As of Fall 2015, neither department sponsors student licenses for proprietary or commercial software on the cluster.

ACCRE does support R, Octave and Python (with packages such as NumPy/SciPy, Pandas, matplotlib, etc).

ACCRE staff can work with you to set up access to additional free software or libraries, as well as commercial software for which you own a license.

It is possible for students to purchase licenses of software such as Matlab or Stata at the Software Store and use these on the cluster.

• Matlab: an additional annual license for use on the cluster must be purchased, at a cost of approximately $100 per year. Once you’ve purchased the license open a ticket with ACCRE staff and you will be granted access to a Matlab installation already on the cluster.
• Stata: the regular perpetual license sold by the software store is issued on a per-user rather than per-machine basis. ACCRE staff can assist you in installing your licensed copy in your home folder on ACCRE.

As of Fall 2015, the following packages are installed for use on ACCRE.

• Packages in brackets require some additional licensing, all others are free to access.
• Run ‘pkginfo’ at the prompt on ACCRE to obtain the most current list.

acml   AMD core math library

ansys   ANSYS

archive

atlas   ATLAS Self-tuning BLAS (GCC) [blas]

atlas_intel14   ATLAS Self-tuning BLAS (INTEL 14) [blas]

atlas_nehalem_gcc   ATLAS Self-tuning BLAS for Nehalem (GCC) [blas]

atlas_nehalem_intel   ATLAS Self-tuning BLAS (GCC) [blas]

atlas_x86-64_gcc   ATLAS Self-tuning BLAS (GCC) [blas]

aztec   aztec parallel iterative solver library for solving sparse linear systems.

blast   FSA-BLAST (Basic Local Alignment Search Tool)

blast_intel   FSA-BLAST (Basic Local Alignment Search Tool)

boost   BOOST 1.53.0 (GCC 4.6, Python 2.6) [boost]

boost_1.58.0   BOOST 1.58.0 (GCC 4.6, Python 2.7.8, OpenMPI 1.8.4) [boost]

boost_1.58.0_gcc490   BOOST 1.58.0 (GCC 4.9, Python 2.7.8, OpenMPI 1.8.4) [boost]

boost_1.58.0_python_3.4.2   BOOST 1.58.0 (GCC 4.6, Python 3.4.2, OpenMPI 1.8.4) [boost]

boost_147_sysgcc   BOOST (GCC) [boost]

boost_151_sysgcc   BOOST (GCC) [boost]

boost_python27_1490   BOOST (GCC) [boost]

calcRoiCovg   calcRoiCovg (GCC 4.6)

casava   CASAVA (1.8.2)

cmake   cmake 3.2.0

cmake2   cmake 2.8.10.2

cuda4.2   CUDA (4.2)

cuda5.0   CUDA (5.0)

cuda6.0   CUDA (6.0)

cuda6.5   CUDA (6.5)

cuda7.0   CUDA (7.0)

cuda7.5   CUDA (7.5)

dakota   Dakota

dakota_atlas_x86-64_gcc   Dakota

dcmtk   dcmtk 3.6.0

ddt   Allinea Distributed Debugging Toolkit version 5.0

ea-utils   ea-utils (FASTQ processing utilities)

ffmpeg   ffmpeg  (version 2.7.2)

ffmpeg-latest   ffmpeg-latest  (version 2.7.2)

fftw2   FFTW2 for ethernet (GCC - MPICH2) [fftw2]

fftw2-intelmpi_intel14_ether   FFTW2 for ethernet (Intel14 - INTELMPI) [fftw2]

fftw2-mpich2_gcc_ether   FFTW2 for ethernet (GCC - MPICH2) [fftw2]

fftw2-mpich2_intel12_ether   FFTW2 for ethernet (Intel12 - MPICH2) [fftw2]

fftw2-mpich2_intel14_ether   FFTW2 for ethernet (Intel14 - MPICH2) [fftw2]

fftw3   FFTW3 (GCC) [fftw3]

fftw3-mpich2_intel_ether   FFTW3 for ethernet (Intel - Mpich2) [fftw3]

fftw3-single-mpich2_intel_ether  FFTW3 single precision for ethernet (Intel - Mpich2) [fftw3]

fftw3_gcc   FFTW3 (GCC) [fftw3]

fftw3_intel   FFTW3 (Intel) [fftw3]

fftw3_intel14   FFTW3 (Intel) [fftw3]

