Software List

This page documents the list of centrally provisioned software (either available as part of the base OS provision, via Linux module or via the EESSI client).

This page is primarily of relevance to Comet.

Software Type

We will generally refer to software on our HPC facilities as being from one of the following categories. The level of support we offer may vary depending on the category of the package in question.

Software Type Category Location Example Support Description
Your code Your home or project directory A custom Python script The Research Software Engineering team can offer basic support and troubleshooting with your own HPC code to get it working or provide advice on potential compatibility issues. If the complexity of the support is deemed to be beyond standard, or the software is of sufficient complexity, you may be advised to engage dedicated RSE software developers at a chargeable day rate. Please use the IT Service ticket system to request assistance.
3rd Party code Your home or project directory A Python library downloaded from Github The Research Software Engineering team can offer basic support and troubleshooting in the download, compilation and configuration of software included in this category. Support is accessible via the normal IT Service ticket system. If the complexity of the support is deemed to be beyond standard, or the software is of sufficient complexity, you may be advised to engage dedicated RSE software developers at a chargeable day rate.
Loaded via Linux module vendor Centrally installed GCC, Matlab or Conda Software which is loaded from a module load command is packaged and has basic testing by our HPC support vendor. Help in the operation of the software is not covered by our vendor. RSE may be able to provide basic guidance via the normal IT Service ticket system, but may not be able to assist with every possible application. Requests for additional/updated software titles in this category will be collated and submitted to our vendor for prioritization and estimate of implementation timescales.
Loaded from EESSI EESSI Remotely installed GCC, Matlab or Conda Software is packaged and basic operation is tested by partners in the EESSI project. Local site-specific help is not offered by the volunteer members of the project. RSE may be able to provide basic guidance via the normal IT Service ticket system, but may not be able to assist with every possible application.

Software Table

This software table describes the packages which are (or are intended to be) available on Comet.

