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Software Available on Bugaboo

Title Version Usage Notes
2014-10-22

(in default path)

4.2.1
N
64-bit Scientific Linux 6.4
ABINIT 7.2.2

module load abinit/7.2.2

ABINIT 7.4.2

(in default PATH)

ABySS 1.5.2

(in default PATH)

ABySS 1.3.5

module load abyss/1.3.5

ALLPATHS-LG Revision 47417

(in default PATH)

AlmaBTE 0.1

(in default path)

AlmaBTE 1.2

module load almabte/1.2

Amber 14

module load amber/14

Amber 12 module load amber
ARB 5.5

(in default PATH)

ASE 3.8.1

In default path

bash (default) 4.1.2
BEAGLE (beagle-lib) 2.1.2

-lhmsbeagle

BEAM 4.11
BEAST 2.4.7

module load beast/2.4.7

BEAST 1.7.5

module load beast/1.7.5 (No add-on)

BEAST 2.4.4

module load beast/2.4.4 (includes all packages)

BEAST 2.1.3

Includes all packages.

BEDTools 2.17.0

(in default path)

BEDTools 2.26.0

module load bedtools/2.26.0

BioPerl 1.6.924

in default path

BioPerl 1.6.924

module load bioperl/1.6.901

Biopython 1.62
BLAS In MKL

-lmkl

BLAS openblas-0.2.6

-lblas (equivalent to -lopenblas)

BLAS GotoBlas2 - 1.13

-lgoto2

BLAST 2.2.31+

module load ncbi-blast+/2.2.31+

BLAST ncbi-blast-2.6.0+

module load ncbi-blast+/2.6.0+

BLAST NCBI BLAST 2.2.26 (Legacy BLAST)

(databases in /usr/local/blastdb)

BLAST mpiblast 1.6.0
BLAST NCBI BLAST+ 2.2.28+

(databases in /usr/local/blastdb)

BLAT 3.5

(in default path)

Blitz++ 0.9
Boost 1.41.0

systems version

Boost 1.54.0

-I/usr/local/boost/include -L/usr/local/boost/lib -Wl,-rpath,/usr/local/boost-1.54.0/lib \
-lboost_name1 -lboost_name2 ...

 where name1, name2, etc. have to be replaced with the actual names of the libraries.

Bowtie 1.0.0

(in default path)

Bowtie2 2.1.0

(in default path)

Bowtie2 2.2.9

module load bowtie2/2.2.9

Bowtie2 2.2.5

module load bowtie2/2.2.5

BWA 0.7.10

(in default path)

BWA 0.7.4

module load bwa/0.7.4

BWA 0.7.7

module load bwa/0.7.7

BWA 0.7.12

module load bwa/0.7.12

C - GNU GCC, Intel, Portland Group (PGI) compilers Intel 16.0.1

module load intel/16.0.1

icc

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

module load intel/13.0.1
icc

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

module load gcc/4.4.7
gcc

C - GNU GCC, Intel, Portland Group (PGI) compilers Intel 14.0.1

module load intel/14.0.1
icc

C - GNU GCC, Intel, Portland Group (PGI) compilers Intel 17.0.1

module load intel/17.0.1

C - GNU GCC, Intel, Portland Group (PGI) compilers Intel 13.1.3

icc
(in default PATH)

C - GNU GCC, Intel, Portland Group (PGI) compilers GNU 4.8.0

gcc
(in default PATH)

C++ - GNU GCC, Intel, Portland Group (PGI) compilers Intel 16.0.1

module load intel/16.0.1
icpc

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

module load intel/13.0.1
icpc

C++ - GNU GCC, Intel, Portland Group (PGI) compilers GNU 4.8.0

g++
(in default PATH)

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

module load gcc/4.4.7
g++

C++ - GNU GCC, Intel, Portland Group (PGI) compilers Intel 14.0.1

module load intel/14.0.1
icpc

C++ - GNU GCC, Intel, Portland Group (PGI) compilers Intel 17.0.1

module load intel/17.0.1

C++ - GNU GCC, Intel, Portland Group (PGI) compilers Intel 13.1.3

icpc
(in default PATH)

Cantera 2.1.1

Linked with sundials-2.5.0 library. Users need to run "module load cantera"

Cd-hit 4.6.1

(in default path)

Cd-hit 3.1.1

module load cd-hit/3.1.1

Cd-hit 4.6.6

module load cd-hit/4.6.6

Celera Whole-Genome Shotgun Assembler 7.0

(in default PATH)

Censor 4.2.28

(in default path)

CGAL 4.6.1

In default path

Chaste 3.0
Circos 0.67-4

The Circos binary, circos, is on the default path.

