
file transfer	rclone	1.39 1.43.1 1.49.5	Website	Rclone is a command line program to sync files and directories to and from: Google Drive, Amazon S3, Dropbox, Google Cloud Storage, Amazon Drive, Microsoft One Drive, Hubic, Backblaze B2, Yandex Disk, or the local filesystem.
framework	mono	5.12.0.301 5.20.1.19	Website	Mono is an open source implementation of Microsoft's .NET Framework based on the ECMA standards for C# and the Common Language Runtime.
language	tcltk	8.6.6	Website	Tcl (Tool Command Language) is a dynamic programming language, suitable for web and desktop applications, networking, administration, testing. Tk is a graphical user interface toolkit.
libs	apr	1.6.3	Website	The Apache Portable Runtime is a supporting library for the Apache web server. It provides a set of APIs that map to the underlying operating system.
libs	apr-util	1.6.1	Website	The Apache Portable Runtime is a supporting library for the Apache web server. It provides a set of APIs that map to the underlying operating system.
libs	atk	2.24.0	Website	ATK is the Accessibility Toolkit. It provides a set of generic interfaces allowing accessibility technologies such as screen readers to interact with a graphical user interface.
libs	benchmark	1.2.0	Website	A microbenchmark support library
libs	cairo	1.14.10	Website	Cairo is a 2D graphics library with support for multiple output devices.
libs	cups	2.2.4	Website	CUPS is the standards-based, open source printing system.
libs	dbus	1.10.22	Website	D-Bus is a message bus system, a simple way for applications to talk to one another.
libs	enchant	1.6.1 2.2.3	Website	Enchant is a library (and command-line program) that wraps a number of different spelling libraries and programs with a consistent interface.
libs	fltk	1.3.4	Website	FLTK (pronounced 'fulltick') is a cross-platform C++ GUI toolkit.
libs	fontconfig	2.12.4	Website	Fontconfig is a library for configuring and customizing font access.
libs	freeglut	3.0.0	Website	FreeGLUT is a free-software/open-source alternative to the OpenGL Utility Toolkit (GLUT) library.
libs	freetype	2.8 2.9.1	Website	FreeType is a software font engine that is designed to be small, efficient, highly customizable, and portable while capable of producing high-quality output (glyph images).
libs	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	gtk+	2.24.30 3.22.18	Website	GTK+, or the GIMP Toolkit, is a multi-platform toolkit for creating graphical user interfaces.
libs	harfbuzz	1.4.8	Website	HarfBuzz is an OpenType text shaping engine.
libs	hunspell	1.6.2	Website	Hunspell is a spell checker.
libs	hyphen	2.8.8	Website	Hyphen is a hyphenation library to use converted TeX hyphenation patterns.
libs	icu	59.1	Website	ICU is a set of C/C++ and Java libraries providing Unicode and Globalization support for software applications.
libs	json-glib	1.4.4	Website	JSON-GLib is a library providing serialization and deserialization support for the JavaScript Object Notation (JSON) format described by RFC 4627.
libs	libaio	0.3.111	Website	libaio provides the Linux-native API for async I/O.
libs	libepoxy	1.4.1	Website	Epoxy is a library for handling OpenGL function pointer management for you.
libs	libexif	0.6.21	Website	A library for parsing, editing, and saving EXIF data.
libs	libffi	3.2.1	Website	libffi is a portable Foreign Function Interface library.
libs	libgcrypt	1.8.2	Website	Libgcrypt is a general purpose cryptographic library originally based on code from GnuPG.
libs	libgd	2.2.5	Website	GD is an open source code library for the dynamic creation of images by programmers.
libs	libgdiplus	5.6	Website	C-based implementation of the GDI+ API
libs	libgpg-error	1.27	Website	Libgpg-error is a small library that originally defined common error values for all GnuPG components.
libs	libidl	0.8.14	Website	The libIDL package contains libraries for Interface Definition Language files. This is a specification for defining portable interfaces.
libs	libjpeg-turbo	1.5.1	Website	libjpeg-turbo is a JPEG image codec that uses SIMD instructions (MMX, SSE2, AVX2, NEON, AltiVec) to accelerate baseline JPEG compression and decompression on x86, x86-64, ARM, and PowerPC systems
libs	libmng	2.0.3	Website	THE reference library for reading, displaying, writing and examining Multiple-Image Network Graphics. MNG is the animation extension to the popular PNG image-format.
libs	libpng	1.2.57 1.6.29	Website	libpng is the official PNG reference library. It supports almost all PNG features, is extensible, and has been extensively tested for over 20 years.
libs	libproxy	0.4.15	Website	libproxy is a library that provides automatic proxy configuration management.
libs	libressl	2.5.3	Website	LibreSSL is a version of the TLS/crypto stack forked from OpenSSL in 2014, with goals of modernizing the codebase, improving security, and applying best practice development processes.
libs	libseccomp	2.3.3	Website	The libseccomp library provides an easy to use, platform independent, interface to the Linux Kernel's syscall filtering mechanism..
libs	libsoup	2.61.2	Website	libsoup is an HTTP client/server library for GNOME.
libs	libtasn1	4.13	Website	Libtasn1 is the ASN.1 library used by GnuTLS, p11-kit and some other packages.
libs	libtiff	4.0.8	Website	libtiff provides support for the Tag Image File Format (TIFF), a widely used format for storing image data.
libs	libunistring	0.9.7	Website	Libunistring provides functions for manipulating Unicode strings and for manipulating C strings according to the Unicode standard.
libs	libuuid	1.0.3	Website	Portable uuid C library.
