modules-anselm.md

Available Modules

Core

Module	Description
lmod
settarg

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.

Bullxde

Module	Description
bullxde

Bullxmpi

Module	Description
bullxmpi

Chem

Module	Description
abinit
cp2k-mpi
lammps
molpro
namd
nwchem
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

Compilers

Module	Description
bupc
chicken
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,...).
gupc
icc	C and C++ compiler from Intel
ifort	Fortran compiler from Intel
java
llvm

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.

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
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
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
guile	Guile is the GNU Ubiquitous Intelligent Language for Extensions, the official extension language for the GNU operating system.
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.
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).
Qt	Qt is a comprehensive cross-platform C++ application framework.
renderproto	Xrender protocol and ancillary headers
SCons	SCons is a software construction tool.
SQLite	SQLite: SQL Database Engine in a C Library
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
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.

Engineering

Module	Description
adams
ansys
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

Lang

Module	Description
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.
NASM	NASM: General-purpose x86 assembler
Perl
Python	Python is a programming language that lets you work more quickly and integrate your systems more effectively.
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	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
libdrm	Direct Rendering Manager runtime library.
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
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.
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.
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).
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.
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
zlib

Libraries

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

Math

Module	Description
GMP	GMP is a free library for arbitrary precision arithmetic, operating on signed integers, rational numbers, and floating point numbers.
ISL	isl is a library for manipulating sets and relations of integer points bounded by linear constraints.
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.
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.
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
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.

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.
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.
OpenBLAS	OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version.
ScaLAPACK	The ScaLAPACK (or Scalable LAPACK) library includes a subset of LAPACK routines redesigned for distributed memory MIMD parallel computers.

Nvidia

Module	Description
cuda

Omics

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

Oscar-Modulefiles

Module	Description

Oscar-Modules

Module	Description
oscar-modules

Perf

Module	Description
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.
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
phono3py	Python is a programming language that lets you work more quickly and integrate your systems more effectively.
phonopy	Python is a programming language that lets you work more quickly and integrate your systems more effectively.
VASP

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

Tools

Module	Description
advisor_xe
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.
dhi-mike
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)
git
gnuplot
grace
gzip	gzip (GNU zip) is a popular data compression program as a replacement for compress
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
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
ruby
scalasca2
scite
scorep
Serf	The serf library is a high performance C-based HTTP client library built upon the Apache Portable Runtime (APR) library
Subversion	Subversion is an open source version control system.
Szip	Szip compression software, providing lossless compression of scientific data
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
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
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
GLib	GLib is one of the base libraries of the GTK+ project
inputproto	X.org InputProto protocol headers.
kbproto	X.org KBProto protocol headers.
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
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).
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.
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.