Available Modules

Os

Module Description
CentOS The CentOS Project is a community-driven free software effort focused on delivering a robust open source ecosystem. For users, we offer a consistent manageable platform that suits a wide variety of deployments. For open source communities, we offer a solid, predictable base to build upon, along with extensive resources to build, test, release, and maintain their code. We’re also expanding the availability of CentOS images across a number of vendors, providing official images for Amazon, Google, and more. For self-hosted cloud, we also provide a generic cloud-init enabled image. For more information about updates and improvements in CentOS 7, please check out the release notes or the release announcement in the mailing list archive.
Debian Debian is a Unix-like computer operating system that is composed entirely of free software, most of which is under the GNU General Public License and packaged by a group of individuals participating in the Debian Project. The Debian Project was first announced in 1993 by Ian Murdock, Debian 0.01 was released on September 15, 1993, and the first stable release was made in 1996. The Debian stable release branch is the most popular Debian edition for personal computers and network servers, and has been used as a base for many other distributions. The project's work is carried out over the Internet by a team of volunteers guided by the Debian Project Leader and three foundational documents: the Debian Social Contract, the Debian Constitution, and the Debian Free Software Guidelines. New distributions are updated continually, and the next candidate is released after a time-based freeze. As one of the earliest operating systems based on the Linux kernel, it was decided that Debian was to be developed openly and freely distributed in the spirit of the GNU Project. This decision drew the attention and support of the Free Software Foundation, which sponsored the project for one year from November 1994 to November 1995. Upon the ending of the sponsorship, the Debian Project formed the non-profit organisation Software in the Public Interest. While all Debian releases are derived from the GNU Operating System and use the GNU userland and the GNU C Library (glibc), other kernels aside from the Linux kernel are also available, such as those based on BSD kernels and the GNU Hurd microkernel.
Fedora The Fedora Project is a global partnership of free software community members. The Fedora Project is sponsored by Red Hat, which invests in our infrastructure and resources to encourage collaboration and incubate innovative new technologies. Some of these technologies may later be integrated into Red Hat products. They are developed in Fedora and produced under a free and open source license from inception, so other free software communities and projects are free to study, adopt, and modify them. Read an overview to learn more about our mission, our community, our governance, and what makes Fedora unique. You can also learn about our vision and core values — the foundations upon which the project is built. We also have information relating to our user base, and the objectives for our technical work.
Ubuntu Ubuntu is a Debian-based Linux operating system for personal computers, tablets and smartphones, where Ubuntu Touch edition is used. It also runs network servers. That is usually with the Ubuntu Server edition, either on physical or virtual servers (such as on mainframes) or with containers, that is with enterprise-class features. It runs on the most popular architectures, including server-class ARM-based. Ubuntu is published by Canonical Ltd, who offer commercial support. It is based on free software and named after the Southern African philosophy of ubuntu (literally, 'human-ness'), which Canonical Ltd. suggests can be loosely translated as "humanity to others" or "I am what I am because of who we all are". Since Ubuntu 11.04 Natty Narwhal Ubuntu has used Unity as its default user interface for the desktop, but following the release of Ubuntu 17.10 it will move to the GNOME 3 desktop instead, as work on Unity ends. Ubuntu is the most popular operating system running in hosted environments, so–called "clouds", as it is the most popular server Linux distribution. Development of Ubuntu is led by UK-based Canonical Ltd., a company of South African entrepreneur Mark Shuttleworth. Canonical generates revenue through the sale of technical support and other services related to Ubuntu. The Ubuntu project is publicly committed to the principles of open-source software development; people are encouraged to use free software, study how it works, improve upon it, and distribute it.

Bio

Module Description
almost all atom molecular simulation toolkit - is a fast and flexible molecular modeling environment that provides powerful and efficient algorithms for molecular simulation, homology modeling, de novo design and ab-initio calculations.
Amber A set of molecular mechanical force fields for the simulation of biomolecules
BCFtools Samtools is a suite of programs for interacting with high-throughput sequencing data. BCFtools - Reading/writing BCF2/VCF/gVCF files and calling/filtering/summarising SNP and short indel sequence variants
bcl2fastq2 bcl2fastq Conversion Software both demultiplexes data and converts BCL files generated by Illumina sequencing systems to standard FASTQ file formats for downstream analysis.
BWA Burrows-Wheeler Aligner (BWA) is an efficient program that aligns relatively short nucleotide sequences against a long reference sequence such as the human genome.
FastQC FastQC is a quality control application for high throughput sequence data. It reads in sequence data in a variety of formats and can either provide an interactive application to review the results of several different QC checks, or create an HTML based report which can be integrated into a pipeline.
GATK The Genome Analysis Toolkit or GATK is a software package developed at the Broad Institute to analyse next-generation resequencing data. The toolkit offers a wide variety of tools, with a primary focus on variant discovery and genotyping as well as strong emphasis on data quality assurance. Its robust architecture, powerful processing engine and high-performance computing features make it capable of taking on projects of any size.
GROMACS 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.
HTSlib A C library for reading/writing high-throughput sequencing data. This package includes the utilities bgzip and tabix
picard A set of tools (in Java) for working with next generation sequencing data in the BAM format.
PLUMED PLUMED is an open source library for free energy calculations in molecular systems which works together with some of the most popular molecular dynamics engines. Free energy calculations can be performed as a function of many order parameters with a particular focus on biological problems, using state of the art methods such as metadynamics, umbrella sampling and Jarzynski-equation based steered MD. The software, written in C++, can be easily interfaced with both fortran and C/C++ codes.
RELION 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).
SAMtools SAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format.
SnpEff Genetic variant annotation and effect prediction toolbox.
Trimmomatic Trimmomatic performs a variety of useful trimming tasks for illumina paired-end and single ended data.The selection of trimming steps and their associated parameters are supplied on the command line.

Cae

Module Description
Adams  
COMSOL  
deMonNano deMonNano is a software package for density functional theory based tight binding calculations. It is part of the deMon (density of Montréal) suite of programs. The present version of the code of deMon for DFT is now known as deMon2k. This code and general information about deMon are available at http://www.demon-software.com
Digimat  
FreeFem++ FreeFem++ is a partial differential equation solver. It has its own language. freefem scripts can solve multiphysics non linear systems in 2D and 3D. Problems involving PDE (2d, 3d) from several branches of physics such as fluid-structure interactions require interpolations of data on several meshes and their manipulation within one program. FreeFem++ includes a fast 2^d-tree-based interpolation algorithm and a language for the manipulation of data on multiple meshes (as a follow up of bamg (now a part of FreeFem++ ). FreeFem++ is written in C++ and the FreeFem++ language is a C++ idiom. It runs on Macs, Windows, Unix machines. FreeFem++ replaces the older freefem and freefem+.
HyperWorks  
Marc  
OpenFOAM OpenFOAM is a free, open source CFD software package. OpenFOAM has an extensive range of features to solve anything from complex fluid flows involving chemical reactions, turbulence and heat transfer, to solid dynamics and electromagnetics.

