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Software Available on Jasper

Title Version Usage Notes
64-bit Linux CentOS 6.6 2.6.32-504.23.4.el6
ABAQUS 6.12-2

wg-abaqs group only

module load application/abaqus/6.12-2

ABAQUS 6.13-1

wg-abaqs group only

module load application/abaqus/6.13-1 

ABINIT 7.8.1

module load application/abinit/7.8.1

ABINIT 7.10.5

module load application/abinit-7.10.5

ABySS 1.3.2

module load application/ABySS/1.3.2

Adaptive Poisson-Boltzmann Solver (APBS) 1.5

module load application/apbs/1.5

ADMIXTURE 1.23

module load application/admixture/1.23

Amber 12

module load application/amber/12

Amber 14

module load application/amber/14  

Annovar 2015Dec14

module load application/annovar/2015Dec14 

ATSAS 2.7.2-5

module load application/atsas/2.7.2-5

Augustus 3.0.2

module load application/augustus/3.0.2

AutoDock 4.2.6

module load application/autodock/4.2.6

AutoDock_vina 1_1_2

module load application/autodock_vina/1_1_2 

BamTools 2.4.0

module load application/bamtools/2.4.0

bash (default) 3.2.25 or later
BCFtools (VCF/BCF file manipulation) 1.3.1

module load application/bcftools/1.3.1

BEAGLE (beagle-lib) 2.1.2

module load library/beagle/2.1.2

bgc 1.03

module load application/bgc/1.03

BLAS In MKL
BLAST NCBI BLAST+ 2.2.30+

Initialize your environment to use NCBI BLAST 2.2.30+ with

module load application/blast/2.2.30

BLAST ncbi-blast-2.3.0

module load application/blast/2.3.0

BLAT 3.5

module load application/blat/3.5

BMTagger 1.0

module load application/bmtagger/1.0 

Boost 1.59.0

module load library/boost/1_59_0

Boost 1.54.0

Initialize your environment to use Boost 1.54.0 with

module load library/boost/1_54_0

Bowtie 1.1.1

module load application/bowtie/1.1.1

Bowtie 1.1.2

module load application/bowtie/1.1.2

Bowtie2 2.2.3

module load application/bowtie2/2.2.3 

BWA 0.7.12

module load application/bwa/0.7.12

C - GNU GCC, Intel, Portland Group (PGI) compilers GNU 4.8.2

(gcc - module load compiler/gcc/4.8.2)

C - GNU GCC, Intel, Portland Group (PGI) compilers Intel 13.0.1

(icc, module load compiler/intel/13.0.1)

C - GNU GCC, Intel, Portland Group (PGI) compilers GNU 4.4.7

(gcc, system compiler)

C - GNU GCC, Intel, Portland Group (PGI) compilers Portland Group 12.10

(pgcc - module load compiler/pgi/12.10)

C - GNU GCC, Intel, Portland Group (PGI) compilers Portland Group 13.9

(pgcc - module load compiler/pgi/13.9)

C - GNU GCC, Intel, Portland Group (PGI) compilers GNU 6.3.0

module load compiler/gcc/6.3.0

C - GNU GCC, Intel, Portland Group (PGI) compilers 4.7.2

(gcc - module load compiler/gcc/4.7.2)

C++ - GNU GCC, Intel, Portland Group (PGI) compilers GNU 4.8.2

(g++, c++ - module load compiler/gcc/4.8.2)

C++ - GNU GCC, Intel, Portland Group (PGI) compilers Intel 13.0.1

(icpc, module load compiler/intel/13.0.1)

C++ - GNU GCC, Intel, Portland Group (PGI) compilers Portland Group 12.10

(pgCC - module load compiler/pgi/12.10)

C++ - GNU GCC, Intel, Portland Group (PGI) compilers Portland Group 13.9

(pgCC - module load compiler/pgi/13.9)

C++ - GNU GCC, Intel, Portland Group (PGI) compilers GNU 6.3.0

module load compiler/gcc/6.3.0

C++ - GNU GCC, Intel, Portland Group (PGI) compilers 4.7.2

(gcc, c++, module load compiler/gcc/4.7.2)

