Applications Overview

Running HPC Applications

Typically, applications are configured as modules and can be loaded if required.

To setup your environment to use a package you need to enter:

module load <package>

Replacing <package> with the relevant module name, followed by the version number, if a version other than the default is required. More information about module commands is available here.

To request the installation of an application please enter the details on the application request page.

In order for an application to be installed on the cluster, we will need to be able to test the installation.
If you cannot provide a suitable set of tests, please contact us and we will work with you to arrange appropriate tests.

List of modules available on Apocrita

Application Versions Default
7zip 16.02 16.02
R 3.3.2, 3.4.0 3.4.0
abaqus 2016 2016
abyss 2.0.2 2.0.2
angsd 0.919 0.919
ansys 18.0.0 18.0.0
arrayfire 3.4.2 3.4.2
asciinema 1.3.0, 1.4.0 1.4.0
aspell 0.60.6 0.60.6
aspera 3.7.2 3.7.2
atlas 3.10.3 3.10.3
augustus 3.2.3 3.2.3
bamtools 2.4.1 2.4.1
bcftools 1.4 1.4
bcl2fastq2 2.19.1 2.19.1
bedtools 2.26.0 2.26.0
blast+ 2.6.0 2.6.0
blobtools 0.9.19.6 0.9.19.6
boost 1.63.0 1.63.0
bowtie 1.2.0 1.2.0
bowtie2 2.3.1, 2.3.2 2.3.2
breakdancer 1.4.5 1.4.5
bucky 1.4.4 1.4.4
busco 3.0 3.0
bwa 0.7.15 0.7.15
canu 1.5 1.5
clustalw 2.1 2.1
cmake 3.8.0 3.8.0
cp2k 4.1.0-intel, 5.1-openmpi-nxn, 4.1 5.1-openmpi-nxn
cuda 8.0.44 8.0.44
cudnn 5.0-cuda8.0, 5.1-cuda8.0, 6.0-cuda8.0 6.0-cuda8.0
dl_poly 4.08-openmpi 4.08-openmpi
emboss 6.6.0 6.6.0
ensembl-vep 89.7 89.7
entrez 201708 201708
exomiser 7.2.3 7.2.3
exonerate 2.4.0 2.4.0
fastqc 0.11.5 0.11.5
ffmpeg 3.2.4, 3.3.3 3.3.3
fftw 3.3.6-pl1-intel, 3.3.6-pl2-gcc 3.3.6-pl1-intel
gamess 201704-R1 201704-R1
gaussian g09_D01, g09 g09_D01
gcc 6.3.0, 7.1.0 7.1.0
gdb 7.12 7.12
genometools 1.5.9 1.5.9
git 2.12.0 2.12.0
glfw 3.2.1 3.2.1
gnuplot 5.2.0 5.2.0
gromacs 5.1.4-gpu, 2016.3-gpu, 2016.3-intelmpi, 2016.3-plumed 2016.3-intelmpi
gsl 2.4 2.4
guidance 2.02 2.02
hdf5-parallel 1.8.18-intel 1.8.18-intel
hmmer 3.1b2, 3.1b2-1 3.1b2-1
htop 2.0.2 2.0.2
htslib 1.4 1.4
idl 8.4.1 8.4.1
imagemagick 7.0.5-4 7.0.5-4
intel 2017.1, 2017.3 2017.3
intelmpi 2017.1, 2017.3 2017.3
intelpython 2.7.12-2017.2, 3.5.2-2017.2, 2.7.12, 3.5.2 3.5.2-2017.2
java 1.8.0_121-oracle 1.8.0_121-oracle
jellyfish 2.2.6 2.2.6
julia 0.5.2, 0.5.2-1 0.5.2
kmc a09d63a4 a09d63a4
lammps 31MAR17, 31MAR17-intel-ompi, 31MAR17-intelmpi 31MAR17
lapack 3.7.0 3.7.0
last 869 869
longranger 2.1.3, 2.1.4 2.1.4
mafft 7.310 7.310
maker 2.31.9-mpi, 2.31.9 2.31.9-mpi
masurca 3.2.2 3.2.2
mathematica 11.0.1 11.0.1
matlab 2016a, 2017a 2017a
mira 4.0.2 4.0.2
mothur 1.39.5 1.39.5
mrbayes 3.2.6-mpi 3.2.6-mpi
multisnv 2.3-12 2.3-12
muscle 3.8.31 3.8.31
namd 2.12-gpu, 2.12-openmpi 2.12-openmpi
nano 2.8.6 2.8.6
newick_utils 1.6 1.6
nwchem 6.6-mpi 6.6-mpi
octave 4.2.1 4.2.1
openbabel 2.4.1 2.4.1
openmpi 1.10.2-pgi, 2.0.2-gcc, 2.1.0-gcc, 2.1.1-intel, 3.0.0-gcc 3.0.0-gcc
parallel 20170422 20170422
paraview 4.4.0, 5.3.0 5.3.0
perl 5.24.1, 5.26.0 5.26.0
pgi 16.10 16.10
phylobayes 4.1c 4.1c
plink 1.9-170906, 2.0-20170920 1.9-170906
prank 170427 170427
python 2.7.13, 2.7.13-1, 2.7.13-3, 2.7.14, 3.6.1, 3.6.2, 3.6.2-2, 3.6.3 3.6.3
qe 6.1.0-mpi 6.1.0-mpi
qt 5.8.0 5.8.0
qualimap 2.2.1 2.2.1
quast 4.5 4.5
raxml 8.2.11 8.2.11
repeatmasker 4.0.7 4.0.7
ruby 2.4.1 2.4.1
samtools 1.4, 1.4.1 1.4.1
scalapack 2.0.2-intel 2.0.2-intel
scilab 6.0.0 6.0.0
seqtk 1.2 1.2
singularity git, 2.2.1, 2.3, 2.3.1, 2.3.2 2.3.2
soapdenovo2 r241 r241
sparsehash 2.0.3 2.0.3
sratools 2.8.2-1 2.8.2-1
stacks 1.46 1.46
star-ccm+ 11.06.011-R8, 12.02.010, 12.02.010-R8 12.02.010-R8
stata 13 13
swig 3.0.12 3.0.12
texinfo 4.8 4.8
trimmomatic 0.36 0.36
trinity 2.4.0 2.4.0
valgrind 3.12.0 3.12.0
vcftools 0.1.15 0.1.15
yasm 1.3.0 1.3.0
zsh 5.4.1, 5.4.2 5.4.2