Chem

Module Description
ABINIT Abinit is a plane wave pseudopotential code for doing condensed phase electronic structure calculations using DFT.
CP2K CP2K is a freely available (GPL) program, written in Fortran 95, to perform atomistic and molecular simulations of solid state, liquid, molecular and biological systems. It provides a general framework for different methods such as e.g. density functional theory (DFT) using a mixed Gaussian and plane waves approach (GPW), and classical pair and many-body potentials.
LAMMPS LAMMPS is a classical molecular dynamics code, and an acronym for Large-scale Atomic/Molecular Massively Parallel Simulator. Has potentials for solid-state materials (metals, semiconductors) and soft matter (biomolecules, polymers) and coarse-grained or mesoscopic systems. It can be used to model atoms or, more generically, as a parallel particle simulator at the atomic, meso, or continuum scale.
libctl libctl is a free Guile-based library implementing flexible control files for scientific simulations.
Libint Libint library is used to evaluate the traditional (electron repulsion) and certain novel two-body matrix elements (integrals) over Cartesian Gaussian functions used in modern atomic and molecular theory.
libxc Libxc is a library of exchange-correlation functionals for density-functional theory. The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.
Molpro  
NAMD NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems.
NWChem NWChem aims to provide its users with computational chemistry tools that are scalable both in their ability to treat large scientific computational chemistry problems efficiently, and in their use of available parallel computing resources from high-performance parallel supercomputers to conventional workstation clusters. NWChem software can handle: biomolecules, nanostructures, and solid-state; from quantum to classical, and all combinations; Gaussian basis functions or plane-waves; scaling from one to thousands of processors; properties and relativity.
Octopus Octopus is a scientific program aimed at the ab initio virtual experimentation on a hopefully ever-increasing range of system types. Electrons are described quantum-mechanically within density-functional theory (DFT), in its time-dependent form (TDDFT) when doing simulations in time. Nuclei are described classically as point particles. Electron-nucleus interaction is described within the pseudopotential approximation.
OpenBabel Open Babel is a chemical toolbox designed to speak the many languages of chemical data. It's an open, collaborative project allowing anyone to search, convert, analyze, or store data from molecular modeling, chemistry, solid-state materials, biochemistry, or related areas.
ORCA  
PLUMED PLUMED is an open source library for free energy calculations in molecular systems which works together with some of the most popular molecular dynamics engines. Free energy calculations can be performed as a function of many order parameters with a particular focus on biological problems, using state of the art methods such as metadynamics, umbrella sampling and Jarzynski-equation based steered MD. The software, written in C++, can be easily interfaced with both fortran and C/C++ codes.
PYXAID  
QuantumESPRESSO Quantum ESPRESSO is an integrated suite of computer codes for electronic-structure calculations and materials modeling at the nanoscale. It is based on density-functional theory, plane waves, and pseudopotentials (both norm-conserving and ultrasoft).
S4MPLE S4MPLE (Sampler For Multiple Protein-Ligand Entities) is a flexible molecular modeling tool, supporting empirical force field-driven conformational sampling and geometry optimization heuristics using a hybrid genetic algorithm (GA).
Scipion  
xdrfile XTC library

Compiler

Module Description
BerkeleyUPC The goal of the Berkeley UPC compiler group is to develop a portable, high performance implementation of UPC for large-scale multiprocessors, PC clusters, and clusters of shared memory multiprocessors.
Clang C, C++, Objective-C compiler, based on LLVM. Does not include C++ standard library -- use libstdc++ from GCC.
GCC The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, as well as libraries for these languages (libstdc++, libgcj,...).
GCCcore The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, as well as libraries for these languages (libstdc++, libgcj,...).
icc C and C++ compiler from Intel
ifort Fortran compiler from Intel
ispc  
LLVM The LLVM Core libraries provide a modern source- and target-independent optimizer, along with code generation support for many popular CPUs (as well as some less common ones!) These libraries are built around a well specified code representation known as the LLVM intermediate representation ("LLVM IR"). The LLVM Core libraries are well documented, and it is particularly easy to invent your own language (or port an existing compiler) to use LLVM as an optimizer and code generator.
OpenCoarrays OpenCoarrays is an open-source software project for developing, porting and tuning transport layers that support coarray Fortran compilers.
PGI C, C++ and Fortran compilers from The Portland Group - PGI

Data

Module Description
GDAL GDAL is a translator library for raster geospatial data formats that is released under an X/MIT style Open Source license by the Open Source Geospatial Foundation. As a library, it presents a single abstract data model to the calling application for all supported formats. It also comes with a variety of useful commandline utilities for data translation and processing.
h5py HDF5 for Python (h5py) is a general-purpose Python interface to the Hierarchical Data Format library, version 5. HDF5 is a versatile, mature scientific software library designed for the fast, flexible storage of enormous amounts of data.
HDF5 HDF5 is a unique technology suite that makes possible the management of extremely large and complex data collections.
netCDF NetCDF (network Common Data Form) is a set of software libraries and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data.
netCDF-Fortran NetCDF (network Common Data Form) is a set of software libraries and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data.
scikit-learn Scikit-learn integrates machine learning algorithms in the tightly-knit scientific Python world, building upon numpy, scipy, and matplotlib. As a machine-learning module, it provides versatile tools for data mining and analysis in any field of science and engineering. It strives to be simple and efficient, accessible to everybody, and reusable in various contexts.
XML-Parser This is a Perl extension interface to James Clark's XML parser, expat.

Debugger

Module Description
aislinn  
DDT  
Forge Allinea Forge is the complete toolsuite for software development - with everything needed to debug, profile, optimize, edit and build C, C++ and FORTRAN applications on Linux for high performance - from single threads through to complex parallel HPC codes with MPI, OpenMP, threads or CUDA.
PerformanceReports Allinea Performance Reports are the most effective way to characterize and understand the performance of HPC application runs. One single-page HTML report elegantly answers a range of vital questions for any HPC site. - Is this application well-optimized for the system and the processors it is running on? - Does it benefit from running at this scale? - Are there I/O, networking or threading bottlenecks affecting performance? - Which hardware, software or configuration changes can we make to improve performance further. - How much energy did this application use?
TotalView  
Valgrind Valgrind: Debugging and profiling tools