freesurfer   freesurfer (version 5.3.0) (freesurfer-x86_64-unknown-linux-gnu-stable5-20130513)

freesurfer51   freesurfer (version 5.1.0) (freesurfer-x86_64-redhat-linux-gnu-stable5-20110522)

fsl   FSL (version 4) [fsl]

fsl5   FSL (version 5) [fsl]

gcc_compiler   GCC Compiler (4.6.1)

gcc_compiler_4.9.0   GCC Compiler (4.9.0)

gcc_compiler_5.2.0   GCC Compiler (5.2.0)

gd

ghc   GHC -- ghc for QIIME

git   Git distributed software source code management

gnuplot   Gnuplot

gotoblas2_intel   GOTOBLAS for nehalem (INTEL14) [gotoblas]

gotoblas2_nehalem_gcc   GOTOBLAS for nehalem (GCC) [gotoblas]

gotoblas2_nehalem_intel   GOTOBLAS for nehalem (INTEL12) [gotoblas]

gotoblas2_opteron_gcc   GOTOBLAS for opteron (GCC) [gotoblas]

gotoblas2_opteron_intel   GOTOBLAS for opteron (INTEL12) [gotoblas]

grace   Grace (2D plotting tool for the X Window System and M*tif)

gsl_gcc   GNU Scientific Library (GCC) [gsl]

gsl_intel   GNU Scientific Library (Intel) [gsl]

gsl_intel14   GNU Scientific Library (Intel) [gsl]

hdf5   HDF5 1.8.8

hdf5_openmpi   HDF5 1.8.14 (Compiled with OpenMPI 1.8.4)

hoomd_0.10.1   HOOMD-BLUE GPU Molecular Dynamics Simulator (version 0.10.1)

hoomd_1.0.1   HOOMD-BLUE GPU Molecular Dynamics Simulator (version 1.0.1)

hoomd_1.0.5   HOOMD-BLUE GPU Molecular Dynamics Simulator (version 1.0.5)

idl-7.1   IDL 7.1 (Keivan Stassun)

idl-8.0   IDL 8.0 (Keivan Stassun)

ImageMagick   ImageMagick (6.7.6) - image manipulation

impute   Impute (including gtool and snptest)

intel_cluster_studio_compiler   Intel Cluster Studio Compiler (Including Intel MPI)

intel_compiler   Intel 12 Compiler, including fortran

intel_compiler2013   Intel 2013 Compiler, including fortran

intel_compiler2013_sp1   Intel 2013 Compiler, including fortran (icc 14.0.3)

jags   JAGS -- Just Another Gibbs Sampler

java   Java - Software Development Kit

java_1.6   Java 1.6 - Software Development Kit

java_1.8   Java 1.8.0 - Software Development Kit

joinx   joinx 1.12 (GCC 4.6)

lammps_intel   LAMMPS for intel and mpich2 [mpich2]

lammps_mic   LAMMPS (ver. 21Jul2015) MD Simulator for Intel Xeon Phi

lapack_atlas   LAPACK with ATLAS (GCC) [lapack]

lapack_atlas_intel14   LAPACK with ATLAS for x86-64 (Intel14) [lapack]

lapack_atlas_nehalem_gcc   LAPACK with ATLAS for Nehalem (GCC) [lapack]

lapack_atlas_nehalem_intel   LAPACK with ATLAS for Nehalem (Intel12) [lapack]

lapack_atlas_x86-64_gcc   LAPACK with ATLAS (GCC) [lapack]

lio   LIO

llvm_compiler   LLVM/Clang (3.3)

lstore-client   L-Store client tools

matlab   Matlab (r2014b) [matlab]

matlab_r2012a   Matlab (r2012a) [matlab]

matlab_r2013a   Matlab (r2013a) [matlab]

matlab_r2014a   Matlab (r2014a) [matlab]

matlab_r2015a   Matlab (r2015a) [matlab]

matlab_r2015b   Matlab (r2015b) [matlab]

meep   Meep 1.2.1 (GCC, MPICH2)

meep_openmpi   Meep 1.2.1 (Compiled with OpenMPI 1.8.4 and Parallel HDF5 1.8.12)

merlin   MERLIN 1.1.2

mono   Mono

mpich2_gcc_ether   MPICH2 for ethernet (GCC) [mpich2]

mpich2_intel14_ether   MPICH2 for ethernet (Intel 2013 compiler) [mpich2]

