Software List

This page documents the list of centrally provisioned software on 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 contact us via team email hpc.researchcomputing@ncl.ac.uk, or 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 direct team email hpc.researchcomputing@ncl.ac.uk, or 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 email hpc.researchcomputing@ncl.ac.uk, or 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 via a container image RSE Centrally installed CASTEP, Bioapps Software which we have built and provided in the form of a container environment in the /nobackup containers folder. We will build and provide updates to these containers but cannot necessarily advise on the use of the software itself.
We can provide some level of assistance for building containers, but depending on the level of complexity or size of user base, this may fall outside of our ability to deliver via our basic support provision and may require engagement of paid RSE services to help develop a solution.

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 AOCC
AMD Optimizing Compiler Libraries vendor Command Line AOCC
Apptainer vendor Command Line Apptainer
cmake vendor Command Line cmake
Docker vendor Command Line Docker
GNU g++ vendor Command Line GCC
GNU gcc vendor Command Line GCC
GNU gfortran vendor Command Line GCC
Gromacs vendor Command Line gromacs / CUDA / OpenCL
libncurses vendor Command Line ncurses
numpy vendor Command Line
Nvidia CUDA SDK vendor Command Line CUDA SDK
Nvidia HPC SDK vendor Command Line HPC SDK
OpenBLAS vendor Command Line
OpenMP vendor Command Line
OpenMPI vendor Command Line
OpenSSL vendor Command Line
Podman vendor Command Line Podman
Python vendor Command Line
PyTorch vendor Command Line PyTorch
R vendor Command Line R
Singularity vendor Command Line See Apptainer
Tensorflow vendor Command Line Tensorflow
zlib vendor Command Line zlib
OpenCL vendor Command Line OpenCL
OpenGL (MESA) vendor Desktop GUI MESA
OpenGL (Nvidia) vendor Desktop GUI VirtualGL / Nvidia OpenGL
VirtualGL vendor Desktop GUI VirtualGL / Nvidia OpenGL
Ansys vendor Commercial Command Line ANSYS
Matlab vendor Commercial Command Line Matlab
Jupyter Lab vendor Desktop GUI Jupyter
Linux X11 desktop vendor Desktop GUI X11 Desktop
R Studio vendor Desktop GUI R Studio
Matlab vendor Commercial Desktop GUI Matlab
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 AFNI
ALE vendor Command Line ALE
ANTS vendor Command Line
BamUtil vendor Command Line Please see Bioapps
BCFTools vendor Command Line Please see Bioapps
bcl2fastq vendor Command Line Obsolete. Replaced by BCL_convert - see BCL_convert
BEDTools vendor Command Line Please see Bioapps
BGEN vendor Command Line
bgenix vendor Command Line
Bioconda vendor Command Line See the alternative Miniforge
Biopython vendor Command Line
BLAST+ vendor Command Line
BOLT-LMM vendor Command Line BOLT-LMM Help, BOLT-LMM compile issues
Bowtie2 vendor Command Line Please see Bioapps
BUGS vendor Command Line
BWA vendor Command Line Please see Bioapps
canu assemblers vendor Command Line
CCP-EM Suite RSE Command Line See CCP-EM Suite.
CDO vendor Command Line
CellBender vendor Command Line
CNVKit vendor Command Line Please see CNVKit
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 See Guppy.
Hail vendor Command Line
HISAT2 vendor Command Line Please see Bioapps
HTSeq vendor Command Line Please see Bioapps
HTSlib vendor Command Line
Hybracter vendor Command Line
ISSM / Ice Sheet and Sea Level System Model vendor Command Line Please see Ice Sheet and Sea Level System Model
JAGS vendor Command Line
JARS vendor Command Line
Julia vendor Command Line
LAMMPS vendor Command Line
last vendor Command Line
ldsc vendor Command Line Please see ldsc
MACS2 vendor Command Line
megan vendor Command Line
merlin vendor Command Line
metaSPAdes vendor Command Line
Model Angelo RSE Command Line See CCP-EM Suite.
