Installed Packages

The packages are taken form public open-sourse repositories and installations are done in bundles.

Basic Editor

gedit, vim, vi, emacs, nano

Basic Compiler

gcc, g++, cc, gfortran, java

Name        : gcc
Arch        : x86_64
Version     : 4.4.7
Release     : 11.el6
Size        : 19 M
Repo        : installed
From repo   : anaconda-base-201505101627.x86_64
Summary     : Various compilers (C, C++, Objective-C, Java, ...)
URL         : http://gcc.gnu.org
License     : GPLv3+ and GPLv3+ with exceptions and GPLv2+ with exceptions
Description : The gcc package contains the GNU Compiler Collection version 4.4.
            : You'll need this package in order to compile C code.

GNU Tools

This bundles a number of GNU tools into a single Rocks group and provides a Modules interface to allow loading of the tool paths into the user environment. For more information about the various packages included in the gnutools, please visit their official web pages:

GNU Autoconf - is an extensible package of M4 macros that produce shell scripts to automatically configure software source code packages.
GNU Automake - is a tool for automatically generating Makefile.in files compliant with the GNU Coding Standards. Automake requires the use of Autoconf.
GNU Binutils - are a collection of binary tools.
GNU GDB - the GNU Project debugger, allows you to see what is going on inside another program while it executes — or what another program was doing at the moment it crashed.
GNU Libtool - is a generic library support script. Libtool hides the complexity of using shared libraries behind a consistent, portable interface.
GNU Texinfo - is the official documentation format of the GNU project.
GNU libunistring - provides functions for manipulating Unicode strings and for manipulating C strings according to the Unicode standard.
libffi - 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.
gnutools - is a portable command-line driven graphing utility.

hdf

This bundles the HDF4 and HDF5 libraries and the h5py Python interface to HDF5. For more information about the various packages included in the hdf please visit their official web pages:

HDF4 - is a library and multi-object file format for storing and managing data between machines.
HDF5 - is a data model, library, and file format for storing and managing data.
The H5PY package is a Pythonic interface to the HDF5 binary data format.

Math [ Upcoming!!, requires Intel MKL Lib]

This bundles a collection of Math packages: eigen, GSL, LAPACK, Parmetis,petsc, ScaLAPACK, slepc, SPRNG, sundials, and superLU.

For more information about the various packages included in the math please visit their official web pages:

eigen - is a C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms.
GSL - is a numerical library for C and C++ programmers.
LAPACK provides routines for solving systems of simultaneous linear equations, least-squares solutions of linear systems of equations, eigenvalue problems, and singular value problems.
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.
petsc - is a suite of data structures and routines for the scalable (parallel) solution of scientific applications modeled by partial differential equations
ScaLAPACK - is a library of high-performance linear algebra routines for parallel distributed memory machines.
slepc is a software library for the solution of large scale sparse eigenvalue problems on parallel computers sundials solves nonlinear and diffential equations
SPRNG is a scalable package for parallel pseudo random number generation which will be easy to use on a variety of architectures, especially in large-scale parallel Monte Carlo applications.
SuperLU - is a general purpose library for the direct solution of large, sparse, nonsymmetric systems of linear equations on high performance machines.

ATLAS

This bundles the ATLAS math package.

The Automatically Tuned Linear Algebra Software (ATLAS) focuses on applying empirical techniques in order to provide portable performance. At present, it provides C and Fortran77 interfaces to a portably efficient BLAS implementation, as well as a few routines from LAPACK. For more information about ATLAS please visit the official web page.

Special Python

This bundles Python 2.7.x and 3.x for side-by-side installation with the system Python and default Rocks Python. Python is a programming language that lets you work more quickly and integrate your systems more effectively.