Title Category License Interface Help
AMD Optimizing Compiler vendor Command Line
AMD Optimizing Compiler Libraries vendor Command Line
cmake vendor Command Line
Docker vendor Command Line
GNU g++ vendor Command Line GCC
GNU gcc vendor Command Line GCC
GNU gfortran vendor Command Line GCC
Gromacs vendor Command Line
libncurses vendor Command Line
numpy vendor Command Line
Nvidia CUDA SDK vendor Command Line
Nvidia HPC SDK vendor Command Line
OpenBLAS vendor Command Line
OpenMP vendor Command Line
OpenMPI vendor Command Line
OpenSSL vendor Command Line
Podman vendor Command Line
Python vendor Command Line
PyTorch vendor Command Line
R vendor Command Line
Singularity vendor Command Line
Tensorflow vendor Command Line
zlib vendor Command Line
OpenCL vendor Command Line
OpenGL (MESA) vendor Desktop GUI
OpenGL (Nvidia) vendor Desktop GUI
VirtualGL vendor Desktop GUI
Ansys vendor Commercial Command Line ANSYS
Matlab vendor Commercial Command Line
Jupyter Lab vendor Desktop GUI
Linux X11 desktop vendor Desktop GUI
R Studio vendor Desktop GUI
Matlab vendor Commercial Desktop GUI
Intel Compiler Suite not installed Commercial Command Line Intel Compiler Suite
Intel MPI Libraries not installed Commercial Command Line Intel Compiler Suite
Intel Math Kernel Libraries not installed Commercial Command Line Intel Compiler Suite
ARPACK vendor Command Line
BLAS vendor Command Line
Boost vendor Command Line
Eigen vendor Command Line
FFTW vendor Command Line
GNU gnuplot vendor Command Line
HDF5 vendor Command Line
Java vendor Command Line
libXmu vendor Command Line
matplotlib vendor Command Line
METIS vendor Command Line
Nektar++ vendor Command Line
OpenCascade CE vendor Command Line
Perl vendor Command Line
PTSCOTCH vendor Command Line
SCOTCH vendor Command Line
Tetgen vendor Command Line
TinyXML vendor Command Line
Triangle vendor Command Line
Vtk vendor Command Line
AFNI vendor Command Line
ALE vendor Command Line
ANTS vendor Command Line
BamUtil vendor Command Line
BCFTools vendor Command Line
bcl2fastq vendor Command Line
BEDTools vendor Command Line
BGEN vendor Command Line
bgenix vendor Command Line
Bioconda vendor Command Line
Biopython vendor Command Line
BLAST+ vendor Command Line
BOLT-LMM vendor Command Line
Bowtie2 vendor Command Line
BUGS vendor Command Line
BWA vendor Command Line
canu assemblers vendor Command Line
CCP-EM Suite vendor Command Line
CDO vendor Command Line
CellBender vendor Command Line
CNVKit vendor Command Line
Code_Saturne vendor Command Line
Convert3D vendor Command Line
CP2K vendor Command Line
Cufflinks vendor Command Line
cutadapt vendor Command Line
DBD-mysql vendor Command Line
diamond vendor Command Line
Disambiguate vendor Command Line
Dorado vendor Command Line
flye vendor Command Line
GATK vendor Command Line
Generic Mapping Tools vendor Command Line
gprMax vendor Command Line
Guppy vendor Command Line
Hail vendor Command Line
HISAT2 vendor Command Line
HTSeq vendor Command Line
HTSlib vendor Command Line
Hybracter vendor Command Line
Ice Sheet and Sea Level System Model vendor Command Line
JAGS vendor Command Line
JARS vendor Command Line
Julia vendor Command Line
LAMMPS vendor Command Line
last vendor Command Line
ldsc vendor Command Line
MACS2 vendor Command Line
Mamba vendor Command Line
megan vendor Command Line
merlin vendor Command Line
metaSPAdes vendor Command Line
Model Angelo vendor Command Line
Mono vendor Command Line
MultiQC vendor Command Line
Netcdf-c vendor Command Line
Netcdf-fortran vendor Command Line
Nextflow vendor Command Line
OpenFOAM vendor Command Line
OpenGeoSys vendor Command Line
OpenSeePy vendor Command Line
parallel vendor Command Line
Paraview vendor Command Line
pgap vendor Command Line
Picard vendor Command Line
piecewiseSEM vendor Command Line
PISM vendor Command Line
Plink vendor Command Line
PRSice vendor Command Line
Pysam vendor Command Line
Python JAX vendor Command Line
Python OpenTURNS vendor Command Line
Python RAY vendor Command Line
QCTOOL vendor Command Line
quantum-espresso vendor Command Line
R-Bioconductor vendor Command Line
R-keras vendor Command Line
Regenie vendor Command Line
Relion vendor Command Line
Remora vendor Command Line
Rerio vendor Command Line
Rstan vendor Command Line
SAIGE vendor Command Line
Salmon vendor Command Line
Sambamba vendor Command Line
Samtools vendor Command Line
SMINA vendor Command Line
Snakemake vendor Command Line
SPAdes vendor Command Line
Stan vendor Command Line
STAR vendor Command Line
StringTie vendor Command Line
Subread vendor Command Line
Szip vendor Command Line
tabix vendor Command Line
Tricycler vendor Command Line
Trim Galore vendor Command Line
Unicycler vendor Command Line
VCFTools vendor Command Line
VEP vendor Command Line
VINA vendor Command Line
XengSort vendor Command Line
xmds2 vendor Command Line
Abaqus vendor Command Line
COMSOL Multiphysics vendor Command Line
NBO vendor Command Line
StarCCM+ vendor Command Line
CryoSparc vendor Desktop GUI
Doppio vendor Desktop GUI
FastQC vendor Desktop GUI
Freesurfer vendor Desktop GUI
FSL vendor Desktop GUI
Gmsh vendor Desktop GUI
GRASS vendor Desktop GUI
jmol vendor Desktop GUI
Mrtrix vendor Desktop GUI
r.avaflow vendor Desktop GUI
Ansys vendor Commercial Desktop GUI ANSYS
COMSOL Multiphysics vendor Desktop GUI
StarCCM+ vendor Desktop GUI
OpenMS vendor Command Line

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