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HPC Software - Software Libraries

Boost C++ Libraries

Boost provides free peer-reviewed portable C++ source libraries.

Boost libraries are intended to be widely useful, and usable across a broad spectrum of applications. The Boost license encourages both commercial and non-commercial use.

[Boost Website - May 2014]

Available versions and module name

1.52.0 (boost or boost-1.52.0)

Default version available

1.52.0

Website

http://www.boost.org/
Expat XML Parser

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).

[Expat Website - June 2014]

Available versions and module name

2.1.0 (expat or expat-2.1.0)

Default version available

2.1.0

Website

http://expat.sourceforge.net/
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 (as well as of even/odd data, i.e. the discrete cosine/sine transforms or DCT/DST).  [FFTW Website - November 2012]

Available versions and module name

3.3.3 (fftw-3.3.3 or fftw)

Default version available

3.3.3

Website

http://www.fftw.org/index.html 

GMP - The GNU Multiple Precision Arithmetic Library

GMP is a free library for arbitrary precision arithmetic, operating on signed integers, rational numbers, and floating point numbers. There is no practical limit to the precision except the ones implied by the available memory in the machine GMP runs on. GMP has a rich set of functions, and the functions have a regular interface. [GMP Website - August 2013]

Available versions and module name

5.1.2 (gmp-5.1.2 or gmp)

Default version available

5.1.2

Website

http://gmplib.org/
GNU Scientific Library (GSL)

The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers. It is free software under the GNU General Public License.

The library provides a wide range of mathematical routines such as random number generators, special functions and least-squares fitting. There are over 1000 functions in total with an extensive test suite.  [GSL Website - November 2012]

Available versions and module name

2.5 (gsl-2.5 or gsl)

1.15 (gsl-1.15)

Default version available

2.5

Website

http://www.gnu.org/software/gsl/

HDF5

HDF5 is a data model, library, and file format for storing and managing data. It supports an unlimited variety of datatypes, and is designed for flexible and efficient I/O and for high volume and complex data. HDF5 is portable and is extensible, allowing applications to evolve in their use of HDF5. The HDF5 Technology suite includes tools and applications for managing, manipulating, viewing, and analysing data in the HDF5 format. [HDF5 Website - June 2014]

Available versions and module name

1.12.0 (hdf5-1.12.0 or hdf5)

1.8.13 (hdf5-1.8.13)

Default version available

1.8.13

Website

http://www.hdfgroup.org/HDF5/

HDFEOS

The HDF-EOS5 is a software library designed built on HDF5* to support the same Grid/Point/Swath functionality in HDF-EOS 2 and to the extent possible it will be built with the same calling sequences as the original HDF-EOS 2 library. [HDF-EOS5 Website - May2017]

Available versions and module name

5.1.5 (hdfeos5-5.1.15 or hdfeos5)

Default version available

5.1.5

Website

http://hdfeos.org/software/library.php#HDF-EOS5

Intel Math Kernel Libraries (Intel® MKL)

The "Intel Math Kernel Libraries (Intel MKL) - which is a computing math library of highly optimized, extensively threaded math routines for applications that require maximum performance. Core math functions include BLAS, LAPACK, ScaLAPACK1, sparse solvers, fast Fourier transforms, vector math, and more."

This Library is part of the Intel Cluster Studio package that is installed on the HPC System.

Available versions and module name

15.0.0 (intel-parallel-studio-2015 or intel-parallel-studio)

13.0.1 (intel-ics or intel-ics-2013)

Default version available

15.0.0

Website

http://software.intel.com/en-us/intel-mkl

libbz2

Available versions and module name

1.0.5-24 (libbz2-1.0.5-24 or libbz2)

Default version available

1.0.5-24

Website
libcurl

Curl is a tool to transfer data from or to a server, using one of the supported protocols (HTTP, HTTPS, FTP, FTPS, SCP, SFTP, TFTP, DICT, TELNET, LDAP or FILE).  The command is designed to work without user interaction. [Curl 7.19.7 man page]

Available versions and module name

7.19.7 (libcurl-7.19.7 or libcurl)

Default version available

7.19.7

Website
libjpeg

Available versions and module name

6.2.0 (libjpeg-6.2.0 or libjpeg)

Default version available

6.2.0

Website
libpng

libpng - Portable Network Graphics (PNG) Reference Library 1.2.31 [libpng 1.2.31 man page]

Available versions and module name

1.2.31 (libjpeg-1.2.31 or libjpeg)

Default version available

1.2.31

Website
MPI

Message Passing Interface (MPI) is a standardized and portable message-passing system designed by a group of researchers from academia and industry to function on a wide variety of parallel computers. The standard defines the syntax and semantics of a core of library routines useful to a wide range of users writing portable message-passing programs in ForTran or the C Programming Language". [http://en.wikipedia.org/wiki/Message_Passing_Interface Website - November 2012]

Available versions and module name

SGI Message Passing Toolkit  - 2.06 (mpt/2.06)

Intel MPI - 4.0 (mpi/intel-4.0)

OpenMPI - 1.8.3 (openmpi)

Default version available

mpt - 2.06

Websites

http://en.wikipedia.org/wiki/Message_Passing_Interface

http://techpubs.sgi.com/library/manuals/3000/007-3773-004/pdf/007-3773-004.pdf

http://software.intel.com/en-us/intel-mpi-library

http://www.open-mpi.org/

OpenBLAS

OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version. . [http://www.openblas.net/ Website - November 2013]

Available versions and module name

0.2.8 (opeblas-0.2.8 or openblas )

Default version available

0.2.8

Websites

http://www.openblas.net/

PCRE (Pearl Compatible Regular Expressions)

The PCRE library is a set of functions that implement regular expression pattern matching using the same syntax and semantics as Perl 5. PCRE has its own native API, as well as a set of wrapper functions that correspond to the POSIX regular expression API. The PCRE library is free, even for building proprietary software.