Climate Data Operators (CDO) 1.6.1

(in default path)

CMake 2.8.11.2

(in default PATH)

CMake 3.3.2

module load cmake/3.3.2

Compilers - C, C++ and Fortran Intel 16.0.1

Initialize your environment to use the Intel 16.0.1 compilers with

module load intel/16.0.1

Compilers - C, C++ and Fortran Intel 17.0.1

module load intel/17.0.1

Compilers - C, C++ and Fortran GCC 4.4.7

Initialize your environment to use the GCC 4.4.7 compilers with

module load gcc/4.4.7

Compilers - C, C++ and Fortran GCC 4.8.0

The GCC 4.8.0 compilers are on the default command PATH.

Compilers - C, C++ and Fortran Intel 13.0.1

Initialize your environment to use the Intel 13.0.1 compilers with

module load intel/13.0.1

Compilers - C, C++ and Fortran Intel 13.1.3

The Intel 13.1.3 compilers are on the default command PATH, but, you can also explicitly initialize your environment to use them with

module load intel/13.1.3

Compilers - C, C++ and Fortran Intel 14.0.2

Initialize your environment to use the Intel 14.0.2 compilers with

module load intel/14.0.2

Compilers - C, C++ and Fortran Intel 15.0.2

Initialize your environment to use the Intel 15.0.2 compilers with

module load intel/15.0.2

CP2K 2.4.0

mpiexec cp2k input_file

CP2K 3.0.0

module load cp2k/3.0.0

POTENTIAL and BASIS files are located in /usr/local/cp2k-3.0.0/data

CPMD 3.15.1

(includes PLUMED 1.3 plugin)

csh Link to tcsh
Cufflinks 2.2.1

It is on default path

Cufflinks 2.1.1

module load cufflinks/2.1.1

ddd 3.3.12
deal.II 8.0.0

to link with the deal_II library use a syntax like:

mpicxx -I/usr/local/deal.II/include <optimizationflags> <sourcefiles> -o <executable> -ldeal_II

E.g., to compile the example program step-1.cc (/usr/local/deal.II/examples/step-1/step-1.cc) use:

mpicxx -I/usr/local/deal.II/include -O3 -xSSSE3 -axSSE4.2,SSE4.1 -ip step-1.cc -o step-1 -ldeal_II

DFTB+ - Density Functional based Tight Binding (DFTB) method with extensions 1.2.2

See the main DFTB+ page for running the software on Bugaboo.

DFTB+ - Density Functional based Tight Binding (DFTB) method with extensions mpi-r4473

This is a development snapshot of the MPI version of DFTB+. See the main DFTB+ page for running the software on Bugaboo.

DIRAC 12.7

module load dirac

dl_meso 2.6

(in default path)

Eigen 3.1.4

(in default search PATH)

Emacs 23.1
ExaML/RAxML - Phylogenetic tree analysis 8.2.9

module load RAxML/8.2.9

binary files, raxmlHPC, raxmlHPC-MPI, raxmlHPC-PTHREADS, raxmlHPC-HYBRID are serial, MPI,  threaded, and threaded-MPI version respectively

ExaML/RAxML - Phylogenetic tree analysis RAxML 7.3.0

module load RAxML/7.3.0

ExaML/RAxML - Phylogenetic tree analysis RAxML 7.7.6

It is on default path

ExaML/RAxML - Phylogenetic tree analysis ExaML 1.0.4
EXCITING lithium

exciting-serial serial version
mpiexec exciting MPI version

Expat 2.0.1

(system version)

FastTree 2.1.7

(in default path)

FFTW 2.1.5
FFTW 3.3.3
Fortran - GNU GCC, Intel, Portland Group (PGI) and Absoft compilers GNU 4.4.7

module load gcc/4.4.7
gfortran

Fortran - GNU GCC, Intel, Portland Group (PGI) and Absoft compilers Intel 13.1.3

ifort
(in default PATH)