libs	libwebp	0.6.1	Website	WebP is a modern image format that provides superior lossless and lossy compression for images on the web.
libs	libxml2	2.9.4	Website	Libxml2 is a XML C parser and toolkit.
libs	libxslt	1.1.32	Website	Libxslt is the XSLT C library developed for the GNOME project. XSLT itself is a an XML language to define transformation for XML.
libs	mesa	17.1.6	Website	Mesa is an open-source implementation of the OpenGL, Vulkan and other specifications.
libs	ncurses	6.0	Website	The ncurses (new curses) library is a free software emulation of curses in System V Release 4.0 (SVr4), and more.
libs	nettle	3.3	Website	Nettle is a cryptographic library that is designed to fit easily in more or less any context.
libs	openjpeg	2.3.1	Website	OpenJPEG is an open-source JPEG 2000 codec written in C language.
libs	orbit	2.14.19	Website	ORBit2 is a CORBA 2.4-compliant Object Request Broker (ORB) featuring mature C, C++ and Python bindings.
libs	pango	1.40.10	Website	Pango is a library for laying out and rendering of text, with an emphasis on internationalization.
libs	pcre	8.40	Website	The PCRE library is a set of functions that implement regular expression pattern matching using the same syntax and semantics as Perl 5.
libs	popt	1.16	Website	Library for parsing command line options.
libs	py-lmdb	0.93	Website	Universal Python binding for the LMDB 'Lightning' Database.
libs	py-mako	1.0.7_py36 1.0.7_py27	Website	Mako is a template library written in Python. It provides a familiar, non-XML syntax which compiles into Python modules for maximum performance.
libs	py-pygobject	3.32.2_py36	Website	PyGObject is a Python package which provides bindings for GObject based libraries such as GTK, GStreamer, WebKitGTK, GLib, GIO and many more.
libs	py-pyqt5	5.9.1_py36	Website	PyQt5 is a comprehensive set of Python bindings for Qt v5.
libs	readline	7.0	Website	The GNU Readline library provides a set of functions for use by applications that allow users to edit command lines as they are typed in.
libs	serf	1.3.9	Website	The serf library is a high performance C-based HTTP client library built upon the Apache Portable Runtime (APR) library.
libs	snappy	1.1.7	Website	A fast compressor/decompressor.
libs	talloc	2.1.14	Website	talloc is a hierarchical, reference counted memory pool system with destructors.
libs	utf8proc	2.4.0	Website	iutf8proc is a small, clean C library that provides Unicode normalization, case-folding, and other operations for data in the UTF-8 encoding.
media	ffmpeg	4.0 4.2.1	Website	FFmpeg is the leading multimedia framework, able to decode, encode, transcode, mux, demux, stream, filter and play pretty much anything that humans and machines have created.
media	libsndfile	1.0.28	Website	Libsndfile is a C library for reading and writing files containing sampled sound (such as MS Windows WAV and the Apple/SGI AIFF format) through one standard library interface.
performance	likwid	4.3.2	Website	Likwid is a simple toolsuite of command line applications for performance oriented programmers.
resource monitoring	nvtop	0.2.2 1.0.0	Website	Nvtop stands for NVidia TOP, a (h)top like task monitor for NVIDIA GPUs.
resource monitoring	remora	1.8.2	Website	Remora is a tool to monitor runtime resource utilization.
scm	git	2.12.2	Website	Git is a free and open source distributed version control system designed to handle everything from small to very large projects with speed and efficiency.
scm	git-lfs	2.4.0	Website	Git Large File Storage (LFS) replaces large files such as audio samples, videos, datasets, and graphics with text pointers inside Git, while storing the file contents on a remote server.
scm	mercurial	4.5.3	Website	Mercurial is a free, distributed source control management tool.
scm	subversion	1.9.7 1.12.2	Website	Subversion is an open source version control system.
tools	clinfo	2.2.18.04.06	Website	clinfo is a simple command-line application that enumerates all possible (known) properties of the OpenCL platform and devices available on the system.
tools	curl	7.54.0	Website	curl is an open source command line tool and library for transferring data with URL syntax.
tools	expat	2.2.3	Website	Expat is a stream-oriented XML parser library written in C.
tools	graphicsmagick	1.3.26	Website	GraphicsMagick is the swiss army knife of image processing.
tools	imagemagick	7.0.7-2	Website	ImageMagick is a free and open-source software suite for displaying, converting, and editing raster image and vector image files.
tools	leveldb	1.20	Website	Symas LMDB is an extraordinarily fast, memory-efficient database we developed for the Symas OpenLDAP Project.
tools	lmdb	0.9.21	Website	Symas LMDB is an extraordinarily fast, memory-efficient database we developed for the Symas OpenLDAP Project.
tools	motif	2.3.7	Website	Motif is the toolkit for the Common Desktop Environment.
tools	parallel	20180122	Website	GNU parallel is a shell tool for executing jobs in parallel using one or more computers.
tools	qt	5.9.1	Website	QT is a cross-platform application framework that is used for developing application software that can be run on various software and hardware platforms.
tools	ripgrep	11.0.1	Website	ripgrep recursively searches directories for a regex pattern.
tools	rocksdb	5.7.3	Website	A library that provides an embeddable, persistent key-value store for fast storage.
tools	x11	7.7	Website	The X.Org project provides an open source implementation of the X Window System.
tools	xkeyboard-config	2.21	Website	The non-arch keyboard configuration database for X Window.

