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
abyss 2.0.2 2.0.2
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 2.3.1
breakdancer 1.4.5 1.4.5
bwa 0.7.15 0.7.15
canu 1.5 1.5
cmake 3.8.0 3.8.0
cp2k 4.1.0-intel, 4.1 4.1
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
fastqc 0.11.5 0.11.5
ffmpeg 3.2.4 3.2.4
fftw 3.3.6-pl1-intel, 3.3.6-pl2-gcc 3.3.6-pl1-intel
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
gromacs 5.1.4-gpu, 2016.3-gpu, 2016.3-intelmpi, 2016.3-plumed 2016.3-intelmpi
hdf5-parallel 1.8.18-intel 1.8.18-intel
hmmer 3.1b2 3.1b2
htop 2.0.2 2.0.2
htslib 1.4 1.4
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
kmc a09d63a4 a09d63a4
lammps 31MAR17, 31MAR17-intel-ompi, 31MAR17-intelmpi 31MAR17
lapack 3.7.0 3.7.0
longranger 2.1.3 2.1.3
maker 2.31.9 2.31.9
masurca 3.2.2 3.2.2
mathematica 11.0.1 11.0.1
matlab 2016a, 2017a 2017a
mothur 1.39.5 1.39.5
mrbayes 3.2.6-mpi 3.2.6-mpi
multisnv 2.3-12 2.3-12
namd 2.12-gpu, 2.12-openmpi 2.12-openmpi
nwchem 6.6-mpi 6.6-mpi
octave 4.2.1 4.2.1
openmpi 1.10.2-pgi, 2.0.2-gcc, 2.1.0-gcc, 2.1.1-intel 2.1.0-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
python 2.7.13, 3.6.1 3.6.1
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
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 2.3.1
soapdenovo2 r241 r241
sparsehash 2.0.3 2.0.3
sratools 2.8.2-1 2.8.2-1
star-ccm+ 11.06.011-R8, 12.02.010, 12.02.010-R8 12.02.010-R8
swig 3.0.12 3.0.12
texinfo 4.8 4.8
trimmomatic 0.36 0.36
valgrind 3.12.0 3.12.0
vcftools 0.1.15 0.1.15
yasm 1.3.0 1.3.0