Along with Python itself, the installs these python modules:

boost

This bundles the boost C++ libraries. For more information about boost please visit the official web page

FFTW

This bundles the FFTW library. 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. For more information about FFTW please visit the official web page

Bio :

This is a default Bundle. The Bio contains a suite of Bio-informatics applications, most commonly in use by the bio-informatics community. The list of applications is as follows: ( list is taken from here)

HMMER - http://hmmer.janelia.org/
NCBI BLAST - From National Center for Biotechnology Information - www.ncbi.nlm.nih.gov/BLAST/
MpiBLAST - From Los Alamos National Laboratory - http://mpiblast.lanl.gov/
biopython - www.biopython.org
ClustalW - From the European BioInformatics Institute - http://www.ebi.ac.uk/clustalw/
MrBayes - From School of Computational Science at the Florida State University - http://mrbayes.csit.fsu.edu/
T_Coffee - From Information Genomique et Structurale at Centre National de la Recherche Scientifique - The T-Coffee Home Page
Emboss - From European Molecular Biology Institute - http://emboss.sourceforge.net/
Phylip - From the Dept. of Biology at the University of Washington - http://evolution.genetics.washington.edu/phylip.html
fasta - From the University of Virginia - http://fasta.bioch.virginia.edu/
Glimmer - From Center for Bioinformatics and Computational Biology at the University of Maryland - http://www.cbcb.umd.edu/software/glimmer/
TIGR Assembler - From the J. Craig Venter Institute - http://www.jcvi.org/cms/research/software/
All the perl utilities mentioned below are from CPAN
perl-bioperl
perl-bioperl-ext
perl-bioperl-run
perl-bioperl-db

Gaussian 09:

We have recently installed Gaussian 09 Version. Users need to add the following to their .login file if they prefer to run in C shell to set the g09root

setenv g09root "/share/apps/gaussian"
setenv GAUSS_SCRDIR "/tmp/$USER/gausian" # user must create this directory before loading it mkdir -p /tmp/$USER/gausian
source $g09root/g09/bsd/g09.login     # sets up G09 run environment.

For Bourne-type shell users need to use these commands instead of the ones above:

g09root="/share/apps/gaussian"
GAUSS_SCRDIR="/tmp/$USER/gausian"
export g09root GAUSS_SCRDIR
. $g09root/g09/bsd/g09.profile

Users need to create a runtime scratch space before they load the Gaussian ENV, use mkdir -p /tmp/$USER/gausian, this will create a folder in /tmp.

As per suggestion, I have not installed GaussView, if you would like to use, please set it in your local area. [expert’s views will highly be appreciated].

Please provide a example script as demo, which will help new users in future.

Packages on Plan (!!!!):

Send me requests (Only For OpenSource Packages).

Already Prepared RPMS (including dependencies)

With the collaboration with TACC/XSEDE and CERN Computing facilities, all these RPMs are produced locally to fit into our HPC