Fortran - GNU GCC, Intel, Portland Group (PGI) and Absoft compilers Intel 16.0.1

module load intel/16.0.1
ifort

Fortran - GNU GCC, Intel, Portland Group (PGI) and Absoft compilers Intel 14.0.1

module load intel/14.0.1
ifort

Fortran - GNU GCC, Intel, Portland Group (PGI) and Absoft compilers GNU 4.4.4

gfortran, gfortran44

Fortran - GNU GCC, Intel, Portland Group (PGI) and Absoft compilers f77

Wrapper script for $FC, $F77, defaulting to ifort

Fortran - GNU GCC, Intel, Portland Group (PGI) and Absoft compilers f90

Wrapper script for $FC, $F90,defaulting to ifort

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

module load intel/13.0.1
ifort

Fortran - GNU GCC, Intel, Portland Group (PGI) and Absoft compilers GNU 4.8.0

gfortran
(in default PATH)

Fortran - GNU GCC, Intel, Portland Group (PGI) and Absoft compilers Intel 17.0.1

module load intel/17.0.1

freebayes 0.9.21

(in default path)

freebayes 1.0.2

module load freebayes/1.0.2

freebayes 0.9.20

module load freebayes/0.9.20

FreeFem++ - Partial Differential Equation Solver 3.23
GAMESS 1May2013

rungms -i inputfile

GapCloser 1.12-r6

(in default searching path)

Gbrowse 2.39
GDAL 1.10.0
gdb 7.6.1
gedit - graphical text editor 2.28.4

See general gedit usage notes.

Git 1.7.1
GLUT freeglut 2.6.0
GMAP (with GSNAP) - Genomic mapping and alignment 2014-10-22

The executables for the software are available on the default path.

GMAP (with GSNAP) - Genomic mapping and alignment 2016-06-09

module load gmap/2016-06-09

GMT - Generic Mapping Tools 4.5.9

(in default PATH)

GNU libgomp 4.4.4

module load gcc/4.4.7

GNU libgomp 4.8.0

-lgomp
(part of default gnu compiler suite)

Gnuplot 4.6.4
Grace/Xmgrace 5.1.23
GRIB-API 1.10.4

(in default PATH)

GRIB-API 1.14.0

module load grib_api/1.14.0 (The main directory located at /usr/local/grib_api-1.14.0)

GROMACS 4.6.5

(in default PATH)

GROMACS 5.0.6

Single precision version compiled with fftw3, Openblas, Lapack.

module load gromacs/5.0.6
mpiexec mdrun_mpi ...

This version has been compiled with Plumed (version 2.1.3) support. This can be enabled with the -plumed flag:

module load gromacs/5.0.6
mpiexec mdrun_mpi -plumed ...

GROMACS 5.1.3 with plumed 2.3b

module load gromacs/5.1.3

GROMACS 5.0.4

Single precision version compiled with fftw3, Openblas, Lapack.

module load gromacs/5.0.4
mpiexec mdrun_mpi ...

This version has been compiled with Plumed (version 2.1.2) support. This can be enabled with the -plumed flag:

module load gromacs/5.0.4
mpiexec mdrun_mpi -plumed ...

GROMACS 4.6.3

module load gromacs/4.6.3

GSL 1.16

-lgsl

GSL fgsl 0.9.4

This is a Fortran interface for the GSL library. Documentation can be found in /usr/local/doc/fgsl, in particular /usr/local/doc/fgsl/examples contains example programs.

Link with -lfgsl

Gulp 4.2.0
Hadoop 1.2.1

See the instructions for running Hadoop on Bugaboo.

HDF 4 4.2.9
HDF 5 1.8.11
hisat2 2.0.4

in default PATH

HMMER 3.1b2

module load hmmer-3.1b2

HMMER 2.3.2

module load hmmer/2.3.2

HMMER 3.1b1

In default path

idb 13.0.1

module load intel/13.0.1-1.117
idb (graphical interface) or idbc (command line interface)

idb 13.1.3

idb (graphical interface) or idbc (commandline interface)
(in default PATH)

IMa2 8.27.12
Ima2p 20151009

(In default path)

Image 2.4.1

module load image/2.4.1

ImageMagick 6.5.4.7
Intel MPI 5.1.2.150

module load mpi/intel

To compile programs use the mpicc, mpicxx, mpif90 commands.