Devel

Module Description
ant 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. The main known usage of Ant is the build of Java applications.
Autoconf Autoconf is an extensible package of M4 macros that produce shell scripts to automatically configure software source code packages. These scripts can adapt the packages to many kinds of UNIX-like systems without manual user intervention. Autoconf creates a configuration script for a package from a template file that lists the operating system features that the package can use, in the form of M4 macro calls.
Automake Automake: GNU Standards-compliant Makefile generator
Autotools This bundle collect the standard GNU build tools: Autoconf, Automake and libtool
Bazel  
Boost Boost provides free peer-reviewed portable C++ source libraries.
CMake CMake, the cross-platform, open-source build system. CMake is a family of tools designed to build, test and package software.
Doxygen Doxygen is a documentation system for C++, C, Java, Objective-C, Python, IDL (Corba and Microsoft flavors), Fortran, VHDL, PHP, C#, and to some extent D.
fontsproto X11 font extension wire protocol
glproto X protocol and ancillary headers
GObject-Introspection GObject introspection is a middleware layer between C libraries (using GObject) and language bindings. The C library can be scanned at compile time and generate a metadata file, in addition to the actual native C library. Then at runtime, language bindings can read this metadata and automatically provide bindings to call into the C library.
gperf GNU gperf is a perfect hash function generator. For a given list of strings, it produces a hash function and hash table, in form of C or C++ code, for looking up a value depending on the input string. The hash function is perfect, which means that the hash table has no collisions, and the hash table lookup needs a single string comparison only.
guile Guile is the GNU Ubiquitous Intelligent Language for Extensions, the official extension language for the GNU operating system.
Guile  
intltool intltool is a set of tools to centralize translation of many different file formats using GNU gettext-compatible PO files.
JUnit A programmer-oriented testing framework for Java.
libICU Binary maven install, Apache Maven is a software project management and comprehension tool. Based on the concept of a project object model (POM), Maven can manage a project's build, reporting and documentation from a central piece of information.
libSM X11 Session Management library, which allows for applications to both manage sessions, and make use of session managers to save and restore their state for later use.
M4 GNU M4 is an implementation of the traditional Unix macro processor. It is mostly SVR4 compatible although it has some extensions (for example, handling more than 9 positional parameters to macros). GNU M4 also has built-in functions for including files, running shell commands, doing arithmetic, etc.
make make-3.82: GNU version of make utility
makedepend The makedepend package contains a C-preprocessor like utility to determine build-time dependencies.
Mako  
Maven Binary maven install, Apache Maven is a software project management and comprehension tool. Based on the concept of a project object model (POM), Maven can manage a project's build, reporting and documentation from a central piece of information.
ncurses The Ncurses (new curses) library is a free software emulation of curses in System V Release 4.0, and more. It uses Terminfo format, supports pads and color and multiple highlights and forms characters and function-key mapping, and has all the other SYSV-curses enhancements over BSD Curses.
PCRE The PCRE library is a set of functions that implement regular expression pattern matching using the same syntax and semantics as Perl 5.
PCRE2 The PCRE library is a set of functions that implement regular expression pattern matching using the same syntax and semantics as Perl 5.
pkg-config pkg-config is a helper tool used when compiling applications and libraries. It helps you insert the correct compiler options on the command line so an application can use gcc -o test test.c pkg-config --libs --cflags glib-2.0 for instance, rather than hard-coding values on where to find glib (or other libraries).
protobuf  
protobuf-python Python Protocol Buffers runtime library.
python-meep Python wrapper for the Meep FDTD solver.
Qt Qt is a comprehensive cross-platform C++ application framework.
Qt5  
renderproto Xrender protocol and ancillary headers
SCons SCons is a software construction tool.
Spack Spack is a package manager for supercomputers, Linux, and macOS. It makes installing scientific software easy. With Spack, you can build a package with multiple versions, configurations, platforms, and compilers, and all of these builds can coexist on the same machine.
Spark Spark is Hadoop MapReduce done in memory
SQLite SQLite: SQL Database Engine in a C Library
squashfs-tools Squashfs is a compressed read-only filesystem for Linux.
SWIG SWIG is a software development tool that connects programs written in C and C++ with a variety of high-level programming languages.
xbitmaps provides bitmaps for x
xcb-proto The X protocol C-language Binding (XCB) is a replacement for Xlib featuring a small footprint, latency hiding, direct access to the protocol, improved threading support, and extensibility.
xextproto XExtProto protocol headers.
xineramaproto X protocol and ancillary headers for xinerama
XKeyboardConfig The non-arch keyboard configuration database for X Window. The goal is to provide the consistent, well-structured, frequently released open source of X keyboard configuration data for X Window System implementations (free, open source and commercial). The project is targeted to XKB-based systems.
xorg-macros X.org macros utilities.
xproto X protocol and ancillary headers
xtrans xtrans includes a number of routines to make X implementations transport-independent; at time of writing, it includes support for UNIX sockets, IPv4, IPv6, and DECnet.

Geo

Module Description
DCW country polygons for GMT
Doris Delft object-oriented radar interferometric software
FEFLOW  
GMT GMT is an open source collection of about 80 command-line tools for manipulating geographic and Cartesian data sets (including filtering, trend fitting, gridding, projecting, etc.) and producing PostScript illustrations ranging from simple x-y plots via contour maps to artificially illuminated surfaces and 3D perspective views; the GMT supplements add another 40 more specialized and discipline-specific tools.
PHREEQC A Computer Program for Speciation, Batch-Reaction, One-Dimensional Transport, and Inverse Geochemical Calculations
PROJ_4 PROJ.4 - Cartographic Projections Library originally written by Gerald Evenden then of the USGS.

Lang

Module Description
Anaconda2 Built to complement the rich, open source Python community, the Anaconda platform provides an enterprise-ready data analytics platform that empowers companies to adopt a modern open data science analytics architecture.
Anaconda3 Built to complement the rich, open source Python community, the Anaconda platform provides an enterprise-ready data analytics platform that empowers companies to adopt a modern open data science analytics architecture.
Bison Bison is a general-purpose parser generator that converts an annotated context-free grammar into a deterministic LR or generalized LR (GLR) parser employing LALR(1) parser tables.
byacc Berkeley Yacc (byacc) is generally conceded to be the best yacc variant available. In contrast to bison, it is written to avoid dependencies upon a particular compiler.
flex Flex (Fast Lexical Analyzer) is a tool for generating scanners. A scanner, sometimes called a tokenizer, is a program which recognizes lexical patterns in text.
Java Java Platform, Standard Edition (Java SE) lets you develop and deploy Java applications on desktops and servers.
libgdiplus An Open Source implementation of the GDI+ API.
Lua  
Mono Mono is an open source implementation of Microsoft's .NET Framework based on the ECMA standards for C# and the Common Language Runtime.
NASM NASM: General-purpose x86 assembler
NodeJS  
OpenCL-builder OpenCL™ is the first open, royalty-free standard for cross-platform, parallel programming of modern processors found in personal computers, servers and handheld/embedded devices. OpenCL (Open Computing Language) greatly improves speed and responsiveness for a wide spectrum of applications in numerous market categories from gaming and entertainment to scientific and medical software. This is builder (formerly runtime) package.
OpenCL-runtime OpenCL™ is the first open, royalty-free standard for cross-platform, parallel programming of modern processors found in personal computers, servers and handheld/embedded devices. OpenCL (Open Computing Language) greatly improves speed and responsiveness for a wide spectrum of applications in numerous market categories from gaming and entertainment to scientific and medical software.
Perl Larry Wall's Practical Extraction and Report Language
Python Python is a programming language that lets you work more quickly and integrate your systems more effectively.
R R is a free software environment for statistical computing and graphics.
Racket Racket is a full-spectrum programming language. It goes beyond Lisp and Scheme with dialects that support objects, types, laziness, and more.
Ruby Ruby is 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.
SIP SIP is a tool that makes it very easy to create Python bindings for C and C++ libraries.
SnuCL An OpenCL Framework for Heterogeneous Clusters
Tcl Tcl (Tool Command Language) is a very powerful but easy to learn dynamic programming language, suitable for a very wide range of uses, including web and desktop applications, networking, administration, testing and many more.