CGAL 4.4

Initialize your environment to use the CGAL library with

module load application/cgal/4.4

CISM 2.0.5

module load application/cism/2.0.5 

or

module load application/cism/2.0.5-serial

may need to do 

ln -s /global/software/cism/cism-2.0.5/bin/cism_driver  ./

CLAPACK 3.2.1

module load library/clapack/3.2.1 

CLHEP 2.3.1.1

module load library/clhep/2.3.1.1 

Climate Data Operators (CDO) 1.7.1rc1

module load application/cdo/1.7.1rc1

CMake 3.0.2

module load utility/cmake/3.0.2 

CNVnator 0.3.2

module load application/cnvnator/0.3.2 

Compilers - C, C++ and Fortran Intel 13.0.1

Initialize your environment to use the Intel 13.0.1 compilers with

module load compiler/intel/13.0.1

Compilers - C, C++ and Fortran GCC 4.8.2

Initialize your environment to use the GCC 4.8.2 compilers with

module load compiler/gcc/4.8.2

Compilers - C, C++ and Fortran GCC 4.7.2

Initialize your environment to use the GCC 4.7.2 compilers with

module load compiler/gcc/4.7.2

Compilers - C, C++ and Fortran GCC 4.4.7

The GCC 4.4.7 compilers are on the default command PATH.

Compilers - C, C++ and Fortran PGI 13.9-0

Initialize your environment to use the Portland Group 13.9-0 compilers with

module load compiler/pgi/13.9

CompuCell3D 3.7.5

module load application/CompuCell3D/3.7.5

CPMD 3_15_3

module load application/cpmd/v3_15_3

csh Link to tcsh
DiScRIBinATE Mar21-2013

module load application/discribinate/Mar21-2013

DL_POLY 4.04

module load application/dl_poly/4.04

DL_POLY Classic 1.9

module load application/dl_poly/class_1.9

DosageConverter 1.0.3

module load application/dosageconverter/1.0.3

Elk 2.1.22 (beta)

This is a mixed OpenMP-MPI code so therefore caution should be used to ensure that an appropriate combination of MPI processes and OpenMP threads is used.

To set up the environment to use Elk, use

module load application/elk/2.1.22

Emacs 23.1.1
Exonerate 2.4.0

module load application/exonerate/2.4.0

Expat 2.1.0

module load library/expat/2.1.0

FastQC 0.11.5

module load application/fastqc/0.11.5 

FFTW 2.1.5

modulel load library/fftw2/2.1.5

FFTW 3.3.1

module load library/fftw/3.3.1

FFTW 3.3.4

module load library/fftw/3.3.4

Fortran - GNU GCC, Intel, Portland Group (PGI) and Absoft compilers GNU 4.8.2 (gfortran)

(gfortran, module load compiler/gcc/4.8.2)

Fortran - GNU GCC, Intel, Portland Group (PGI) and Absoft compilers Intel 13.0.1

(ifort, module load compiler/intel/13.0.1)

Fortran - GNU GCC, Intel, Portland Group (PGI) and Absoft compilers GNU 4.4.7

(gfortran, gfortran44 - module load compiler/gcc/4.4.6)

Fortran - GNU GCC, Intel, Portland Group (PGI) and Absoft compilers Portland Group 12.10

(pgf77, pgf90, pgf95 - module load compiler/pgi/12.10)

Fortran - GNU GCC, Intel, Portland Group (PGI) and Absoft compilers Portland Group 13.9

(pgf77, pgf90, pgf95 - module load compiler/pgi/13.9)

Fortran - GNU GCC, Intel, Portland Group (PGI) and Absoft compilers GNU 6.3.0

module load compiler/gcc/6.3.0

Fortran - GNU GCC, Intel, Portland Group (PGI) and Absoft compilers 4.7.2

module load compiler/gcc/4.7.2

GAMESS 1May2013

module load application/gamess/20130501  

rungms jobName 00

Gar2ped 13-dec-1996

module load application/gar2ped/13-dec-1996

GATE 7.2

module load application/gate/7.2

Gaussian G09 D.01

For U of A researchers only.  Initialize your environment with:

module load uofa/gaussian/g09-d1

gdb 7.0.1-37.el5_7.1
Geant4 10.02.p01

module load application/geant4/10.02.p01

gedit - graphical text editor 2.28.4

See general gedit usage notes.

GHMM 0.9-rc3

module load application/ghmm/0.9-rc3

Git 1.7.10.1

module load application/git/1.7.10.1

GMAP (with GSNAP) - Genomic mapping and alignment 2014-12-02

module load application/gmap/2014-12-02

GNU binutils 2.28

module load utility/binutils/2.28

Gnuplot 4.2
GOTTCHA 1.0b

module load application/gottcha/1.0b  

Grace/Xmgrace 5.1.22

xmgrace is on the default command PATH, in /usr/bin.