To run programs use the mpiexec command.

Intel MPI 4.1.1p-036

Before using Intel MPI contact support@westgrid.ca

Ipopt 3.10.3
JAGS 3.3.0
Java OpenJDK 1.7.0_45

module load java/1.7.0

Java OpenJDK 1.6.0_24

module load java/1.6.0

Java OpenJDK 1.8.0_51

(in default path)

ksh 20100621
LAMMPS 7Dec15

mpiexec lmp

LAMMPS 5Nov16

module load lammps/20161105
mpiexec lmp

LAMMPS 11Aug17

module load lammps-20170811
mpiexec lmp

LAMMPS 30jul16

module load lammps/20160730

mpiexec lmp

LAMMPS 27Aug13

module load lammps/20130827

mpiexec lmp

LAMMPS 9Dec14

module load lmp/20141209
mpiexec lmp

LAPACK 3.5.0

-llapack -lblas

LAPACK In MKL

-lmkl

LepMAP 3.0.1

module load LepMAP/3.0.1

libjpeg 1.2.1

(libjpeg-turbo variant)

libpng 1.2.49
libtiff 3.9.4
links 2.2
MATLAB R2015a

module load matlab/2015a
(SFU only) 

MATLAB R2016a

(in default path)

(SFU only)

MATLAB R2015b

module load matlab/2015b (SFU only)

MATLAB R2013a

(default version; SFU only)

MATLAB R2011b module load matlab/2011b
(version 7.13.0.564; SFU only)
MATLAB R2012a module load matlab/2012a
(SFU only)
MATLAB R2014a

(SFU only)

MATLAB Compiler Runtime (MCR) 8.3

For use with standalone applications compiled with the version of the MATLAB compiler distributed with R2014a of MATLAB.

Installed to /usr/local/matlab-mcr/v83.

See full instructions for creating standalone applications.

MATLAB Compiler Runtime (MCR) 8.5

For use with standalone applications compiled with the version of the MATLAB compiler distributed with R2015a of MATLAB.

Installed to /usr/local/matlab-mcr/v85

MATLAB Compiler Runtime (MCR) 8.0

For use with standalone applications compiled with the version of the MATLAB compiler distributed with R2012b of MATLAB.

Installed to /usr/local/matlab-mcr/v80.

See full instructions for creating standalone applications.

MATLAB Compiler Runtime (MCR) 8.1

For use with standalone applications compiled with the version of the MATLAB compiler distributed with R2013a of MATLAB.

Installed to /usr/local/matlab-mcr/v81.

See full instructions for creating standalone applications.

MATLAB Compiler Runtime (MCR) 7.16

For use with standalone applications compiled with the version of the MATLAB compiler distributed with R2011b of MATLAB.

Installed to /usr/local/matlab-mcr/v716.

See full instructions for creating standalone applications.

 

MATLAB Compiler Runtime (MCR) 9.0.1

For use with standalone applications compiled with the version of the MATLAB compiler distributed with R2016a of MATLAB.

Installed to /usr/local/matlab-mcr/v901 (but may also be referenced as /global/software/mcr/v901).

MATLAB Compiler Runtime (MCR) 7.14

For use with standalone applications compiled with the version of the MATLAB compiler distributed with R2010b of MATLAB.

Installed to /usr/local/matlab-mcr/v714.

See full instructions for creating standalone applications.

MATLAB Compiler Runtime (MCR) 8.4

Installed to /usr/local/matlab-mcr/v84

MATLAB Compiler Runtime (MCR) 8.2

For use with standalone applications compiled with the version of the MATLAB compiler distributed with R2013b of MATLAB.

Installed to /usr/local/matlab-mcr/v82.

See full instructions for creating standalone applications.

MATLAB Compiler Runtime (MCR) 7.17

For use with standalone applications compiled with the version of the MATLAB compiler distributed with R2012a of MATLAB.

Installed to /usr/local/matlab-mcr/v717.

See full instructions for creating standalone applications.