Lib

Module Description
astroid The aim of this module is to provide a common base representation of python source code for projects such as pychecker, pyreverse, pylint… Well, actually the development of this library is essentially governed by pylint’s needs. It used to be called logilab-astng.
Embree Embree is a collection of high-performance ray tracing kernels, developed at Intel.
ETSF_IO A library of F90 routines to read/write the ETSF file format has been written. It is called ETSF_IO and available under LGPL.
FOX FOX is a C++ based Toolkit for developing Graphical User Interfaces easily and effectively. It offers a wide, and growing, collection of Controls, and provides state of the art facilities such as drag and drop, selection, as well as OpenGL widgets for 3D graphical manipulation.
freeglut freeglut is a completely OpenSourced alternative to the OpenGL Utility Toolkit (GLUT) library.
glibc The Glibc package contains the main C library. This library provides the basic routines for allocating memory, searching directories, opening and closing files, reading and writing files, string handling, pattern matching, arithmetic, and so on.
GLM  
isort isort is a Python utility / library to sort imports alphabetically, and automatically separated into sections. It provides a command line utility, Python library and plugins for various editors to quickly sort all your imports.
libdrm Direct Rendering Manager runtime library.
libevent  
libffi The libffi library provides a portable, high level programming interface to various calling conventions. This allows a programmer to call any function specified by a call interface description at run-time.
libfontenc X11 font encoding library
libgd GD is an open source code library for the dynamic creation of images by programmers.
libjpeg-turbo libjpeg-turbo is a fork of the original IJG libjpeg which uses SIMD to accelerate baseline JPEG compression and decompression. libjpeg is a library that implements JPEG image encoding, decoding and transcoding.
libmatheval GNU libmatheval is a library (callable from C and Fortran) to parse and evaluate symbolic expressions input as text.
libMesh The libMesh library provides a framework for the numerical simulation of partial differential equations using arbitrary unstructured discretizations on serial and parallel platforms. A major goal of the library is to provide support for adaptive mesh refinement (AMR) computations in parallel while allowing a research scientist to focus on the physics they are modeling.
libpng libpng is the official PNG reference library
libpthread-stubs The X protocol C-language Binding (XCB) is a replacement for Xlib featuring a small footprint, latency hiding, direct access to the protocol, improved threading support, and extensibility.
libreadline 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. Both Emacs and vi editing modes are available. The Readline library includes additional functions to maintain a list of previously-entered command lines, to recall and perhaps reedit those lines, and perform csh-like history expansion on previous commands.
libsndfile 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.
LIBSVM  
LibTIFF tiff: Library and tools for reading and writing TIFF data files
libtool GNU libtool is a generic library support script. Libtool hides the complexity of using shared libraries behind a consistent, portable interface.
libunistring This library provides functions for manipulating Unicode strings and for manipulating C strings according to the Unicode standard.
libunwind The primary goal of libunwind is to define a portable and efficient C programming interface (API) to determine the call-chain of a program. The API additionally provides the means to manipulate the preserved (callee-saved) state of each call-frame and to resume execution at any point in the call-chain (non-local goto). The API supports both local (same-process) and remote (across-process) operation. As such, the API is useful in a number of applications
libxcb The X protocol C-language Binding (XCB) is a replacement for Xlib featuring a small footprint, latency hiding, direct access to the protocol, improved threading support, and extensibility.
libxml2 Libxml2 is the XML C parser and toolchain developed for the Gnome project (but usable outside of the Gnome platform).
libxslt  
libyaml  
libzip libzip is a C library for reading, creating, and modifying zip archives. Files can be added from data buffers, files, or compressed data copied directly from other zip archives. Changes made without closing the archive can be reverted. The API is documented by man pages.
lxml The lxml XML toolkit is a Pythonic binding for the C libraries libxml2 and libxslt.
MATIO  
mpi4py MPI for Python (mpi4py) provides bindings of the Message Passing Interface (MPI) standard for the Python programming language, allowing any Python program to exploit multiple processors.
nettle  
OpenCoarrays OpenCoarrays is an open-source software project for developing, porting and tuning transport layers that support coarray Fortran compilers.
PROJ Program proj is a standard Unix filter function which converts geographic longitude and latitude coordinates into cartesian coordinates
pylint Pylint is a Python source code analyzer which looks for programming errors, helps enforcing a coding standard and sniffs for some code smells (as defined in Martin Fowler's Refactoring book).
PyYAML PyYAML is a YAML parser and emitter for the Python programming language.
QCA QCA aims to provide a straightforward and cross-platform crypto API, using Qt datatypes and conventions. QCA separates the API from the implementation, using plugins known as Providers
QGIS A Free and Open Source Geographic Information System
Qwt The Qwt library contains GUI Components and utility classes which are primarily useful for programs with a technical background. Beside a framework for 2D plots it provides scales, sliders, dials, compasses, thermometers, wheels and knobs to control or display values, arrays, or ranges of type double.
scipy Test utilities for code working with files and commands
SIONlib SIONlib is a scalable I/O library for parallel access to task-local files. The library not only supports writing and reading binary data to or from several thousands of processors into a single or a small number of physical files, but also provides global open and close functions to access SIONlib files in parallel. This package provides a stripped-down installation of SIONlib for use with performance tools (e.g., Score-P), with renamed symbols to avoid conflicts when an application using SIONlib itself is linked against a tool requiring a different SIONlib version.
snappy  
spatialindex The purpose of this library is to provide: * An extensible framework that will support robust spatial indexing methods. * Support for sophisticated spatial queries. Range, point location, nearest neighbor and k-nearest neighbor as well as parametric queries (defined by spatial constraints) should be easy to deploy and run. * Easy to use interfaces for inserting, deleting and updating information.
SpatiaLite SpatiaLite is an open source library intended to extend the SQLite core to support fully fledged Spatial SQL capabilities.
tbb Intel Threading Building Blocks 4.0 (Intel TBB) is a widely used, award-winning C++ template library for creating reliable, portable, and scalable parallel applications. Use Intel TBB for a simple and rapid way of developing robust task-based parallel applications that scale to available processor cores, are compatible with multiple environments, and are easier to maintain. Intel TBB is the most proficient way to implement future-proof parallel applications that tap into the power and performance of multicore and manycore hardware platforms.
Tensorflow An open-source software library for Machine Intelligence
zlib 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.