BEDTools-2.15.0-1.el6.x86_64.rpm
GotoBLAS2-1.13-0.x86_64.rpm
PLAPACK-R3.2-1.el6.x86_64.rpm
PnetCDF-1.4.1-1.el6.x86_64.rpm
R-2.15.1-1.el6.x86_64.rpm
  R-devel-2.15.1-1.el6.x86_64.rpm
  R-core-2.15.1-1.el6.x86_64.rpm
  libRmath-2.15.1-1.el6.x86_64.rpm
  libRmath-devel-2.15.1-1.el6.x86_64.rpm
  libicu-4.2.1-9.1.el6_2.x86_64.rpm
  texinfo-tex-4.13a-8.el6.x86_64.rpm
SHRiMP-2_2_3-1.x86_64.rpm
abyss-1.3.7-1.x86_64.rpm
ant-1.7.1-13.el6.x86_64.rpm
   java-1.6.0-openjdk-1.6.0.36-1.13.8.1.el6_7.x86_64.rpm
   java-1.6.0-openjdk-devel-1.6.0.36-1.13.8.1.el6_7.x86_64.rpm
   xerces-j2-2.7.1-12.7.el6_5.x86_64.rpm
   xml-commons-resolver-1.1-4.18.el6.x86_64.rpm
   xml-commons-apis-1.3.04-3.6.el6.x86_64.rpm
arpack-3.1.3-1.el6.x86_64.rpm
atlas-3.8.4-2.el6.x86_64.rpm
boost-1.41.0-25.el6.x86_64.rpm
   boost-date-time-1.41.0-25.el6.x86_64.rpm
   boost-filesystem-1.41.0-25.el6.x86_64.rpm
   boost-graph-1.41.0-25.el6.x86_64.rpm
   boost-iostreams-1.41.0-25.el6.x86_64.rpm
   boost-program-options-1.41.0-25.el6.x86_64.rpm
   boost-python-1.41.0-25.el6.x86_64.rpm
   boost-regex-1.41.0-25.el6.x86_64.rpm
   boost-serialization-1.41.0-25.el6.x86_64.rpm
   boost-signals-1.41.0-25.el6.x86_64.rpm
   boost-system-1.41.0-25.el6.x86_64.rpm
   boost-test-1.41.0-25.el6.x86_64.rpm
   boost-thread-1.41.0-25.el6.x86_64.rpm
   boost-wave-1.41.0-25.el6.x86_64.rpm
   libicu-4.2.1-9.1.el6_2.x86_64.rpm
bowtie-0.12.7-2.el6.x86_64.rpm
bwa-0.5.9-1.el6.x86_64.rpm
charm-6.0-0.x86_64.rpm
darshan-runtime-mpich-2.3.0-1.x86_64.rpm
darshan-runtime-openmpi-2.3.0-1.x86_64.rpm
darshan-util-2.3.0-1.x86_64.rpm
elemental-0.83-1.el6.x86_64.rpm
espresso-ab-1.0-1.el6.x86_64.rpm
fftw2-2.1.5-21.el6.x86_64.rpm
fftw-3.2.1-3.1.el6.x86_64.rpm
geos-3.3.2-1.el6.x86_64.rpm
glpk-4.40-1.1.el6.x86_64.rpm
gnuplot-4.2.6-2.el6.x86_64.rpm
   gnuplot-common-4.2.6-2.el6.x86_64.rpm
   wxBase-2.8.12-1.el6.centos.x86_64.rpm
   wxGTK-2.8.12-1.el6.centos.x86_64.rpm
gromacs-4.5.7-1.el6.x86_64.rpm
   gromacs-common-4.5.7-1.el6.noarch.rpm
   gromacs-libs-4.5.7-1.el6.x86_64.rpm
   fftw-3.2.1-3.1.el6.x86_64.rpm
java-1.7.0-openjdk-1.7.0.85-2.6.1.3.el6_7.x86_64.rpm
   java-1.7.0-openjdk-devel-1.7.0.85-2.6.1.3.el6_7.x86_64.rpm
   jpackage-utils-1.7.5-3.14.el6.noarch.rpm
   tzdata-java-2015f-1.el6.noarch.rpm
lammps-20150409-12.el6.x86_64.rpm
   lammps-common-20150409-12.el6.x86_64.rpm
libgtextutils-0.6-5.el6.x86_64.rpm
libTAU-1.0.0-1.el6.x86_64.rpm
meep-1_2_1-1.x86_64.rpm
   guile-1.8.7-5.el6.x86_64.rpm
mpi4py-common-1.3-5.el6.noarch.rpm
   mpi4py-mpich2-1.3-5.el6.x86_64.rpm
   mpi4py-openmpi-1.3-5.el6.x86_64.rpm
   mpich2-1.2.1-2.3.el6.x86_64.rpm
mpich2-1.2.1-2.3.el6.x86_64.rpm
ncbi-blast-2.2.29+-1.x86_64.rpm
ncl-6.0.0-3.el6.x86_64.rpm
   ncl-common-6.0.0-3.el6.noarch.rpm