 

Matplotlib 1.3.0
MEME Suite 4.9.0

module load meme/4.9.0

MEME Suite 4.11.3

(in default path)
Note: this is version 4.11.3-1 (patch 1 applied)

Mercurial 2.7
Mesa 9.0
MetaVelvet 1.2.02

in default PATH. Please note, The binary file name is meta-velvetg. If it hangs during the run please run comand "ulimit -s 20000" perior to use meta-velvetg.

METIS 5.0.3

-lmetis

METIS ParMETIS 4.0.3

-lparmetis

Migrate (Migrate-n) - Population genetics program to estimate migration rates and population sizes 3.6

migrate-n-mpi is on the default command PATH.

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

MKL 11.1.1

-lmkl

MMG3D 4.0.0
Molden 5.0.6

(in default PATH)

MOM 5.1.0

module load mom
MOM_run.csh --type <program>--experiment <name>--npes <#>

where <program> is one of CM2M, EBM, ESM2M, ICCM, MOM_SIS, MOM_solo and <name> is one of the cases that come with the MOM code like atlantic1, baltic1, box1, etc; <#> needs to be replaced with the number of processes to be used for the calculation - within a submission script this should be set to the preset system variable $PBS_NP.

Documentation is in /usr/local/mom/doc; the example and test cases are in /usr/local/mom/data. By default the directory work within the current directory is used as working directory. The MOMROOT environment variable can set to use a different directory structure. In that case the directory $MOMROOT/work is used as working directory and input files need to be copied to $MOMROOT/work/<name>/INPUT.

Mothur 1.31.2

The executable, mothur,  is in the default PATH.

MrBayes 3.2.4(parallel)

mpiexec mb

MrBayes 3.2.2 (parallel)

module load mrbayes/3.2.2
mpiexec mb

MUMPS 4.10.0
Muscle 3.8.31

(in default PATH)

MVAPICH2 2.1

module load mpi/mvapich

To compile programs use the mpicc, mpicxx, mpifort commands.

To run programs use the mpiexec command.

MySQL 5.5.34
NAMD 2.9
nano 2.0.9
NCAR Graphics and NCL 6.2.0

Set up your environment (bash shell example) with

export NCARG_ROOT=/usr/local/ncarg

before running ncl.

NCO 4.3.4

(in default PATH)

Ncview 2.1.2
NEdit 5.5
Nemo 2.3.42 - Parallel version

It is on default path.

NetCDF 4.3.0

C interface of the netcdf library (both serial and MPI version installed)
link with -lnetcdf

NetCDF 4.2

C++ interface to the netcdf library (version 4); both serial and MPI version installed
link using -lnetcdf_c++4

NetCDF 4.2

Fortran interface to the netcdf library (version 4); serial and MPI version installed
link using -lnetcdff

Netpbm 10.47.05
NetworkX 1.8.1
NLopt 2.3
Octave 3.8.2

(in default PATH)

Open Babel 2.3.2

(in default PATH)

Open MPI 1.6.5

(default MPI distribution)

OpenBUGS 3.2.2
OpenFOAM, OpenFOAM+ and OpenFOAM Extend 2.2.1

module load openfoam

OpenFOAM, OpenFOAM+ and OpenFOAM Extend v1606+

To set up your environment to use version v1606+ from the OpenFOAM+ distribution, use

module load openfoam/1606

OpenFOAM, OpenFOAM+ and OpenFOAM Extend foam-extend-3.1

module load openfoam/foam-extend-3.1

OpenFOAM, OpenFOAM+ and OpenFOAM Extend 2.3.0

module load openfoam/2.3.0

OpenSees 2.3.0
orthomcl 2.0.9

module load orthomcl/2.0.9

p4est 0.3.4.1
Pandaseq 2.5.0
ParaView 4.0.1

(in default PATH)

Perl 5.10.1
PETSc 3.4.4

(in default PATH)
included packages: mpi, blas, lapack, blacs, scalapack, hdf5, netcdf, netcdf-cxx, fftw, boost, mumps, metis, parmetis, hypre, ml, cholmod, ufmpack, superlu, superlu_dist, ptscotch, petsc4py, mpi4py, numpy