Math

Module Description
Eigen  
FIAT The FInite element Automatic Tabulator FIAT supports generation of arbitrary order instances of the Lagrange elements on lines, triangles, and tetrahedra. It is also capable of generating arbitrary order instances of Jacobi-type quadrature rules on the same element shapes.
GEOS GEOS (Geometry Engine - Open Source) is a C++ port of the Java Topology Suite (JTS)
GMP GMP is a free library for arbitrary precision arithmetic, operating on signed integers, rational numbers, and floating point numbers.
h5py HDF5 for Python (h5py) is a general-purpose Python interface to the Hierarchical Data Format library, version 5. HDF5 is a versatile, mature scientific software library designed for the fast, flexible storage of enormous amounts of data.
Harminv Harminv is a free program (and accompanying library) to solve the problem of harmonic inversion - given a discrete-time, finite-length signal that consists of a sum of finitely-many sinusoids (possibly exponentially decaying) in a given bandwidth, it determines the frequencies, decay constants, amplitudes, and phases of those sinusoids.
ISL isl is a library for manipulating sets and relations of integer points bounded by linear constraints.
Keras Keras is a minimalist, highly modular neural networks library, written in Python and capable of running on top of either TensorFlow or Theano.
libcerf libcerf is a self-contained numeric library that provides an efficient and accurate implementation of complex error functions, along with Dawson, Faddeeva, and Voigt functions.
libsmm Library for small matrix multiplies.
libxsmm LIBXSMM is a library for small dense and small sparse matrix-matrix multiplications targeting Intel Architecture (x86).
MATLAB  
METIS METIS is a set of serial programs for partitioning graphs, partitioning finite element meshes, and producing fill reducing orderings for sparse matrices. The algorithms implemented in METIS are based on the multilevel recursive-bisection, multilevel k-way, and multi-constraint partitioning schemes.
MPC  
MPFR The MPFR library is a C library for multiple-precision floating-point computations with correct rounding.
MUMPS  
numpy NumPy is the fundamental package for scientific computing with Python. It contains among other things: a powerful N-dimensional array object, sophisticated (broadcasting) functions, tools for integrating C/C++ and Fortran code, useful linear algebra, Fourier transform, and random number capabilities. Besides its obvious scientific uses, NumPy can also be used as an efficient multi-dimensional container of generic data. Arbitrary data-types can be defined. This allows NumPy to seamlessly and speedily integrate with a wide variety of databases.
Octave GNU Octave is a high-level interpreted language, primarily intended for numerical computations.
ParMETIS 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. ParMETIS extends the functionality provided by METIS and includes routines that are especially suited for parallel AMR computations and large scale numerical simulations. The algorithms implemented in ParMETIS are based on the parallel multilevel k-way graph-partitioning, adaptive repartitioning, and parallel multi-constrained partitioning schemes.
Qhull Qhull computes the convex hull, Delaunay triangulation, Voronoi diagram, halfspace intersection about a point, furthest-site Delaunay triangulation, and furthest-site Voronoi diagram. The source code runs in 2-d, 3-d, 4-d, and higher dimensions. Qhull implements the Quickhull algorithm for computing the convex hull.
ScientificPython ScientificPython is a collection of Python modules for scientific computing. It contains support for geometry, mathematical functions, statistics, physical units, IO, visualization, and parallelization.
scipy Test utilities for code working with files and commands
SCOTCH Software package and libraries for sequential and parallel graph partitioning, static mapping, and sparse matrix block ordering, and sequential mesh and hypergraph partitioning.
sympy SymPy is a Python library for symbolic mathematics. It aims to become a full-featured computer algebra system (CAS) while keeping the code as simple as possible in order to be comprehensible and easily extensible. SymPy is written entirely in Python and does not require any external libraries.
Theano Theano is a Python library that allows you to define, optimize, and evaluate mathematical expressions involving multi-dimensional arrays efficiently.

Mpi

Module Description
impi The Intel(R) MPI Library for Linux* OS is a multi-fabric message passing library based on ANL MPICH2 and OSU MVAPICH2. The Intel MPI Library for Linux OS implements the Message Passing Interface, version 2 (MPI-2) specification.
MPI_NET MPI.NET is a high-performance, easy-to-use implementation of the Message Passing Interface (MPI) for Microsoft's .NET environment
MPICH MPICH v3.x is an open source high-performance MPI 3.0 implementation. It does not support InfiniBand (use MVAPICH2 with InfiniBand devices).
MPT  
MVAPICH2 This is an MPI 3.0 implementation. It is based on MPICH2 and MVICH.
OpenMPI The Open MPI Project is an open source MPI-2 implementation.

Numlib

Module Description
Armadillo Armadillo is an open-source C++ linear algebra library (matrix maths) aiming towards a good balance between speed and ease of use. Integer, floating point and complex numbers are supported, as well as a subset of trigonometric and statistics functions.
arpack-ng ARPACK is a collection of Fortran77 subroutines designed to solve large scale eigenvalue problems.
ATLAS ATLAS (Automatically Tuned Linear Algebra Software) is the application of the AEOS (Automated Empirical Optimization of Software) paradigm, with the present emphasis on the Basic Linear Algebra Subprograms (BLAS), a widely used, performance-critical, linear algebra kernel library.
CGAL  
Clp  
CNTKCustomMKL The default CNTK math library is the Intel Math Kernel Library (Intel MKL). CNTK supports using the Intel MKL via a custom library version (CNTK custom MKL).
FFTW FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) in one or more dimensions, of arbitrary input size, and of both real and complex data.
GSL 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.
Hypre Hypre is a library for solving large, sparse linear systems of equations on massively parallel computers. The problems of interest arise in the simulation codes being developed at LLNL and elsewhere to study physical phenomena in the defense, environmental, energy, and biological sciences.
imkl Intel Math Kernel Library is a library of highly optimized, extensively threaded math routines for science, engineering, and financial applications that require maximum performance. Core math functions include BLAS, LAPACK, ScaLAPACK, Sparse Solvers, Fast Fourier Transforms, Vector Math, and more.
LAPACK LAPACK is written in Fortran90 and provides routines for solving systems of simultaneous linear equations, least-squares solutions of linear systems of equations, eigenvalue problems, and singular value problems.
LAPACKE LAPACKE C Interface to LAPACK header files and library
LIBLINEAR  
MPI-LIBLINEAR MPI LIBLINEAR is an extension of LIBLINEAR on distributed environments. The usage and the data format are the same as LIBLINEAR. It supports L2-regularized logistic regression, L2-regularized logistic regression, L2-regularized L2-loss linear SVM (primal trust-region Newton), L2-regularized L1-loss linear SVM (dual), L2-regularized logistic regression (primal limited common directions), L2-regularized L2-loss linear SVM (primal limited common directions). Module created by the PERMON Team (http://permon.it4i.cz).
NLopt NLopt is a free/open-source library for nonlinear optimization, providing a common interface for a number of different free optimization routines available online as well as original implementations of various other algorithms.
OpenBLAS OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version.
PETSc PETSc, pronounced PET-see (the S is silent), is a suite of data structures and routines for the scalable (parallel) solution of scientific applications modeled by partial differential equations.
PFFT PFFT is a software library for computing massively parallel, fast Fourier transformations on distributed memory architectures. PFFT can be understood as a generalization of FFTW-MPI to multidimensional data decomposition.
qrupdate qrupdate is a Fortran library for fast updates of QR and Cholesky decompositions.
ScaLAPACK The ScaLAPACK (or Scalable LAPACK) library includes a subset of LAPACK routines redesigned for distributed memory MIMD parallel computers.
SLEPc SLEPc (Scalable Library for Eigenvalue Problem Computations) is a software library for the solution of large scale sparse eigenvalue problems on parallel computers. It is an extension of PETSc and can be used for either standard or generalized eigenproblems, with real or complex arithmetic. It can also be used for computing a partial SVD of a large, sparse, rectangular matrix, and to solve quadratic eigenvalue problems.
SuiteSparse SuiteSparse is a collection of libraries manipulate sparse matrices.
Trilinos The Trilinos Project is an effort to develop algorithms and enabling technologies within an object-oriented software framework for the solution of large-scale, complex multi-physics engineering and scientific problems. A unique design feature of Trilinos is its focus on packages.