GROMACS 5.1.2 with plumed 2.2.2

module load application/gromacs/5.1.2plumed 

GROMACS 4.5.5

Initialize the environment with module load application/gromacs/4.5.5 .

GROMACS 4.6.1

Initialize the environment with module load application/gromacs/4.6.1 .

GROMACS 5.1

module load application/gromacs/5.1

gmx <command>

gmx_d <command>

mdrun_mpi

mdrun_mpi_d

GSL 1.16

module load library/gsl/1.16

Gulp 4.3

module load application/gulp/4.3

HDF 5 1.8.9

module load library/hdf5/1.8.9 

module load library/hdf5/1.8.9-parallel

module load library/hdf5/1.8.9-intel

module load library/hdf5/1.8.9-intel-parallel

HMMER 3.1b2

module load application/hmmer/3.1b2

HTSlib 1.2.1

module load application/htslib/1.2.1

idb Intel 13.0.1

(idb, module load compiler/intel/13.0.1)

ImageMagick 6.5.4.7
IMPUTE (genotype imputation) 2.3.2

module load application/impute2/2.3.2

Intel MPI 4.1.0.024

Feb.12, 2014: Currently unavailable due to incompatibilities with the queuing system.  Please email support@westgrid.ca for alternatives.

module load library/intelmpi/4.1.0.024

InterProScan 5.3-46.0

module load application/interproscan/5.3-46.0

InterProScan 5.20-59.0

module load application/interproscan/5.20-59.0

JAGS 4.2.0

module load application/jags/4.2.0

Java Oracle JDK 1.8.0 update 92

module load application/jdk/1.8.0_92

Java OpenJDK 1.8.0_45
JELLYFISH 1.1.11

module load application/jellyfish/1.1.11        

Julia 0.4.5

module load application/julia/0.4.5 

Kraken 0.10.5-beta

module load application/kraken/0.10.5-beta  

ksh Y
LAMMPS 28Jun14

module load application/lammps/28Jun14

lmp_jasper

LAPACK In MKL
LibYAML 0.14

module load library/yaml/0.1.4

Lis 1.7.36

module load application/lis/1.7.36-gnu

or

module load application/lis/1.7.36-intel 

Mach 1.0.18

module load application/mach/1.0.18

Maker 2.31.8

modulel load application/maker/2.31.8  

Please use only one node. i.e. nodes=1:ppn=x

Maple 17

U oF A only

module load uofa/maple/17

Mathematica 8.0

U of A only

module load uofa/Mathematica/8.0

MATLAB R2014a

module load uofa/matlab/R2014a

(UofA only)

MATLAB R2013a module load uofa/matlab/R2013a

(UofA only)
MEGAHIT 1.1.0-pre

module load application/megahit/1.1.0-pre

Megan 5_10_3

module load application/megan/5_10_3

License file: /global/software/megan/MEGAN5-academic-license.txt

Memprot 1.7

module load application/memprot/1.7

Mercurial 3.5

module load utility/mercurial/3.5

Migrate (Migrate-n) - Population genetics program to estimate migration rates and population sizes 3.6.4

Initialize your environment to use Migrate with

module load application/migrate/3.6.4

See the generic Running Instructions section of the WestGrid Migrate page for more information.

Minimac2 2014.9.15

module load application/minimac2/2014.9.15

Minimac3 2.0.1

module load application/minimac3/2.0.1

MKL In Intel 12 environment
Mono (C# environment) 3.10.0

module load load application/mono/3.10.0

Mono (C# environment) 4.2.1

Initialize your environment to use Mono 4.2.1 on Jasper with

module load application/mono/4.2.1

MPFR 3.1.2

module load library/mpfr/3.1.2

MrBayes 3.2.6 (parallel)

module load application/mrbayes/3.2.6

muParser 2_2_3

module load library/muparser/2_2_3

NAMD 2.10

module load application/namd/2.10

mpiexec namd2 ...

nano 1.3.12

pico is just a link to nano

NCAR Graphics and NCL 6.3.0

Initialize your enivronment to use NCAR Command Language 6.3.0 on Jasper with

module load application/ncl_ncarg/6.3.0

NCO 4.3.9

module load application/nco/4.3.9 

Ncview 2.1.1

module load application/ncview/2.1.1

NEdit 5.5
NetCDF 4.1.3

module load library/netcdf/4.1.3

NetworkX 1.7

module load application/python/2.7.3

NWChem 6.1.1

module load application/nwchem/6.1.1

Octave 4.0.3

module load application/octave/4.0.3

Octave 3.4.3

In default path.

