Software

Compilers

Name Description Version(s)
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,…)
4.5.3
4.6.3
4.6.4
4.7.2
4.7.3
C and C++ compiler from Intel
2011.13.367
2013.3.163
2013.5.192
2013_sp1.1.106
Fortran compiler from Intel
2011.13.367
2013.3.163
2013.5.192
2013_sp1.1.106

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Toolchains

Toolchains are basically a (set of) compilers together with a bunch of libraries that provide additional support that is
commonly required to build software

Name Description Version(s)
gmvapich2
GNU Compiler Collection (GCC) based compiler toolchain, including MVAPICH2 for MPI support
1.6.7
1.7.9a2
1.7.12
gmvolf
GNU Compiler Collection (GCC) based compiler toolchain, including MVAPICH2 for MPI support, OpenBLAS  (BLAS and LAPACK support), FFTW and ScaLAPACK
1.7.12
gompi
GNU Compiler Collection (GCC) based compiler toolchain, including OpenMPI for MPI support
1.1.0-no-OFED
1.3.12
1.4.10
goolf
GNU Compiler Collection (GCC) based compiler toolchain, including OpenMPI for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK.
1.4.10
goolfc
GCC based compiler toolchain with CUDA support, and including OpenMPI for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK.
1.3.12
iccifort
Intel Cluster Toolkit Compiler Edition provides Intel C,C++ and fortran compilers
2011.13.367
2013.5.192
Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & Intel MKL.
4.1.13
5.3.0
5.5.0
6.1.5

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Biology

Name Description Version(s)
The BEDTools utilities allow one to address common genomics tasks such as finding feature overlaps and computing coverage. The utilities are largely based on four widely-used file formats: BED, GFF/GTF, VCF, and SAM/BAM.
2.17.0-goolf-1.4.10
2.18.1-goolf-1.4.10
A tool to map bisulfite converted sequence reads and determine cytosine methylation states
0.10.1-goolf-1.4.10
Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences.
2.0.2-goolf-1.4.10
Burrows-Wheeler Aligner (BWA) is an efficient program that aligns relatively short nucleotide sequences against a long reference sequence such as the human genome.
0.7.4-goolf-1.4.10
cutadapt removes adapter sequences from high-throughput sequencing data. This is usually necessary when the read length of the sequencing machine is longer than the molecule that is sequenced, for example when sequencing microRNAs.
1.3-goolf-1.4.10-Python-2.7.3
A Python library for phylogenetics and phylogenetic computing: reading, writing, simulation, processing and manipulation of phylogenetic trees (phylogenies) and characters.
3.12.0-goolf-1.4.10-Python-2.7.3
The Genome Analysis Toolkit or GATK is a software package developed at the Broad Institutevto 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.
3.0-0-Java-1.7.0_10
The MethPipe software package is a computational pipeline for analyzing bisulfite sequencing data (BS-seq, WGBS and RRBS).
3.0.1-goolf-1.4.10
A set of tools (in Java) for working with next generation sequencing data in the BAM format.
1.109
pBWA is a parallel implementation of the popular software BWA. It was developed by modifying the BWA source code with the OpenMPI C library on the SHARCNET. pBWA has been successfully tested on other systems with the most basic OpenMPI installs. pBWA currently implements three commands from BWA: aln, samse, and sampe. pBWA retains and improves upon the multithreading provided by BWA while adding efficient parallelization for the above listed functions. pBWA has shown that its wall-time speedup is bounded only by the size of the parallel system available as pBWA can run on any number of nodes and/or cores simultaneously.
0.5.9_1.21009-goolf-1.4.10
SAM (Sequence Alignment/Map) format is a generic format for storing large nucleotide sequence alignments.
0.1.18-goolf-1.4.10
TopHat is a fast splice junction mapper for RNA-Seq reads.
2.0.4-goolf-1.4.10

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CFD/Finite Element

Name Description Version(s)
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.
2.1.1-goolf-1.4.10
ParFlow is an integrated, parallel watershed model that makes use of high-performance computing to simulate surface and subsurface fluid flow.
605-goolf-1.4.10

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Chemistry

Name Description Version(s)
Abinit is a plane wave pseudopotential code for doing condensed phase electronic structure calculations using DFT.
7.4.3-x86_64_linux_gnu4.5
7.4.3-goolf-1.4.10 (parallel version)
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.
20111205-goolf-1.4.10
2.4.0-goolf-1.4.10
2.4.0-goolf-1.4.10-ipi
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.
1.1.4-goolf-1.4.10
NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems.
2.9-gmvapich2-1.7.12-CUDA
2.9-gmvolf-1.7.12-CUDA
2.9-goolf-1.4.10
2.9-goolfc-1.3.12
CVS-2013-12-30-goolf-1.4.10
CVS-2013-12-30-goolfc-1.3.12
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.
6.1.1-goolf-1.4.10-2012-06-27-Python-2.7.3
6.1.1-ictce-4.1.13-2012-06-27-Python-2.7.3
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).
 5.0.2-goolf-1.4.10