Perf

Module Description
Advisor Vectorization Optimization and Thread Prototyping - Vectorize & thread code or performance “dies” - Easy workflow + data + tips = faster code faster - Prioritize, Prototype & Predict performance gain
Cube Cube, which is used as performance report explorer for Scalasca and Score-P, is a generic tool for displaying a multi-dimensional performance space consisting of the dimensions (i) performance metric, (ii) call path, and (iii) system resource. Each dimension can be represented as a tree, where non-leaf nodes of the tree can be collapsed or expanded to achieve the desired level of granularity.
ipp Intel Integrated Performance Primitives (Intel IPP) is an extensive library of multicore-ready, highly optimized software functions for multimedia, data processing, and communications applications. Intel IPP offers thousands of optimized functions covering frequently used fundamental algorithms.
MAP  
OPARI2 OPARI2, the successor of Forschungszentrum Juelich's OPARI, is a source-to-source instrumentation tool for OpenMP and hybrid codes. It surrounds OpenMP directives and runtime library calls with calls to the POMP2 measurement interface.
OTF2 The Open Trace Format 2 is a highly scalable, memory efficient event trace data format plus support library. It will become the new standard trace format for Scalasca, Vampir, and Tau and is open for other tools.
PAPI PAPI provides the tool designer and application engineer with a consistent interface and methodology for use of the performance counter hardware found in most major microprocessors. PAPI enables software engineers to see, in near real time, the relation between software performance and processor events. In addition Component PAPI provides access to a collection of components that expose performance measurement opportunites across the hardware and software stack.
perfboost  
perfcatcher  
PerfReports  
PerfSuite  
Vampir The Vampir software tool provides an easy-to-use framework that enables developers to quickly display and analyze arbitrary program behavior at any level of detail. The tool suite implements optimized event analysis algorithms and customizable displays that enable fast and interactive rendering of very complex performance monitoring data.
VampirServer The Vampir software tool provides an easy-to-use framework that enables developers to quickly display and analyze arbitrary program behavior at any level of detail. The tool suite implements optimized event analysis algorithms and customizable displays that enable fast and interactive rendering of very complex performance monitoring data.

Phys

Module Description
ALAMODE ALAMODE is an open source software designed for analyzing lattice anharmonicity and lattice thermal conductivity of solids. By using an external DFT package such as VASP and Quantum ESPRESSO, you can extract harmonic and anharmonic force constants straightforwardly with ALAMODE. Using the calculated anharmonic force constants, you can also estimate lattice thermal conductivity, phonon linewidth, and other anharmonic phonon properties from first principles.
CASMcode CASM (https://github.com/prisms-center/CASMcode) is an open source software package designed to perform first-principles statistical mechanical studies of multi-component crystalline solids. CASM interfaces with first-principles electronic structure codes, automates the construction and parameterization of effective Hamiltonians and subsequently builds highly optimized (kinetic) Monte Carlo codes to predict finite-temperature thermodynamic and kinetic properties. CASM uses group theoretic techniques that take full advantage of crystal symmetry in order to rigorously construct effective Hamiltonians for almost arbitrary degrees of freedom in crystalline solids. This includes cluster expansions for configurational disorder in multi-component solids and lattice-dynamical effective Hamiltonians for vibrational degrees of freedom involved in structural phase transitions.
DynaPhoPy Software to calculate crystal microscopic anharmonic properties from molecular dynamics (MD) using the normal-mode-decomposition technique. These properties include the phonon frequency shifts and linewidths, as well as the renormalized force constanst and thermal properties by using quasiparticle theory. This code includes interfaces for MD outputs from VASP and LAMMPS .PHONOPY code is used to obtain harmonic phonon modes.
Elk An all-electron full-potential linearised augmented-plane wave (FP-LAPW) code with many advanced features. Written originally at Karl-Franzens-Universität Graz as a milestone of the EXCITING EU Research and Training Network, the code is designed to be as simple as possible so that new developments in the field of density functional theory (DFT) can be added quickly and reliably.
LMGC90 LMGC90 is a free and open source software dedicated to multiple physics simulation of discrete material and structures. Module created by Jiri Tomcala from the PERMON Team (http://permon.it4i.cz) and Josef Hrabal from IT4I Supercomputing Services
Meep Meep (or MEEP) is a free finite-difference time-domain (FDTD) simulation software package developed at MIT to model electromagnetic systems.
Netgen Netgen/NGSolve is a high performance multiphysics finite element software. It is widely used to analyze models from solid mechanics, fluid dynamics and electromagnetics. Due to its flexible Python interface new physical equations and solution algorithms can be implemented easily.
phono3py  
phonopy Python is a programming language that lets you work more quickly and integrate your systems more effectively.
Sen2Cor Sen2Cor is a processor for Sentinel-2 Level 2A product generation and formatting; it performs the atmospheric-, terrain and cirrus correction of Top-Of- Atmosphere Level 1C input data. Sen2Cor creates Bottom-Of-Atmosphere, optionally terrain- and cirrus corrected reflectance images; additional, Aerosol Optical Thickness-, Water Vapor-, Scene Classification Maps and Quality Indicators for cloud and snow probabilities. Its output product format is equivalent to the Level 1C User Product: JPEG 2000 images, three different resolutions, 60, 20 and 10 m.
Siesta SIESTA is both a method and its computer program implementation, to perform efficient electronic structure calculations and ab initio molecular dynamics simulations of molecules and solids. This version si compiled with OpenMP and MPI support.
VASP 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. To use VASP, You need academic licenses from University of Wiena. Follow the instructions https://www.vasp.at/index.php/faqs. Then send us please a list of authorized users and their ID for which you need this access. Please use only http://support.it4i.cz/rt. We are responsible to verify your licenses. After succesfull verification You will be granted to use VASP in our enviroment.