Open MPI 1.8.4

module load library/openmpi/1.8.4-intel

Open MPI 1.6.5

module load library/openmpi/1.6.5-intel

module load library/openmpi/1.6.5-noDlopen

module load library/openmpi/1.6.5-valgrind

OpenBUGS 3.2.2

module load application/openbugs/3.2.2

OpenCV 2.4.12

module load application/opencv/2.4.12

OpenFOAM, OpenFOAM+ and OpenFOAM Extend 3.0.1

module load application/OpenFOAM/3.0.1

source $OPENFOAM_SETUP

OpenFOAM, OpenFOAM+ and OpenFOAM Extend 2.4.0

module load application/OpenFOAM/2.4.0

source $OPENFOAM_SETUP

OpenFOAM, OpenFOAM+ and OpenFOAM Extend 2.3.0

Set up your environment to use OpenFOAM with

module load application/OpenFOAM/2.3.0
source $OPENFOAM_SETUP

openkim 1.5.0

module load application/openkim/1.5.0

ORCA 2_9_1

module load application/orca/2_9_1

parallel-netcdf 1.3.1

module load library/parallel-netcdf/1.3.1

PEAR 0.9.6

module load application/pear/0.9.6

Perl 5.20.0

module load application/perl/5.20.0

Perl 5.14.4

module load application/perl/5.14.4

module load application/perl/5.14.4t

(with threading support)

Perl 5.16.3

module load application/perl/5.16.3 

Perl 5.18.2

module load application/perl/5.18.2

Perl 5.19.11

module load application/perl/5.19.11

module load application/perl/5.19.11t

(with threading support)

PETSc 3.7.6

module load application/petsc/3.7.6  

PETSc 3.5.1

module load application/petsc/3.5.1

PETSc 3.0.0-p7

module load application/petsc/3.0.0-p7

module load application/petsc/3.0.0-p7-debug

PETSc 3.3-p6

module load application/petsc/3.3-p6

PHAST (Phylogenic Analysis with Space/Time Models) 1.3

Initialize your environment to use PHAST 1.3 on Jasper with

module load application/phast/1.3

Phonopy 1.10.0

module load application/phonopy/1.10.0

Phonopy 1.8.1

module load application/phonopy/1.8.1

PLINK 1.07

module load application/plink/1.07  

PLINK 1.90

module load  application/plink/1.90  

PLUMED 2.2.2

module load application/plumed/2.2.2

PRINSEQ 0.20.4

module load application/prinseq/0.20.4

Python Anaconda 2.4.1

module load application/anaconda/anaconda2  

Python 2.7.3

Initialize your environment with:

module load application/python/2.7.3

This installation includes NumPy 1.6.2, SciPy 0.11.0 and matplotlib 1.2.0 .

Python 2.6.8

module load application/python/2.6.8 

Python 2.7.8

module load application/python/2.7.8

Qt 4.8.5

module load library/qt/4.8.5

Quantum ESPRESSO 6.0

module load application/espresso/6.0

Quantum ESPRESSO 5.2.1

Initialize your environment to use Quantum ESPRESSO 5.2.1 with

module load application/espresso/5.2.1

Quantum ESPRESSO 5.4.0

module load application/espresso/5.4.0

Quantum ESPRESSO 5.1

module load application/espresso/5.1

R 3.1.2

module load application/R/3.1.2

R 3.3.1

module load application/R/3.3.1

or

module load application/R/3.3.1-mkl

compiled with intel compiler and mkl library

R 3.2.5

module load application/R/3.2.5

RAPSearch (protein similarity search) 2.12_pair

module load application/rapsearch/2.12_pair

RAPSearch (protein similarity search) 2.23

module load application/rapsearch/2.23

Relion 1.4

module load application/relion/1.4

RepeatMasker open-4-0-6

module load application/repeatmasker/open-4-0-6

RepeatMasker open-4-0-5

module load application/repeatmasker/open-4-0-5

RNAmmer 1.2

module load application/rnammer/1.2

ROOT (data analysis framework) 5.34.17

Initialize your environment to use ROOT 5.34.17 with

module load application/root/v5.34.17

Rosetta Software Suite 2015.25.57927

module load application/rosetta/2015.25.57927

RSEM 1.2.20

module load application/rsem/1.2.20

RSEM 1.2.31

module load application/rsem/1.2.31

RStudio 0.98

module load application/rstudio/0.98

Ruby 1.8.7
SAMtools and HTSlib utilities 1.3.1

module load application/samtools/1.3.1

SAMtools and HTSlib utilities 1.1

module load application/samtools/1.1

ScaLAPACK MKL

ScaLAPACK is available through the Math Kernel Library (MKL).