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	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	5.1 6.0 7.0.1 7.0.4 7.0.5 7.1.1 7.1.4 7.3.1.20 7.4.1.5 7.6.4	Website	NVIDIA cuDNN is a GPU-accelerated library of primitives for deep neural networks.
deep learning	h2o	3.22.0.1	Website	TensorFlow™ is an open source software library for numerical computation using data flow graphs.
deep learning	py-horovod	0.12.1_py36 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	2.0.8_py27 2.1.5_py36 2.2.4_py27 2.2.4_py36 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	0.2.0_py27 0.2.0_py36 0.3.0_py36 1.0.0_py27 1.0.0_py36 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	1.4.0_py27 1.5.0_py27 1.5.0_py36 1.6.0_py36 1.7.0_py27 1.8.0_py27 1.9.0_py27 1.9.0_py36 1.12.0_py27 1.12.0_py36 2.0.0_py36 1.6.0_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	tensorrt	3.0.1 3.0.4 4.0.1.6 5.0.2.6	Website	NVIDIA TensorRT™ is a high-performance deep learning inference optimizer and runtime that delivers low latency, high-throughput inference for deep learning applications.
deep learning	torch	20180202	Website	Torch is a scientific computing framework with wide support for machine learning algorithms that puts GPUs first.
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_py36 0.19.1_py27	Website	Scikit-learn is a free software machine learning library for the Python programming language.
numerical analysis	matlab	R2017a R2017b R2018a R2019a	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	fftw	3.3.6 3.3.8	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 2.3	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	imkl	2017.u2 2018.u1 2018 2019	Website	Intel Math Kernel Library (Intel MKL) is a library of optimized math routines for science, engineering, and financial applications. Core math functions include BLAS, LAPACK, ScaLAPACK, sparse solvers, fast Fourier transforms, and vector math.[3] The routines in MKL are hand-optimized specifically for Intel processors
numerical library	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	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	nagcl	cll6i26dcl	Website	The NAG C Library is the largest and most comprehensive collection of mathematical and statistical algorithms for C and C++.
numerical library	nagfl	fll6i26dcl	Website	The NAG Fortran Library is the largest and most comprehensive collection of numerical and statistical algorithms in Fortran.
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	openblas	0.2.19 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-numpy	1.14.3_py36 1.17.2_py36 1.14.3_py27	Website	NumPy is the fundamental package for scientific computing with Python.
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_py36 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	xblas	1.0.248	Website	Extra precise basic linear algebra subroutines.
optimization	gurobi	7.5.1 8.0.1_py27 8.0.1_py36	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.
scientific computing	py-scipystack	1.0_py36 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	R	3.4.0 3.6.1 3.5.1	Website	R is a free software environment for statistical computing and graphics. Usage on Sherlock
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 2.9.2_py36	Website	rpy2 is an interface to R running embedded in a Python process.
statistics	r-rstan	2.17.3	Website	RStan is the R interface to Stan, an open-source software for facilitating statistical inference at the frontiers of applied statistics.
statistics	rstudio	1.1.423	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	14 16 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 1.1.1_py36	Website	SymPy is a Python library for symbolic mathematics.