System

Module Description
eudev eudev is a fork of systemd-udev with the goal of obtaining better compatibility with existing software such as OpenRC and Upstart, older kernels, various toolchains and anything else required by users and various distributions.
hwloc The Portable Hardware Locality (hwloc) software package provides a portable abstraction (across OS, versions, architectures, ...) of the hierarchical topology of modern architectures, including NUMA memory nodes, sockets, shared caches, cores and simultaneous multithreading. It also gathers various system attributes such as cache and memory information as well as the locality of I/O devices such as network interfaces, InfiniBand HCAs or GPUs. It primarily aims at helping applications with gathering information about modern computing hardware so as to exploit it accordingly and efficiently.
libpciaccess Generic PCI access library.

Toolchain

Module Description
foss GNU Compiler Collection (GCC) based compiler toolchain, including OpenMPI for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK.
GNU Compiler-only toolchain with GCC and binutils.
gompi GNU Compiler Collection (GCC) based compiler toolchain, including OpenMPI for MPI support.
iccifort Intel C, C++ and Fortran compilers
ictce Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & Intel MKL.
iimpi Intel C/C++ and Fortran compilers, alongside Intel MPI.
intel Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & Intel MKL.
iomkl Intel Cluster Toolchain Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MKL & OpenMPI.
iompi  
libc The Glibc package contains the main C library. This library provides the basic routines for allocating memory, searching directories, opening and closing files, reading and writing files, string handling, pattern matching, arithmetic, and so on.
PRACE The PRACE Common Production Environment (PCPE) is a set of software tools and libraries that are planned to be available on all PRACE execution sites. The PCPE also defines a set of environment variables that try to make compilation on all sites as homogeneous and simple as possible.
prace PRACE Common Production Environment (PCPE) Initialisation of the PRACE common production environment. This allows you to assume that the following tools/libraries are available by default in your PATH/environment. * Fortran, C, C++ Compilers * MPI * BLAS, LAPACK, BLACS, ScaLAPACK * FFTW * HDF5, NetCDF The compiler commands on are: * mpif90 - Fortran compiler * mpicc - C compiler * mpicxx - C++ compiler For more information on the PCPE please see the documentation at: http://www.prace-ri.eu/PRACE-Common-Production For help using this system, please see Local User Guide available at: http://prace-ri.eu/Best-Practice-Guide-Anselm-HTML

Tools

Module Description
ANSYS  
APR Apache Portable Runtime (APR) libraries.
APR-util Apache Portable Runtime (APR) util libraries.
Bash Bash is an sh-compatible command language interpreter that executes commands read from the standard input or from a file. Bash also incorporates useful features from the Korn and C shells (ksh and csh).
binutils binutils: GNU binary utilities
bzip2 bzip2 is a freely available, patent free, high-quality data compressor. It typically compresses files to within 10% to 15% of the best available techniques (the PPM family of statistical compressors), whilst being around twice as fast at compression and six times faster at decompression.
ClusterShell  
CORALbenchmark  
cURL libcurl is a free and easy-to-use client-side URL transfer library, supporting DICT, FILE, FTP, FTPS, Gopher, HTTP, HTTPS, IMAP, IMAPS, LDAP, LDAPS, POP3, POP3S, RTMP, RTSP, SCP, SFTP, SMTP, SMTPS, Telnet and TFTP. libcurl supports SSL certificates, HTTP POST, HTTP PUT, FTP uploading, HTTP form based upload, proxies, cookies, user+password authentication (Basic, Digest, NTLM, Negotiate, Kerberos), file transfer resume, http proxy tunneling and more.
DMTCP 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.
EasyBuild EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.
expat Expat is an XML parser library written in C. It is a stream-oriented parser in which an application registers handlers for things the parser might find in the XML document (like start tags)
Ghostscript Ghostscript is a versatile processor for PostScript data with the ability to render PostScript to different targets. It used to be part of the cups printing stack, but is no longer used for that.
git 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.
globus  
GLPK The GLPK (GNU Linear Programming Kit) package is intended for solving large-scale linear programming (LP), mixed integer programming (MIP), and other related problems. It is a set of routines written in ANSI C and organized in the form of a callable library.
Graph500 Reference code of the Graph500 benchmark.
gzip gzip (GNU zip) is a popular data compression program as a replacement for compress
Hadoop  
help2man  
HPL HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the High Performance Computing Linpack Benchmark.
Inspector Intel Inspector XE 2013 is an easy to use memory error checker and thread checker for serial and parallel applications
IOR The IOR software is used for benchmarking parallel file systems using POSIX, MPIIO, or HDF5 interfaces.
itac The Intel Trace Collector is a low-overhead tracing library that performs event-based tracing in applications. The Intel Trace Analyzer provides a convenient way to monitor application activities gathered by the Intel Trace Collector through graphical displays.
JOE JOE is a full featured terminal-based screen editor which is distributed under the GNU General Public License (GPL)
LicenseChecker  
likwid Toolsuite of command line applications for performance oriented programmers
Lmod  
LSMS  
MATLAB  
Mercurial Mercurial is a free, distributed source control management tool. It efficiently handles projects of any size and offers an easy and intuitive interface.
MIKE MIKE Powered by DHI is a part of DHI, the global organisation dedicated to solving challenges in water environments worldwide.
networkx NetworkX is a Python package for the creation, manipulation, and study of the structure, dynamics, and functions of complex networks.
numactl The numactl program allows you to run your application program on specific cpu's and memory nodes. It does this by supplying a NUMA memory policy to the operating system before running your program. The libnuma library provides convenient ways for you to add NUMA memory policies into your own program.
osm2pgsql  
PAPI PAPI provides the tool designer and application engineer with a consistent interface and methodology for use of the performance counter hardware found in most major microprocessors. PAPI enables software engineers to see, in near real time, the relation between software performance and processor events. In addition Component PAPI provides access to a collection of components that expose performance measurement opportunites across the hardware and software stack.
parallel parallel: Build and execute shell commands in parallel
pigz  
QBOX  
QEMU QEMU is a generic and open source machine emulator and virtualizer.
RStudio RStudio is a set of integrated tools designed to help you be more productive with R. It includes a console, syntax-highlighting editor that supports direct code execution, as well as tools for plotting, history, debugging and workspace management.
Scalasca  
Score-P  
SDE Intel Software Development Emulator is a pintool that enables the development of applications using instruction set extensions that are not currently implemented in hardware.
SentinelToolboxes  
Serf The serf library is a high performance C-based HTTP client library built upon the Apache Portable Runtime (APR) library
Singularity  
Subversion Subversion is an open source version control system.
Szip Szip compression software, providing lossless compression of scientific data
Tar tar: The GNU tape archiver
tcsh Tcsh is an enhanced, but completely compatible version of the Berkeley UNIX C shell (csh). It is a command language interpreter usable both as an interactive login shell and a shell script command processor. It includes a command-line editor, programmable word completion, spelling correction, a history mechanism, job control and a C-like syntax.
tmux  
turbovnc TurboVNC is a derivative of VNC (Virtual Network Computing) that is tuned to provide peak performance for 3D and video workloads.
util-linux Set of Linux utilities
VDE2 VDE is an ethernet compliant virtual network that can be spawned over a set of physical computer over the Internet. VDE is part of virtualsquare project.
VirtualGL 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.
VTune Intel VTune Amplifier XE 2016 is the premier performance profiler for C, C++, C#, Fortran, Assembly and Java.
Wine Wine (originally an acronym for "Wine Is Not an Emulator") is a compatibility layer capable of running Windows applications on several POSIX-compliant operating systems, such as Linux, Mac OSX, & BSD.
x86_adapt  
XZ xz: XZ utilities

