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.
bowtie2  
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.
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.

Cae

Module Description
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
OpenFOAM  

Chem

Module Description
ABINIT  
cp2k-mpi  
lammps  
libxc  
molpro  
namd  
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.
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 ORCA is a flexible, efficient and easy-to-use general purpose tool for quantum chemistry with specific emphasis on spectroscopic properties of open-shell molecules. It features a wide variety of standard quantum chemical methods ranging from semiempirical methods to DFT to single- and multireference correlated ab initio methods. It can also treat environmental and relativistic effects.
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.
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).
xdrfile XTC library

Compiler

Module Description
bupc  
chicken  
Clang C, C++, Objective-C compiler, based on LLVM. Does not include C++ standard library -- use libstdc++ from GCC.
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,...). [NOTE: This module does not include Objective-C, Java or Ada]
gupc  
icc C and C++ compiler from Intel
ifort Fortran compiler from Intel
ispc  
java  
LLVM  
OpenCoarrays A transport layer for 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.
HDF5 HDF5 is a unique technology suite that makes possible the management of extremely large and complex data collections.
netCDF  
netCDF-Fortran  
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.

Debugger

Module Description
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?

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.
Caffe Caffe is a deep learning framework made with expression, speed, and modularity in mind. It is developed by the Berkeley Vision and Learning Center (BVLC) and community contributors.
CMake CMake, the cross-platform, open-source build system. CMake is a family of tools designed to build, test and package software.
Doxygen  
fontsproto X11 font extension wire protocol
gflags The gflags package contains a C++ library that implements commandline flags processing. It includes built-in support for standard types such as string and the ability to define flags in the source file in which they are used.
glog A C++ implementation of the Google logging module.
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.
JUnit A programmer-oriented testing framework for Java.
LevelDB LevelDB is a fast key-value storage library written at Google that provides an ordered mapping from string keys to string values.
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.
LMDB OpenLDAP's Lightning Memory-Mapped Database (LMDB) library.
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  
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.
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 Google Protocol Buffers
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.
SQLite SQLite: SQL Database Engine in a C Library
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.
xcb-util  
xcb-util-image  
xcb-util-keysyms  
xcb-util-renderutil  
xcb-util-wm  
xextproto XExtProto protocol headers.
xineramaproto X protocol and ancillary headers for xinerama
xorg-macros X.org macros utilities.
xproto  
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.

Engineering

Module Description
adams  
beopest  
blender  
Code_Saturne  
comsol  
digimat  
Discovery_Studio  
dytran  
fds  
hypermesh  
hyperworks  
lsdyna  
lsprepost  
lux  
marc  
matlab  
maxwell  
modflow-2005  
modflow-nwt  
nastran  
openfoam  
paraview  
pest  
wien2k  

Environments

Module Description
bullxde  
PrgEnv-gnu  
PrgEnv-intel  

Geo

Module Description
Doris Delft object-oriented radar interferometric software
PHREEQC A Computer Program for Speciation, Batch-Reaction, One-Dimensional Transport, and Inverse Geochemical Calculations

Init

Module Description

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 Lua is a powerful, fast, lightweight, embeddable scripting language. Lua combines simple procedural syntax with powerful data description constructs based on associative arrays and extensible semantics. Lua is dynamically typed, runs by interpreting bytecode for a register-based virtual machine, and has automatic memory management with incremental garbage collection, making it ideal for configuration, scripting, and rapid prototyping.
Mono An open source, cross-platform, implementation of C# and the CLR that is binary compatible with Microsoft.NET.
NASM NASM: General-purpose x86 assembler
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.
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.
Tcl  
Yasm Yasm: Complete rewrite of the NASM assembler with BSD license