Physics#

Field	Module name	Version(s)	URL	Description
astronomy	heasoft	6.22.1 6.26.1	Website	HEAsoft is a Unified Release of the FTOOLS (General and mission-specific tools to manipulate FITS files) and XANADU (High-level, multi-mission tasks for X-ray astronomical spectral, timing, and imaging data analysis) software packages.
climate modeling	cdo	1.9.7.1	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	1.9.5.1_py36 1.9.5.1_py27	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.
materials science	atat	3.36	Website	Alloy Theoretic Automated Toolkit: a software toolkit for modeling coupled configurational and vibrational disorder in alloy systems.
photonics	meep	1.3 1.4.3	Website	Meep is a free finite-difference time-domain (FDTD) simulation software package to model electromagnetic systems.
photonics	mpb	1.5 1.6.2	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.

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	imp	2.8.0	Website	IMP's broad goal is to contribute to a comprehensive structural characterization of biomolecules ranging in size and complexity from small peptides to large macromolecular assemblies, by integrating data from diverse biochemical and biophysical experiments.
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	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	relion	2.0.3 2.1	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	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	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	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	2.3.4.1	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	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	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	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	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 2.7.1	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 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	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_py36 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-multiqc	1.6_py36 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 0.15.3_py36	Website	Pysam is a python module for reading, manipulating and writing genomic data sets.
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	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	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.
neurology	afni	17.2.07 18.2.04	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	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-caiman	1.4.4_py36	Website	A Python toolbox for large scale Calcium Imaging data Analysis and behavioral analysis.
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_py36 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.

Chemistry#

Field	Module name	Version(s)	URL	Description
cheminformatics	py-rdkit	2018.09.1_py36 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 g16.B01	Website	Gaussian is a general purpose computational chemistry software package.
computational chemistry	libint	1.1.4 2.0.3	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 2018-1 2018-2 2019-2	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.
cristallography	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 2018	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	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

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	cmake	3.8.1 3.11.1 3.13.1	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_py36 3.0.5_py27	Website	SCons is an Open Source software construction tool.
compiler	gcc	7.1.0 7.3.0 8.1.0 9.1.0 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 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	3.8.1 4.0.0 5.0.0 7.0.0	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	npl6a61na	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	pgi	17.4 18.4 19.4	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	1.10.0p1 1.10.2	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	Website	The NCO toolkit manipulates and analyzes data stored in netCDF-accessible formats.
data	netcdf	4.4.1.1	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	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 0.23.0_py36	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_py36 3.6.1_py27 3.6.1_py36 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. Usage on Sherlock
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.
framework	dotnet	2.1.500	Website	.NET is a free, cross-platform, open source developer platform for building many different types of applications.
language	chapel	1.19.0	Website	Chapel is a modern programming language designed for productive parallel computing at scale.
language	cuda	8.0.61 9.1.85 9.2.88 9.2.148 10.0.130 10.1.105 10.1.168 10.2.89 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 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	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	0.6.4 1.0.0 1.1.0 1.2.0	Website	Julia is a high-level, high-performance dynamic programming language for numerical computing. Usage on Sherlock
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	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. Usage on Sherlock
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_py36 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	6.1.0_py36 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_py36 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	3.6.1 2.7.13	Website	Python is an interpreted, interactive, object-oriented programming language. Usage on Sherlock
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 1.69.0	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 4.0.1	Website	libctl is a library for supporting flexible control files in scientific simulations.
lib	libgpuarray	0.7.5	Website	Library to manipulate tensors on the GPU.
lib	nccl	1.3.4 2.0.4 2.1.15 2.2.13 2.3.7 2.4.8	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	2.8.0_py36 2.7.1_py27	Website	The h5py package is a Pythonic interface to the HDF5 binary data format.
lib	py-netcdf4	1.3.1_py36 1.3.1_py27	Website	netcdf4-python is a Python interface to the netCDF C library.
lib	py-numba	0.35.0_py36 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-scikit-image	0.13.0_py27 0.14.0_py27 0.15.0_py27 0.15.0_py36	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 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	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	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 3.0.1 4.0.0 4.0.1 3.1.2	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	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	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	1.2.1 1.4.0 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++.
runtime	starpu	1.3.2	Website	StarPU is a unified runtime system that offers support for heterogeneous multicore architectures
sdk	google-cloud-sdk	240.0.0	Website	Command-line interface for Google Cloud Platform products and services.