Vis

Module Description
cairo Cairo is a 2D graphics library with support for multiple output devices. Currently supported output targets include the X Window System (via both Xlib and XCB), Quartz, Win32, image buffers, PostScript, PDF, and SVG file output. Experimental backends include OpenGL, BeOS, OS/2, and DirectFB
ffmpeg A complete, cross-platform solution to record, convert and stream audio and video.
fixesproto X.org FixesProto protocol headers.
FLTK FLTK is a cross-platform C++ GUI toolkit for UNIX/Linux (X11), Microsoft Windows, and MacOS X. FLTK provides modern GUI functionality without the bloat and supports 3D graphics via OpenGL and its built-in GLUT emulation.
fontconfig Fontconfig is a library designed to provide system-wide font configuration, customization and application access.
freetype FreeType 2 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). It can be used in graphics libraries, display servers, font conversion tools, text image generation tools, and many other products as well.
gettext GNU `gettext' is an important step for the GNU Translation Project, as it is an asset on which we may build many other steps. This package offers to programmers, translators, and even users, a well integrated set of tools and documentation
GL2PS GL2PS: an OpenGL to PostScript printing library
GLib GLib is one of the base libraries of the GTK+ project
gnuplot Portable interactive, function plotting utility
GPI-2 GPI-2 is an API for the development of scalable, asynchronous and fault tolerant parallel applications.
grace Grace is a WYSIWYG 2D plotting tool for X Windows System and Motif.
GraphicsMagick GraphicsMagick is the swiss army knife of image processing.
HarfBuzz HarfBuzz is an OpenType text shaping engine.
inputproto X.org InputProto protocol headers.
JasPer The JasPer Project is an open-source initiative to provide a free software-based reference implementation of the codec specified in the JPEG-2000 Part-1 standard.
kbproto X.org KBProto protocol headers.
libepoxy Epoxy is a library for handling OpenGL function pointer management for you
libGLU The OpenGL Utility Library (GLU) is a computer graphics library for OpenGL.
libICE X Inter-Client Exchange library for freedesktop.org
libX11 X11 client-side library
libXau The libXau package contains a library implementing the X11 Authorization Protocol. This is useful for restricting client access to the display.
libXdamage X Damage extension library
libXdmcp The libXdmcp package contains a library implementing the X Display Manager Control Protocol. This is useful for allowing clients to interact with the X Display Manager.
libXext Common X Extensions library
libXfixes X Fixes extension library
libXfont X font libary
libXft X11 client-side library
libXinerama Xinerama multiple monitor library
libXrender X11 client-side library
libXt libXt provides the X Toolkit Intrinsics, an abstract widget library upon which other toolkits are based. Xt is the basis for many toolkits, including the Athena widgets (Xaw), and LessTif (a Motif implementation).
matplotlib matplotlib is a python 2D plotting library which produces publication quality figures in a variety of hardcopy formats and interactive environments across platforms. matplotlib can be used in python scripts, the python and ipython shell, web application servers, and six graphical user interface toolkits.
Mesa Mesa is an open-source implementation of the OpenGL specification - a system for rendering interactive 3D graphics.
motif Motif refers to both a graphical user interface (GUI) specification and the widget toolkit for building applications that follow that specification under the X Window System on Unix and other POSIX-compliant systems. It was the standard toolkit for the Common Desktop Environment and thus for Unix.
OpenCV OpenCV (Open Source Computer Vision Library) is an open source computer vision and machine learning software library. OpenCV was built to provide a common infrastructure for computer vision applications and to accelerate the use of machine perception in the commercial products.
opencv-python Theano is a Python library that allows you to define, optimize, and evaluate mathematical expressions involving multi-dimensional arrays efficiently.
OpenDX Open source visualization software package based on IBM's Visualization Data Explorer.
OSPRay A Ray Tracing Based Rendering Engine for High-Fidelity Visualization
p4vasp p4vasp is a visualization suite for the Vienna Ab-initio Simulation Package (VASP). It contains an extensible GUI framework, that can be used to view material structure, density of states, band-structure and more.
Pango Pango is a library for laying out and rendering of text, with an emphasis on internationalization. Pango can be used anywhere that text layout is needed, though most of the work on Pango so far has been done in the context of the GTK+ widget toolkit. Pango forms the core of text and font handling for GTK+-2.x.
ParaView ParaView is a scientific parallel visualizer.
Pillow Pillow is the 'friendly PIL fork' by Alex Clark and Contributors. PIL is the Python Imaging Library by Fredrik Lundh and Contributors.
pixman Pixman is a low-level software library for pixel manipulation, providing features such as image compositing and trapezoid rasterization. Important users of pixman are the cairo graphics library and the X server.
PyQt PyQt is a set of Python v2 and v3 bindings for Digia's Qt application framework.
scikit-image Scikit-learn integrates machine learning algorithms in the tightly-knit scientific Python world, building upon numpy, scipy, and matplotlib. As a machine-learning module, it provides versatile tools for data mining and analysis in any field of science and engineering. It strives to be simple and efficient, accessible to everybody, and reusable in various contexts.
seekpath SeeK-path is a python module to obtain and visualize band paths in the Brillouin zone of crystal structures. The definition of k-point labels follows crystallographic convention, as defined and discussed in the HPKOT paper. Moreover, the Bravais lattice is detected properly using the spacegroup symmetry. Also the suggested band path provided in the HPKOT paper is returned. Systems without time-reversal and inversion-symmetry are also properly taken into account.
SUMO Simulation of Urban MObility (SUMO) is an open source, highly portable, microscopic and continuous road traffic simulation package designed to handle large road networks.
Tix Tix, the Tk Interface eXtension, is a powerful set of user interface components that expands the capabilities of your Tcl/Tk and Python applications. Using Tix together with Tk will greatly enhance the appearance and functionality of your application.
Tk Tk is an open source, cross-platform widget toolchain that provides a library of basic elements for building a graphical user interface (GUI) in many different programming languages.
Togl A Tcl/Tk widget for OpenGL rendering.
VisIt VisIt is an Open Source, interactive, scalable, visualization, animation and analysis tool
VTK The Visualization Toolkit (VTK) is an open-source, freely available software system for 3D computer graphics, image processing and visualization. VTK consists of a C++ class library and several interpreted interface layers including Tcl/Tk, Java, and Python. VTK supports a wide variety of visualization algorithms including: scalar, vector, tensor, texture, and volumetric methods; and advanced modeling techniques such as: implicit modeling, polygon reduction, mesh smoothing, cutting, contouring, and Delaunay triangulation.
X11  
Xvfb Xvfb is an X server that can run on machines with no display hardware and no physical input devices. It emulates a dumb framebuffer using virtual memory.