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.
freeglut freeglut is a completely OpenSourced alternative to the OpenGL Utility Toolkit (GLUT) library.
GLM OpenGL Mathematics (GLM) is a header only C++ mathematics library for graphics software based on the OpenGL Shading Language (GLSL) specifications.
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  
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.
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  
libunistring This library provides functions for manipulating Unicode strings and for manipulating C strings according to the Unicode standard.
libxcb  
libxml2  
libxslt Libxslt is the XSLT C library developed for the GNOME project (but usable outside of the Gnome platform).
libyaml LibYAML is a YAML 1.1 parser and emitter written in C.
lxml The lxml XML toolkit is a Pythonic binding for the C libraries libxml2 and libxslt.
MATIO matio is an C library for reading and writing Matlab MAT files.
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 Nettle is a cryptographic library that is designed to fit easily in more or less any context: In crypto toolkits for object-oriented languages (C++, Python, Pike, ...), in applications like LSH or GNUPG, or even in kernel space.
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.
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 Snappy is a compression/decompression library. It does not aim for maximum compression, or compatibility with any other compression library; instead, it aims for very high speeds and reasonable compression.
spGPU spGPU is a set of custom matrix storages and CUDA kernels for sparse linear algebra computing on GPU. It isn't a replacement for cuBLAS/cuSPARSE that should be used for a full featured linear algebra environment on GPU.
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  
zlib  

Libraries

Module Description
adios  
dataspaces  
fftw2  
fftw2-mpi  
fftw3  
fftw3-mpi  
gpi2  
gsl  
hdf5  
hdf5-parallel  
ipp  
magma  
mkl  
mxml  
netcdf  
netcdf-cxx  
netcdf-fortran  
netcdf-parallel  
opencl-rt  
opencl-sdk  
petsc  
plasma  
szip  
tbb  
trilinos  

Math

Module Description
Eigen  
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 Test utilities for code working with files and commands
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.
MATLAB MATLAB is a high-level language and interactive environment that enables you to perform computationally intensive tasks faster than with traditional programming languages such as C, C++, and Fortran.
METIS  
MLD2P4 MLD2P4 (Multi-Level Domain Decomposition Parallel Preconditioners Package based on PSBLAS) is a package of parallel algebraic multi-level preconditioners. It implements various versions of one-level additive and of multi-level additive and hybrid Schwarz algorithms. In the multi-level case, a purely algebraic approach is applied to generate coarse-level corrections, so that no geometric background is needed concerning the matrix to be preconditioned. The matrix is assumed to be square, real or complex, with a symmetric sparsity pattern.
MPFR  
numpy Test utilities for code working with files and commands
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.
PSBLAS Most computationally intensive applications work on irregular and sparse domains that complicate their implementation on parallel machines. The major goal of the Parallel Sparse Basic Linear Algebra Subroutines (PSBLAS) project is to provide a framework to enable easy, efficient and portable implementations of iterative solvers for linear systems, while shielding the user from most details of their parallelization. The interface is designed keeping in view a Single Program Multiple Data programming model on distributed memory machines.
PSBLAS-ext PSBLAS - Extended formats and NVIDIA GPU support
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  
Theano Theano is a Python library that allows you to define, optimize, and evaluate mathematical expressions involving multi-dimensional arrays efficiently.

Mpi

Module Description
bullxmpi  
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.
lam  
MPICH MPICH v3.x is an open source high-performance MPI 3.0 implementation. It does not support InfiniBand (use MVAPICH2 with InfiniBand devices).
mvapich2  
OpenMPI The Open MPI Project is an open source MPI-2 implementation.
openmpi  

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  
cuDNN  
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.
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.
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  
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.

Omics

Module Description
fastqc  
gatk  
hpg-aligner  
hpg-fastq  
hpg-variant  
ngsPipeline  
picard  
samtools  
snpEff  

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.
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 is 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.
PDT Program Database Toolkit (PDT) is a framework for analyzing source code written in several programming languages and for making rich program knowledge accessible to developers of static and dynamic analysis tools. PDT implements a standard program representation, the program database (PDB), that can be accessed in a uniform way through a class library supporting common PDB operations.
Scalasca Scalasca is a software tool that supports the performance optimization of parallel programs by measuring and analyzing their runtime behavior. The analysis identifies potential performance bottlenecks -- in particular those concerning communication and synchronization -- and offers guidance in exploring their causes.
Score-P The Score-P measurement infrastructure is a highly scalable and easy-to-use tool suite for profiling, event tracing, and online analysis of HPC applications.
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.