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Data Processing

Name
Description
Version(s)
Library contains GRIB2 encoder/decoder (“C” version).
1.2.3-goolf-1.4.10
Library contains GRIB2 encoder/decoder and search/indexing routines.
1.2.4-goolf-1.4.10
HDF (also known as HDF4) is a library and multi-object file format for storing and managing data between machines.
4.2.7-patch1-goolf-1.4.10
HDF5 is a unique technology suite that makes possible the management of extremely large and complex data collections.
1.8.7-goolf-1.4.10
1.8.9-goolf-1.4.10
1.8.9-ictce-5.3.0
1.8.10-patch1-goolf-1.4.10
1.8.10-ictce-4.1.13-gpfs
1.8.10-ictce-5.3.0-gpfs
NCL is an interpreted language designed specifically for scientific data analysis and
visualization.
6.0.0-goolf-1.4.10
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.
4.1.3-goolf-1.4.10
4.1.3-ictce-5.3.0
4.2-goolf-1.4.10
4.2.1.1-goolf-1.4.10
4.2.1.1-ictce-4.1.13
4.2.1.1-ictce-5.3.0
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.
4.2-goolf-1.4.10
4.2-ictce-4.1.13
4.2-ictce-5.3.0
Silo is a library for reading and writing a wide variety of scientific data to binary, disk files.
4.9.1-goolf-1.4.10

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Debugging

Name
Description
Version(s)
Berkeley Lab Checkpoint/Restart (BLCR) for LINUX
0.8.5-goolf-1.4.10

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Development

Name
Description
Version(s)
Boost provides free peer-reviewed portable C++ source libraries.
1.51.0-goolf-1.4.10-Python-2.7.3
CMake, the cross-platform, open-source build system. CMake is a family of tools designed to build, test and package software.
2.8.12-goolf-1.4.10
2.8.12-ictce-5.3.0
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.
1.8.1.1-goolf-1.4.10
1.8.1.1-ictce-5.3.0
1.8.3.1-goolf-1.4.10
1.8.3.1-ictce-4.1.13
1.8.3.1-ictce-5.3.0
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.
1.4.16-GCC-4.5.3
1.4.16-GCC-4.6.3
1.4.16-GCC-4.7.2
1.4.16-GCC-4.7.3
1.4.16-goolf-1.4.10
1.4.16-ictce-4.1.13
1.4.16-ictce-5.3.0
The makedepend package contains a C-preprocessor like utility to determine build-time dependencies.
1.0.4-goolf-1.4.10
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.
5.9-GCC-4.7.3
5.9-goolf-1.4.10
5.9-ictce-4.1.13
5.9-ictce-5.3.0

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 Weather Modelling

Name Description Version(s)
The Earth System Modeling Framework (ESMF) is software for building and coupling weather, climate, and related models.
5.3.0-goolf-1.4.10
WRF Preprocessing System (WPS) for WRF. The Weather Research and Forecasting (WRF) Model is a next-generation mesoscale numerical weather prediction system designed to serve both operational forecasting and atmospheric research needs.
3.4-ictce-5.3.0-dmpar
The Weather Research and Forecasting (WRF) Model is a next-generation mesoscale numerical weather prediction system designed to serve both operational forecasting and atmospheric research needs.
3.4-ictce-5.3.0-dmpar

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Programming Languages

Name Description Version(s)
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.
2.5-GCC-4.5.3
2.5-GCC-4.6.3
2.5-goolf-1.4.10
2.5-ictce-5.3.0
2.7-GCC-4.7.2
2.7-GCC-4.7.3
2.7-goolf-1.4.10
2.7-ictce-4.1.13
2.7-ictce-5.3.0
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.
2.5.35-gmvapich2-1.6.7
2.5.35-goolf-1.4.10
2.5.35-ictce-5.3.0
2.5.37-goolf-1.4.10
2.5.37-ictce-4.1.13
2.5.37-ictce-5.3.0
Java Platform, Standard Edition (Java SE) lets you develop and deploy Java applications on desktops and servers.
1.7.0_10
1.7.0_21
NASM-2.07: General-purpose x86 assembler
2.07-goolf-1.4.10
Python is a programming language that lets you work more quickly and integrate your systems more effectively.
2.7.3-goolf-1.4.10
2.7.3-ictce-4.1.13
2.7.3-ictce-5.3.0
3.2.3-goolf-1.4.10
R is a free software environment for statistical computing and graphics.
2.15.2-goolf-1.4.10
3.0.2-goolf-1.4.10
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.
8.5.12
8.5.12-goolf-1.4.10
8.5.14-goolf-1.4.10