PCRE was originally written for the Exim MTA, but is now used by many high-profile open source projects, including ApachePHPKDEPostfixAnalog, and Nmap. PCRE has also found its way into some well known commercial products, like Apple Safari. Some other interesting projects using PCRE include ChickenFeriteOnyxHypermailLeafnodeAskemos, and Wenlin. [PCRE Website - November 2013]

Available versions and module name

8.33 (pcre-8.33 or prce)

Default version available

8.33

Websites

http://www.pcre.org/

szip

Szip compression software, providing lossless compression of scientific data, has been provided with HDF software products as of HDF5 Release 1.6.0 and HDF4 Release 2.0. [Szip Compression in HDF Products - June 2014]

Available versions and module name

2.1 (szip-2.1 or szip)

Default version available

2.1

Websites

http://www.hdfgroup.org/doc_resource/SZIP/

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. Open source and business-friendly, Tcl is a mature yet evolving language that is truly cross platform, easily deployed and highly extensible. [Tcl Developer Xchange! Website - February 2014]

Available versions and module name

8.5.5 (tcl-8.5.5 or tck)

Default version available

8.5.5

Websites

http://www.tcl.tk/

tk

Tk is a graphical user interface toolkit that takes developing desktop applications to a higher level than conventional approaches. Tk is the standard GUI not only for Tcl, but for many other dynamic languages, and can produce rich, native applications that run unchanged across Windows, Mac OS X, Linux and more. [Tcl Developer Xchange! Website - February 2014]

Available versions and module name

8.5.5 (tk-8.5.5 or tk)

Default version available

8.5.5

Websites

http://www.tcl.tk/

UDUNITS

The UDUNITS package supports units of physical quantities. Its C library provides for arithmetic manipulation of units and for conversion of numeric values between compatible units. The package contains an extensive unit database, which is in XML format and user-extendable. The package also contains a command-line utility for investigating units and converting values. [UDUNITS Website - June 2014]

Available versions and module name

2.2.12 (udunits-2.2.12 or udunits)

Default version available

2.2.12

Websites

http://www.unidata.ucar.edu/software/udunits/

If, for whatever reason, you would like to use the older versions of the compilers, or other available software, you can simply "unload" the current module and load the older version. See Software Module Information webpage.

Software list

Bioinformatics
  • AmpliconNoise
  • ARB
  • BLAST (Legacy BLAST- Not BLAST+)
  • BLAST+
  • Bowtie2
  • CD-HIT
  • cdbtools
  • ChimeraSlayer
  • clearcut
  • Cufflinks
  • Cytoscape
  • FastQC
  • FastTree
  • Fastx-Toolkit
  • Gepard
  • HMMER
  • IGV
  • infernal
  • Kraken
  • metavelvet
  • mothur
  • MUSCLE
  • Ngopt
  • ParsInsert
  • Pear
  • Pplacer
  • QIIME
  • RAxML
  • rRNASelector
  • RSEM
  • RTAX
  • SAM Tools
  • SAMStat
  • SourceTracker
  • TopHat
  • Trimmomatic
  • Trinityrnaseq
  • UCLUST
  • UProC
  • USEARCH
  • Velvet
  • Velvet Optmiser
Compilers
  • Glasgow Haskell Compiler
  • GNU Bison
  • GNU Compiler
  • GNU Fortran Compiler
  • Go Compiler
  • Intel C and C++ Compiler
  • Intel Fortran Compiler
  • Mono C# Compiler and associated libraries
Data Mining and Analysis Applications
  • NCL (NCAR Command Language)
  • Ncview
  • NetCDF
  • NetCDF-Fortran
  • RapidMiner
  • STIR (Tomographic Imaging)
  • Weka
Development tools
  • Apache Maven
  • GNU Emacs
  • IntelliJ IDEA
  • RStudio
Documentation Tools
  • Tex Live
  • Tex Info
Engineering Applications
  • ANSYS (Fluent and Mechanical)
  • ABAQUS
  • AVL Fire
  • Comsol Multiphysics
Geospatial Tools
  • GDAL
  • GEOS
  • Panoply
Graphics Applications
  • Circos
  • ImageJ
  • ImageMagick
  • PLPlot
  • Xfig
Interpreters
  • Perl
  • Python (with many Modules Installed)
Mathematics and Statics
  • Mathematica
  • Grid Mathematica
  • Matlab
  • Matlab-Simulink
  • Octave
  • OpenBUGS
  • R
  • SPSS (by IBM)
Run Time Environments
  • Java
Simulation Software
  • APSIM
Software Libraries
  • Boost C++ Libraries
  • Expat XML Parser
  • FFTW
  • GMP (GNU Multiple Precision Arithmetic Library)
  • GNU Scientific Library (GSL)
  • HDF5
  • HDF-EOS5
  • Intel Math Kernel Libraries (Intel® MKL)
  • libbz2
  • libcurl
  • libjpeg
  • libpng
  • MPI
  • OpenBLAS
  • PCRE (Perl Compatible Regular Expressions)
  • szip
  • tcl
  • tk
  • UDUNITS
Text Tools and Software
  • Flex