PETSc 3.5.1

-I/usr/local/petsc-3.5.1/include -L/usr/local/petsc-3.5.1/lib -lpetsc

included packages: mpi, blas, lapack, blacs, scalapack, hdf5, netcdf, netcdf-cxx, fftw, boost, mumps, metis, parmetis, hypre, ml, suitesparse, superlu, superlu_dist, ptscotch, petsc4py, mpi4py, numpy

PETSc 3.4.4-cmplx

This version uses complex variables, i.e., it was compiled with scalar-type=complex. To compile with this version use

-I/usr/local/petsc-cmplx/include -lpetsc-cmplx

PETSc 3.5.1-cmplx

This version uses complex variables, i.e., it was compiled with scalar-type=complex. To compile with this version use

-I/usr/local/petsc-3.5.1-cmplx/include -L/usr/local/petsc-3.5.1-cmplx/lib -lpetsc-cmplx

PostgreSQL 9.4.12

module load postgres/9.4.12

PostgreSQL 9.3.2

module load postgresql/9.3.2

(Note: the server version is 9.4.12)

 

PROJ.4 4.8.0

(in default search path)

Python 2.6.6

module load python/2.6.6

Python 2.7.4

(default)

Python 3.3.1

module load python/3.3.1

QIIME 2017.8

module load qiime2/2017.8

QIIME 1.7.0

To set up the environment to use QIIME, use:

module load qiime/1.7.0

QIIME 1.8.0

To setup the environment to use QIIME, use:

     module load qiime

Qt 4.8.4

/usr/local/qt

Quantum ESPRESSO 5.0.3

(in default PATH)

Pseudo potentials are in /usr/local/espresso/pseudo - that directory should be specified using the pseudo_dir specification in the input file.

Quantum ESPRESSO 5.4.0

module load espresso/5.4.0

Quantum ESPRESSO 5.2.1

Initialize your environment to use Quantum ESPRESSO 5.2.1 with

module load espresso/5.2.1

Quantum ESPRESSO 5.1.2

module load espresso/5.1.2

Pseudopotentials are in /usr/local/espresso-pseudopotentials - that directory should be specified using the pseudo_dir specification in the input file.

Quantum ESPRESSO 6.1

module load espresso/6.1

Quantum ESPRESSO 5.0.2

module load espresso/5.0.2

R 3.1.1

(in default PATH)

R 3.3.1

module load R/3.3.1

R 3.0.1

module load R/3.0.1

Rasmol 2.7.5
RITA 1.0.1 (Rank-specific setup only)
RNAmmer 1.2

in default path

ROOT (data analysis framework) 6.06

(in default path)

Rosetta Software Suite 3.5

(both serial and MPI versions are installed; the MPI executables have a .mpi suffix)

module load rosetta

Rosetta Software Suite 2014.22

(both serial and MPI versions are installed; the MPI executables have a .mpi suffix)

module load rosetta/2014.22

RSEM 1.2.6
Ruby 1.8.7
SAMtools and HTSlib utilities 0.1.19

module load samtools/0.1.19

SAMtools and HTSlib utilities 1.1

(in default path)

SAMtools and HTSlib utilities 0.1.18

module load samtools/0.1.18

SAMtools and HTSlib utilities 1.3

module load samtools/1.3

SAMtools and HTSlib utilities 1.2

Initialize your environment to use Samtools 1.2 on Bugaboo with

module load samtools/1.2

SAS 9.3

(sas - in default path) Licensed for SFU researchers only.

ScaLAPACK 2.0.2

Link with -lscalapack -llapack -lblas.

ScaLAPACK MKL

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

Link with: -lmkl_scalapack_lp64 -lmkl_blacs_openmpi_lp64 -lmkl

SCons 2.3.3
SCOTCH 6.0.0

includes esmupms, ptscotch, ptesmumps

Seismic Un*x Release 42

module load cwp-su

sh Link to bash
ShengBTE - solving Boltzmann Transport Equation for phonons 1.1.0-f86c1a7

module load ShengBTE/1.1.0-f86c1a7

ShengBTE - solving Boltzmann Transport Equation for phonons 1.0.2

(in default path)

SHRiMP 2.2.3

module load shrimp

SIESTA 3.1

module load siesta/3.1

SIESTA 3.2 patch level 5

(in default path)