SCons 2.3.2

module load utility/scons/2.3.2

SCOTCH 6.0.0

module load application/scotch 6.0.0

Seismic Un*x Release 42

module load application/cwp_su/42

sh Link to bash
SHAPEIT (estimation of haplotypes) 2.r837

module load application/shapeit/v2.r837

ShengBTE - solving Boltzmann Transport Equation for phonons 1.0.2

Set up your environment to use ShengBTE with

module load application/ShengBTE/1.0.2

ShengBTE - solving Boltzmann Transport Equation for phonons 1.1.0

module load application/ShengBTE/1.1.0

SIESTA 3.2

module load application/siesta/3.2

SignalP 4.1c

module load application/signalp/4.1c

Sire 14_4

module load application/sire/14_4

Smoldyn 2.39

module load application/smoldyn/2.39

SNAP 2013-11-29

module load application/snap/2013-11-29

SNPTEST 2.5.2

Before running the snptest executable on Jasper, initialize your environment with

module load application/snptest/2.5.2

Spglib 1.8.2.2

module load library/spglib/1.8.2.2

Stacks 1.40

module load /global/software/stacks/stacks-1.40/bin

Stacks 1.27

Initialize your environment with

module load application/stacks/1.27

Stacks 1.35

module load application/stacks/1.35

Structure 2.3.4

Either one of

module load application/structure/2.3.4

or

application/structure-frontend/2.3.4

Subread 1.5.2

module load application/subread/1.5.2

Subversion 1.6.11
SVDetect r0.8b

module load application/svdetect/r0.8b

Swig 3.0.5

module load application/swig/3.0.5

Szip 2.1 module load library /szip/2.1

/global/software/szip-2.1/
tcsh NA
TMHMM 2.0c

module load application/tmhmm/2.0c

TopHat 2.0.14

module load application/tophat/2.0.14

TransDecoder 2.1.0

module load application/transdecoder/2.1.0

Treemix 1.12

module load application/treemix/1.12

Trilinos 12.6.3

module load application/trilinos/12.6.3

Trimmomatic 0.36

module load application/trimmomatic/0.36

java -jar $JAR PE ...

or

java -jar $JAR SE ...

Trinity 2.4.0

module load application/trinity/2.4.0

Trinity 2.1.1

module load application/trinity/2.1.1

Trinity 2.0.6

module load application/trinity/2.0.6

Trinity r20131110

module load application/trinity/r20131110

Trinotate r20140708

module load application/trinotate/r20140708

Trinotate 3.0.0

module load application/trinotate/3.0.0

VASP 5.3.5

Initialize your environment with

module load application/vasp/5.3.5

The vasp and makeparam executables were compiled with the flag -DNGZhalf
.

For vasp-tbdyn and makeparam-tbdyn: -DNGZhalf
 -Dtbdyn
 .

For vasp-full and makeparam-full: without -DNGZhalf and without -Dtbdyn .
 
The various potentials are in /global/software/vasp/vasp.5.3.5/pseudo/.

VCFtools 0.1.13

module load application/vcftools/0.1.13

Vim 7.0
VMD 1.9.2

module load application/vmd/1.9.2

VTK - Visualization Toolkit 5.10.1

module load application/vtk/5.10.1

Wannier90 2.0.1

module load application/wannier90/2.0.1

WHAM/WHAMG - WHole-genome Alignment Metrics 1.7.0

module load application/wham/1.7.0

WRF WPS 3.7.1

module load application/wrf/3.7.1

WRF WRF 3.6.1

module load application/wrf/3.6.1

WRF WPS 3.6.1

module load application/wrf/3.6.1

WRF WRF 3.7.1

module load application/wrf/3.7.1

XCrySDen 1.5.60

module load application/xcrysden/1.5.60

and use vnc to connect

Xerces-C++ 3.1.1

module load application /xerces-c/3.1.1