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.
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.
phono3py This software calculates phonon-phonon interaction related properties
phonopy Phonopy is an open source package of phonon calculations based on the supercell approach.
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.

Prace

Module Description
GLOBUS  
PRACE  

System

Module Description
CUDA CUDA (formerly Compute Unified Device Architecture) is a parallel computing platform and programming model created by NVIDIA and implemented by the graphics processing units (GPUs) that they produce. CUDA gives developers access to the virtual instruction set and memory of the parallel computational elements in CUDA GPUs.
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.
gimkl GNU Compiler Collection (GCC) based compiler toolchain, next to Intel MPI and Intel MKL (BLAS, (Sca)LAPACK, FFTW).
gimpi GNU Compiler Collection (GCC) based compiler toolchain, next to Intel MPI.
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
iimpi Intel C/C++ and Fortran compilers, alongside Intel MPI.
intel  
iomkl Intel Cluster Toolchain Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MKL & OpenMPI.
iompi Intel C/C++ and Fortran compilers, alongside Open MPI.

Tools

Module Description
advisor_xe  
ANSYS ANSYS simulation software enables organizations to confidently predict how their products will operate in the real world. We believe that every product is a promise of something greater.
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.
cmake  
cube  
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.
elmer  
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  
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.
gnuplot  
grace  
gzip gzip (GNU zip) is a popular data compression program as a replacement for compress
help2man  
inspector_xe  
intelpcm  
ipm  
itac  
JOE JOE is a full featured terminal-based screen editor which is distributed under the GNU General Public License (GPL)
likwid  
Lmod  
MATLAB  
memoryscape  
Mercurial Mercurial is a free, distributed source control management tool. It efficiently handles projects of any size and offers an easy and intuitive interface.
mercurial  
MIKE  
mono  
mpi.net  
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.
octave  
opari2  
openssh-x509  
oscar-modules  
otf2  
papi  
parallel  
python  
R  
racket  
relion  
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.
ruby  
scite  
Serf The serf library is a high performance C-based HTTP client library built upon the Apache Portable Runtime (APR) library
Singularity Singularity is a container platform focused on supporting "Mobility of Compute"
Subversion Subversion is an open source version control system.
Szip  
tcl  
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.
tk  
tmux  
totalview  
turbovnc  
util-linux Set of Linux utilities
valgrind  
vampir  
virtualgl  
VTune Intel VTune Amplifier XE 2016 is the premier performance profiler for C, C++, C#, Fortran, Assembly and Java.
vtune_xe  
XZ xz: XZ utilities

Virtualization

Module Description
qemu  
vde2  
wine  

Vis

Module Description
ATK ATK provides the set of accessibility interfaces that are implemented by other toolkits and applications. Using the ATK interfaces, accessibility tools have full access to view and control running applications.
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.
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.
Gdk-Pixbuf The Gdk Pixbuf is a toolkit for image loading and pixel buffer manipulation. It is used by GTK+ 2 and GTK+ 3 to load and manipulate images. In the past it was distributed as part of GTK+ 2 but it was split off into a separate package in preparation for the change to GTK+ 3.
gettext  
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
grace Grace is a WYSIWYG 2D plotting tool for X Windows System and Motif.
GraphicsMagick GraphicsMagick is the swiss army knife of image processing.
GST-plugins-base GStreamer is a library for constructing graphs of media-handling components. The applications it supports range from simple Ogg/Vorbis playback, audio/video streaming to complex audio (mixing) and video (non-linear editing) processing.
GStreamer GStreamer is a library for constructing graphs of media-handling components. The applications it supports range from simple Ogg/Vorbis playback, audio/video streaming to complex audio (mixing) and video (non-linear editing) processing.
GTK+ The GTK+ 2 package contains libraries used for creating graphical user interfaces for applications.
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.
libGLU  
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.
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
libXinerama  
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  
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.
OSPRay A Ray Tracing Based Rendering Engine for High-Fidelity Visualization
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.
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.
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.
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  
x264 x264 is a free software library and application for encoding video streams into the H.264/MPEG-4 AVC compression format, and is released under the terms of the GNU GPL.