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Libraries

Name Description Version(s)
A library of F90 routines to read/write the ETSF file format has been written. It is called ETSF_IO and available under LGPL.
1.0.4-goolf-1.4.10
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.
1.3.0-goolf-1.4.10
libpng is the official PNG reference library
1.5.11-ictce-5.3.0
1.5.13-goolf-1.4.10
1.5.14-goolf-1.4.10
1.6.6-goolf-1.4.10
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.
6.2-goolf-1.4.10
6.2-ictce-4.1.13
6.2-ictce-5.3.0
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.
1.2.7-goolf-1.4.10
1.2.7-ictce-4.1.13
1.2.7-ictce-5.3.0

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Mathematics

Name Description Version(s)
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.
1.6.2-goolf-1.4.10-Python-2.7.3
R is a free software environment for statistical computing and graphics.
2.15.2-goolf-1.4.10
3.0.2-goolf-1.4.10
Theano is a Python library that allows you to define, optimize, and evaluate mathematical expressions involving multi-dimensional arrays efficiently.
0.5.0-ictce-5.3.0-Python-2.7.3
0.6.0-goolf-1.4.10-Python-2.7.3

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MPI

Name Description Version(s)
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.
4.1.0.027
4.1.0.030
4.1.1.036
4.1.3.045
This is an MPI 3.0 implementation. It is based on MPICH2 and MVICH.
1.7-GCC-4.5.3
1.7-GCC-4.6.3
1.9a2-GCC-4.7.2
1.9-GCC-4.7.3
1.9-iccifort-2011.13.367
1.9rc1-GCC-4.7.3
The Open MPI Project is an open source MPI-2 implementation
1.4.5-GCC-4.6.3-no-OFED
1.6.3-iccifort-2011.13.367
1.6.3-iccifort-2013.5.192
1.6.4-GCC-4.6.4
1.6.4-GCC-4.7.2

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Numerical Libraries

Name Description Version(s)
ARPACK is a collection of Fortran77 subroutines designed to solve large scale eigenvalue problems.
3.1.3-ictce-5.3.0
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.
3.8.4-gompi-1.1.0-no-OFED-LAPACK-3.4.0
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.
3.3.3-gmvapich2-1.7.12
3.3.3-gompi-1.3.12
3.3.3-gompi-1.4.10
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.
1.15-goolf-1.4.10
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.
2.8.0b-goolf-1.4.10
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.
10.3.12.361
11.0.3.163
11.0.5.192
11.1.1.106
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.
3.4.0-gompi-1.1.0-no-OFED
OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version.
0.2.6-gmvapich2-1.7.12-LAPACK-3.4.2
0.2.6-gompi-1.3.12-LAPACK-3.4.2
0.2.6-gompi-1.4.10-LAPACK-3.4.2
The ScaLAPACK (or Scalable LAPACK) library includes a subset of LAPACK routines redesigned for distributed memory MIMD parallel computers.
2.0.2-gmvapich2-1.7.12-OpenBLAS-0.2.6-LAPACK-3.4.2
2.0.2-gompi-1.3.12-OpenBLAS-0.2.6-LAPACK-3.4.2
2.0.2-gompi-1.4.10-OpenBLAS-0.2.6-LAPACK-3.4.2

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Physics

Name Description Version(s)
UDUNITS supports conversion of unit specifications between formatted and binary forms, arithmetic manipulation of units, and conversion of values between compatible scales of measurement.
2.1.24-goolf-1.4.10

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System-level software

Name Description Version(s)
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.
5.0.35-1
5.5.22
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.
1.6.2-GCC-4.6.4
1.6.2-GCC-4.7.2
1.6.2-iccifort-2013.5.192
1.6-iccifort-2011.13.367

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Utilities

Name Description Version(s)
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.
1.0.6-goolf-1.4.10
1.0.6-ictce-4.1.13
1.0.6-ictce-5.3.0
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.
7.27.0-goolf-1.4.10
7.29.0-goolf-1.4.10
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)
2.1.0-goolf-1.4.10
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.
2.0-goolf-1.4.10
2.0-ictce-5.3.0
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.
2.0.8-goolf-1.4.10
2.0.8-ictce-4.1.13
Szip compression software, providing lossless compression of scientific data
2.1-goolf-1.4.10
2.1-ictce-4.1.13
2.1-ictce-5.3.0
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.
6.18.01-ictce-5.3.0

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Visualization

Name Description Version(s)
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
1.12.14-goolf-1.4.10
Fontconfig is a library designed to provide system-wide font configuration, customization and application access.
2.10.91-goolf-1.4.10
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.
2.4.11-goolf-1.4.10
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.
1.900.1-goolf-1.4.10
1.900.1-ictce-5.3.0
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.
0.28.2-goolf-1.4.10

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