mpich2_intel_ether   MPICH2 for ethernet (Intel12 compiler) [mpich2]

mpiexec   MPIEXEC (from Ohio Supercomputer Center)

mricron   MRIcron a cross-platform NIfTI format image view

mvapich2_2.1+cuda_7.0   mvapich2 2.1 (GCC 4.6, CUDA 7.0) [mpi]

mysql-client   MySQL client

nedit   NEdit 5.5 GCC

nedit_intel   NEdit 5.5 Intel

octave   Octave

openmpi_1.6.4   OpenMPI 1.6.4 (GCC 4.6) [mpi]

openmpi_1.8.4   OpenMPI 1.8.4 (GCC 4.6) [mpi]

openmpi_1.8.4+cuda_7.0   OpenMPI 1.8.4 (GCC 4.6, CUDA 7.0) [mpi]

openmpi_gcc   OpenMPI 1.4.4 (GCC-compiled) [mpi]

openmpi_intel   OpenMPI 1.4.4 (INTEL-compiled) [mpi]

openmpi_intel14   OpenMPI 1.4.4 (INTEL14-compiled) [mpi]

oracle   Oracle Client version

orthagogue   orthagogue

perl   Perl (5.14.2)

perl_5.16.2   Perl (5.16.2)

perl_thread   Perl (5.14.2) with multithreaded support

petsc   Petsc (3.4)

phoebe   Physics of Eclipsing Binaries

plink   Plink Genome Association Analysis Toolset

plink2   Plink2 (1.90 beta) Genome Association Analysis Toolset

python   Python (2.7.2)

python2   Python (2.7.2)

python2.7.4   Python (2.7.4)

python2.7.8   Python (2.7.8)

python2.7.8_intel14   Python (2.7.8, Intel-compiled + Intel MKL)

python3   Python (3.2.2)

python3.4.2   Python (3.4.2)

python_xnat   python_xnat for NI research (2.7.3)

qemu   QEMU Machine Emulator / Virtual Machine (1.5.1)

qtdt   QTDT 2.6.1

R   R (2.14.0) statistical programming language (GCC 4.6 / x86_64)

R_2.15.0   R (2.15.0) statistical programming language (GCC 4.6 / x86_64)

R_3.0.0   R (3.0.0) statistical programming language (GCC 4.6 / x86_64)

R_3.0.2   R (3.0.2) statistical programming language (GCC 4.6 / x86_64)

R_3.1.1   R (3.1.1) statistical programming language (GCC 4.6 / x86_64)

R_3.1.1_intel   R (3.1.1) statistical programming language (Intel 14 / x86_64)

R_3.2.0   R (3.2.0) statistical programming language (Intel 14 / x86_64)

R_3.2.0_gcc   R (3.2.0) statistical programming language (GCC 4.6 / x86_64)

R_gpu   R (2.14.0) GPU version - statistical programming language (GCC 4.6 / x86_64)

R_x86-64_gcc   R (2.14.0) statistical programming language (GCC 4.6 / x86_64)

R_x86-64_intel   R (2.14.0) statistical programming language (Intel 12 / x86_64)

relion   RELION 1.3 (OpenMPI 1.8.4)

ruby   Ruby 2.1.1

ruby1.8   Ruby 1.8.7

ruby1.9.3   Ruby 1.9.3

ruby2.0.0   Ruby 2.0.0

ruby2.2.0   Ruby 2.2.0

ruby2.2.0_intel   Ruby 2.2.0

sas   SAS 9.3 [sas]

scalapack_mpich2_gcc   SCALAPACK with mpich2 (gcc) [scalapack]

scalapack_mpich2_intel   SCALAPACK with mpich2 (gcc) [scalapack]

shogun   Shogun Machine Learning Toolbox (4.0.0) with Python (2.7.8) Modular

solar   Sequential Oligogenic Linkage Analysis Routines (7.2.5)

spark   Apache Spark (1.5.0 w/ Java 1.8, Python 3.4.2, R 3.2.0)

sparsehash   Sparsehash (2.0.2)

stata   [stata]

subversion   Subversion

supermongo   Supermongo Plotting Programme [supermongo]

swig   Swig (3.0.5)

swig2   Swig (2.0.4)

tabix   Tabix 0.2.4 (GCC 4.6, Python 2.7.2, Perl 5)

valgrind   valgrind

valgrind_3.8.1   valgrind