   udunits2-2.1.19-1.el6.x86_64.rpm
nco-4.0.5-2.el6.x86_64.rpm
   gsl-1.13-1.el6.x86_64.rpm
   netcdf-4.1.1-3.el6.4.x86_64.rpm
      hdf5-1.8.5.patch1-7.el6.x86_64.rpm
   udunits2-2.1.19-1.el6.x86_64.rpm
numpy-1.4.1-9.el6.x86_64.rpm
nwchem-6.5.26243-13.el6.x86_64.rpm
nwchem-common-6.5.26243-13.el6.noarch.rpm
octave-3.4.3-1.el6.x86_64.rpm
   GraphicsMagick-c++-1.3.18-2.el6.x86_64.rpm
   GraphicsMagick-1.3.18-2.el6.x86_64.rpm
   blas-3.2.1-4.el6.x86_64.rpm
   fltk-1.1.10-1.el6.x86_64.rpm
   glpk-4.40-1.1.el6.x86_64.rpm
   gnuplot-4.2.6-2.el6.x86_64.rpm
   gnuplot-common-4.2.6-2.el6.x86_64.rpm
   hdf5-1.8.5.patch1-7.el6.x86_64.rpm
   qhull-2003.1-14.el6.x86_64.rpm
   qrupdate-1.1.2-1.el6.x86_64.rpm
   suitesparse-3.4.0-9.el6.x86_64.rpm
   texinfo-4.13a-8.el6.x86_64.rpm
   wxBase-2.8.12-1.el6.centos.x86_64.rpm
   wxGTK-2.8.12-1.el6.centos.x86_64.rpm
picard-tools-1.112-1.el6.x86_64.rpm
plplot-5.9.7-3.el6.1.x86_64.rpm
   gnu-free-sans-fonts-20100919-3.el6.noarch.rpm
   gnu-free-serif-fonts-20100919-3.el6.noarch.rpm
   lasi-1.1.0-6.el6.x86_64.rpm
   numpy-1.4.1-9.el6.x86_64.rpm
   plplot-libs-5.9.7-3.el6.1.x86_64.rpm
   python-nose-0.10.4-3.1.el6.noarch.rpm
   python-setuptools-0.6.10-3.el6.noarch.rpm
rhino-1.7-0.7.r2.2.el6.noarch.rpm
   jline-0.9.94-0.8.el6.noarch.rp
samtools-0.1.18-2.el6.x86_64.rpm
scalapack-common-2.0.2-6.el6.x86_64.rpm
slepc-3.4.4-1.x86_64.rpm
sprng-4.4-1.el6.x86_64.rpm
   mpich2-1.2.1-2.3.el6.x86_64.rpm
sparsehash-devel-1.7-3.el6.noarch.rpm
sratoolkit-2.3.4-1.el6.x86_64.rpm
sundials-2.5.0-1.el6.x86_64.rpm
trinityrnaseq-r20140717-5.x86_64.rpm
   bowtie-1.1.1-1.el6.x86_64.rpm
   java-1.6.0-openjdk-1.6.0.36-1.13.8.1.el6_7.x86_64.rpm
   java-1.6.0-openjdk-devel-1.6.0.36-1.13.8.1.el6_7.x86_64.rpm
   samtools-0.1.18-2.el6.x86_64.rpm
valgrind-3.8.1-3.2.el6.x86_64.rpm
saga-2.1.1-1.el6.x86_64.rpm
   cfitsio-3.240-3.el6.x86_64.rpm
   gdal-1.7.3-15.el6.x86_64.rpm
   gdal-devel-1.7.3-15.el6.x86_64.rpm
   gdal-java-1.7.3-15.el6.x86_64.rpm
   geos-3.3.2-1.el6.x86_64.rpm
   libdap-3.11.0-1.el6.x86_64.rpm
   libgeotiff-1.2.5-6.el6.x86_64.rpm
   libgeotiff-devel-1.2.5-6.el6.x86_64.rpm
   libmspack-0.4-0.1.alpha.el6.x86_64.rpm
   librx-1.5-24.el6.x86_64.rpm
   netcdf-4.1.1-3.el6.4.x86_64.rpm
   ogdi-3.2.0-0.14.beta2.el6.x86_64.rpm
   postgresql-libs-8.4.20-1.el6_5.x86_64.rpm
   proj-4.7.0-1.el6.x86_64.rpm
   unixODBC-2.2.14-14.el6.x86_64.rpm
   wxBase3-3.0.0-7.el6.x86_64.rpm
   wxGTK3-3.0.0-7.el6.x86_64.rpm
   xerces-c-3.0.1-20.el6.x86_64.rpm

Dislaimer:

The information about the packages are taken from web (mostly, through google-search). by S. Jena

Document version: V1.1.1 12/06/2017
Document version: V1.1.0 23/03/2017
Document version: V1.2.0 16/03/2018