SignalP 4.1c

in default path

SLEPc 3.4.4-cmplx

This version uses complex variables, i.e., it was compiled with scalar-type=complex. To compile with this version use

-I/usr/local/slepc-cmplx/include -lslepc-cmplx

SLEPc 3.5.1

compile with:

-I/usr/local/slepc-3.5.1/include -L/usr/local/slepc-3.5.1/lib -lslepc

SLEPc 3.5.1-cmplx

This version uses complex variables, i.e., it was compiled with scalar-type=complex. To compile with this version use

-I/usr/local/slepc-3.5.1-cmplx/include -L/usr/local/slepc-3.5.1-cmplx/lib -lslepc-cmplx

SLEPc 3.4.4

-lslepc

smalt 0.7.6

(in default path)

smalt 0.7.5

module load smalt/0.7.5

SOAPdenovo 2.04-r241

Compiled with Intel and in default path

Stacks 1.34

module load stacks/1.34

Stacks 1.24

module load stacks/1.24

Stacks 1.27

Stacks executables have been installed in the default PATH.

Subversion 1.6.11
SuiteSparse 4.3.1
Szip 2.1
tcsh 6.17
TecIO 2013
TetGen 1.4.3
TMHMM 2.0c

in default path

TopHat 2.0.12

It is on default path

TopHat 2.0.9

module load tophat/2.0.9

TPP 4.5.0 (in default path)

Web interface here: https://joffre.westgrid.ca/

Trans-ABySS 1.5.1

module load trans-ABySS/1.5.1

Trans-ABySS 1.4.4

module load trans-ABySS/1.4.4

Trilinos 11.4.1
Trinity 2.4.0

module load trinity/2.4.0

Trinity 2.1.1

module load trinity/2.1.1

Trinity r20140413p1

in default PATH

Trinotate 2.0.2

In default path

VASP 5.4.1

module load vasp/5.4.1

VASPSolv and VTST modules had been built in this version.

VASP 4.6.36

(in default path) to run: mpiexec vasp or mpiexec vasp-gamma

VASP 5.3.5

(in default path) to run: mpiexec vasp5 or mpiexec vasp5-gamma

VASP 5.3.3

module load vasp/5.3.3

VASP 5.4.4

module load vasp/5.4.4

VCFtools 0.1.13

module load vcftools/0.1.13

Velvet 1.2.10

Velvet binaries are in the default command PATH. These were compiled with the OpenMP parallelization (multi-threading) option.

Vim 7.2.411
VISAT 4.7
VMD 1.9.1
VTK - Visualization Toolkit 5.2

/usr/local/vtk

wkhtmltox 0.12.1
WRF WRF 3.5

includes wrf-chem (in default PATH)

WRF WRF portal 2.84

graphical frontend for wps and wrf: wrf-dwiz prepares and runs wps applications; wrf-portal can additionally run wrf applications as well.

WRF WRF 3.7.1

module load wrf/3.7.1

includes wrf-chem (version 3.7.1) and wrf-hydro (version 3.0)

This version includes all fixes that were released until Sep. 8, 2016 (including the tmn_update fix).

WRF WRF 3.6.1

module load wrf/3.6.1

Includes wrf-chem

WRF WPS 3.7.1

module load wrf/3.7.1

the geog directory is /usr/local/wrf-geog-3.7

WRF WPS 3.6.1

module load wrf/3.6.1

The geog directory is in /usr/local/wrf-geog-3.6

WRF WRF 3.8.1

in default PATH

includes wrf-chem (version 3.8.1) and wrf-hydro (version 3.0)

(this version has been fixed with respect to the tmn_update bug mentioned under WRF-3.8.1 known problems)

WRF WPS 3.8.1

in default PATH

the geog directory is /usr/local/wrf-geog-3.8

WRF WPS 3.5

module load wrf/3.5
the geog directory is /usr/local/wrf-geog

Xerces-C++ 3.0.1
xv 3.10a
YAeHMOP 3.1.0b2

module load yaehmop

zlib 1.2.8

-I/usr/local/zlib/include -L/usr/local/zlib/lib -Wl,-rpath,/usr/local/zlib-1.2.8/lib -lz

zlib 1.2.3
zsh 4.2.6