Available Software

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See also: Software, Modules, Programming Tools

Contents

  • This page lists application software available.
  • Software listed below is available at all sites unless indicated otherwise.
  • Multiple versions of the same piece of software may be available. The default version is not necessarily the most recent one. We advise you to use Modules to discover which versions are available.
  • The users of Fundy group restricted packages should source additional settings described here.

Astronomy and Astrophysics

Software Default/ Latest version Modulefile Command(s)
DS9 6.0 ds9 ds9
IRAF 2.14.1 -- --
Starlab 4.4.4 starlab various commands
SExtractor 2.19.5 sextractor sex, ldactoasc

Atomic and Molecular Science

Software Default/ Latest version Modulefile Command(s)
ABINIT 6.12.3/ 8.4.2 abinit abinit
aenet 1.0.0/ 1.0.0 aenet generate.x, train.x, predict.x
AmberTools 13 ambertools various commands
CPMD 3.13.2/ 3.15.3 cpmd cpmd.x, cpmd2cube.x, trimcube.x
DFTB+ 1.2.2 dftb+ dftb+
DL_POLY 3.10 dl_poly DLPOLY.Y
DL_MESO 2.2
ESPResSo 3.1.2/ 3.3.0 espressomd Espresso
GAMESS(US) 12jan2009/ 1may2013 gamess rungms
GAMESSPLUS v2010-2 gamessplus rungmsplus
Gaussian (Placentia) g09.D01 gaussian g09
GROMACS 4.5.5/ 2018.1 gromacs grompp, mdrun, mdrun_mpi,...
JuNoLo 1.02 junolo vdw.exe
LAMMPS 29Jul11/ 1Jul13 lammps lammps
Molden 5.0 molden molden
NAMD 2.9 namd namd2
NWChem with NBO5 6.1.1/ 6.6 nwchem nwchem
Open Babel 2.3.1 openbabel babel
Qbox 1.56.2 qbox qb
Quantum ESPRESSO 5.0.2+/ 5.1.1 espresso pw.x, cp.x,...
Q-Chem 3.2.0.2
SIESTA 3.2/ 4.0 siesta siesta
VASP 5.2.12/ 5.4.4 vasp vasp, vasp.gamma, vasp.noncollinear
VMD 1.9 vmd vmd
XPLOR-NIH 2.23 xplor-nih xplor
YAeHMOP 3.0 yaehmop viewkel, bind,...
WebMO (Placentia) 9.0.009e

Biology and Genetics

Software Default/ Latest version Modulefile Command(s)
ABySS 1.3.2 abyss abyss-pe, ABYSS
BEAST 1.8.2 beast beast
BWA 0.7.15 bwa bwa
BIMr 1.0 bimr BIMr
Diamond 0.7.8 diamong diamond
BioPerl 1.6 perl perl
BLAST 2.6.0+ blast blastn, makeblastdb
Bowtie 2.3.2 bowtie bowtie2, bowtie2-build
Cufflinks 2.1.1 cufflinks cufflinks, cuffmerge,...
HMMER 3.1b1 hmmer hmmscan, hmmsearch,...
HumANN 0.99 humann various commands
IM 12172009 im IM, IMa
IQ-TREE 1.5.5 iqtree iqtree, iqtree-omp
InterProScan 5.11-51.0 interproscan interproscan.sh
LAMARC 2.1.6 lamarc lamarc, lam_conv
MEGAN 5.7.1 megan5 MEGAN
MetaPhlAn 1.7.8/ 2.0 metaphlan metaphlan.py
Migrate 3.6.11 migrate migrate-n
MIRA 3.9.18/ 4.0.2 mira mira
MrBayes 3.2.1 mrbayes mb
PhyML 2.4.4 phyml phyml_linux
PLINK 1.07 plink plink
RAPSearch 2.24 rapsearch rapsearch
SAMtools 0.1.18/ 1.4.1 samtools samtools
Structure 2.2.3 structure structure.exe
Trinity 2.2.0 trinity Trinity
QIIME 1.2.19 with Python 2.7.2 swarm

Earth, Ocean and Atmospheric Science

Software Default/ Latest version Modulefile Command(s)
CDO 1.6.1/ 1.9.0 cdo cdo, ncdump
Elmer FEM r5675 elmerfem ElmerSolver, ElmerSolver_mpi
Ferret 6.84/ 6.93 ferret ferret
GDAL 1.10.1 gdal gdalinfo
GMT 4.5.7/ 5.2.1 gmt GMT
ISSM r11321 issm issm.exe
NCO 4.3.4/ 4.6.8 nco ncap2, ncbo, ncks...
PROJ 4.8.0 proj proj
wgrib2 2.0.1 wgrib2 wgrib2

Engineering

Software Default/ Latest version Modulefile Command(s)
ANSYS (Placentia) 14.5
Elmer FEM r5675 elmerfem ElmerSolver, ElmerSolver_mpi
EnergyPlus 8.1/ 8.5.0 energyplus runenergyplus
LS-DYNA (Glooscap) 7.0.0 lsdyna lsdyna_mpp_d and others
OpenFOAM and OpenFOAM+ 2.2.1/ 3.0/ 1616 openfoam blockMesh, icoFoam,...
SU2 5.0.0/6.0.1 su2 SU2_CFD and others

Mathematics, Statistics and Computer Science

Software Default/ Latest version Modulefile Command(s)
DiVinE 2.5.2 divine divine
GAP 4.4.10 gap gap.sh
Gurobi
(Placentia and Glooscap)
7.5.1 gurobi gurobi.sh, gurobi_cl
Macaulay2 1.1 macaulay2 M2
MATLAB
(Placentia and Fundy)
various --
MPI-Spin 1.1 mpi-spin ms, mscc
R 3.1.2/ 3.3.0 r R
Sage 4.8 sage sage
Spin 5.1.6 spin spin, xspin

Graphics & Visualization

Software Default/ Latest version Modulefile Command(s)
ImageMagick 6.7.4-0 imagemagick convert, mogrify, animate,...
FFmpeg 0.9 ffmpeg ffmpeg
FSL 5.0.9 fsl flirt, melodic,...
Ghostscript 9.06 ghostscript gs
ParaView 4.1.0/ 4.3.1 paraview paraview
PGPLOT 5.2.2 pgplot pgplot
Gnuplot 4.6.0 gnuplot gnuplot
HDFView 2.8 hdfview hdfview
JasPer 1.900.1 jasper jasper, imgcmp, imginfo,...
Ncview 2.1.1 ncview ncview, ncdump
Grace 5.1.22/ 5.1.24 grace xmgrace
feh 1.3.4 feh feh
NCL/NCARG 6.1.2/ 6.2.1 ncl ncl, ncargex
VTK 5.8.0 vtk vtk

Editors

Software Default/ Latest version Modulefile Command(s)
Emacs 24.3 emacs emacs
XEmacs 21.4.22 xemacs xemacs
nano 2.2.6 nano nano
Vim 7.3 vim vim, vi

File Transfer and Compression

Software Default/ Latest version Modulefile Command(s)
GridFTP 4.2.1
bzip2 1.0.6 compression bzip2, bunzip2
Gzip 1.6 compression gzip, gunzip
GNU Tar 1.28 compression tar
XZ Utils 5.2.0 compression xz
Zip 3.0 compression zip, zipcloak, zipnote,...
UnZip 6.0 compression unzip, unzipsfx, funzip
zlib 1.1.13 compression --
PBZIP2 1.2.8 compression pbzip2
pigz 2.3.4 compression pigz
PXZ 4.999 compression pxz
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