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 Please see OpenGeoSys
OpenSeePy vendor Command Line
parallel vendor Command Line
Paraview vendor Command Line
pgap RSE Command Line Please see pgap
Picard vendor Command Line Please see Bioapps
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
Bioconductor vendor Command Line Most of Bioconductor is installed as part of the Bioapps container image. See that page for more details and a list of all installed libraries.
R-keras vendor Command Line
Regenie vendor Command Line See Regenie.
Relion RSE Command Line See CCP-EM Suite.
Remora vendor Command Line
Rerio vendor Command Line
Rstan vendor Command Line
SAIGE vendor Command Line Please see SAIGE
Salmon vendor Command Line
Sambamba vendor Command Line Please see Bioapps
Samtools vendor Command Line Please see Bioapps
SMINA vendor Command Line
Snakemake vendor Command Line
SPAdes vendor Command Line
Stan vendor Command Line
STAR vendor Command Line
StringTie vendor Command Line Please see Bioapps
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 not installed Commercial Command Line COMSOL
NBO vendor Command Line
StarCCM+ vendor Command Line
CryoSparc vendor Desktop GUI
Doppio RSE Desktop GUI See CCP-EM Suite.
FastQC vendor Desktop GUI
Freesurfer vendor Desktop GUI
FSL vendor Desktop GUI FSL
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 not installed Commercial Desktop GUI COMSOL
StarCCM+ vendor Desktop GUI
DEXSeq RSE Command Line Please see Bioapps
OpenMS vendor Command Line
Amber MD RSE Command Line and Desktop GUI Please see Amber MD
Ambertools RSE Command Line and Desktop GUI Please see Amber MD
ChimeraX vendor Desktop GUI Please see ChimeraX
Avogadro 2 vendor Desktop GUI Please see Avogadro 2
ORCA vendor Command Line Use module load Orca
Visual Studio Code / VSCode vendor Desktop GUI Please see VSCode
CASTEP RSE Command Line Please see CASTEP
Conda vendor Command Line See the alternative Miniforge
Mamba vendor Command Line See the alternative Miniforge
MuSpAn self install Command Line Please see the MuSpAn install guide
Stata/MP vendor Command Line Please see StataMP
PLUMED RSE Command Line Please see Amber MD
MBX RSE Command Line Please see Amber MD
Suitesparse RSE Command Line Please see Amber MD
APBS RSE Command Line Please see Amber MD
Torchani RSE Command Line Please see Amber MD
Gaussian vendor Commercial Command Line Please see Gaussian / GaussView
GaussView vendor Commercial Desktop GUI Please see Gaussian / GaussView
CCP-EM v2 RSE Non-commercial, academic use Command Line Please see CCP-EM Suite container
CCP-EM v1 RSE Non-commercial, academic use Command Line Please see CCP-EM Suite container
CCP4 RSE Command Line + Desktop GUI Please see CCP-EM Suite container
ARP/wARP RSE Command Line Please see CCP-EM Suite container
CheckMySequence, DoubleHelix, FindMySequence RSE Command Line Please see CCP-EM Suite container
CryoDRGN RSE Command Line Please see CCP-EM Suite container
CTFFind 4 RSE Command Line Please see CCP-EM Suite container
Doppio RSE Non-commercial, academic use Desktop GUI Please see CCP-EM Suite container
EMDA RSE Command Line Please see CCP-EM Suite container
EMDB Validation Analysis RSE Command Line Please see CCP-EM Suite container
Locscale RSE Command Line Please see CCP-EM Suite container
MetalCoord RSE Command Line Please see CCP-EM Suite container
Modeller (Salilabs) RSE Non-commercial, academic use Command Line Please see CCP-EM Suite container
RIBFIND RSE Command Line Please see CCP-EM Suite container
Relion RSE Desktop GUI Please see CCP-EM Suite container
Resmap RSE Command Line Please see CCP-EM Suite container
TEMPy RSE Command Line Please see CCP-EM Suite container
TEMPy-REFF RSE Command Line Please see CCP-EM Suite container
UCSF Motioncor 3 RSE Command Line Please see CCP-EM Suite container
Topaz RSE Command Line Please see CCP-EM Suite container
merlin vendor Command Line Now installed. See Merlin.
OpenMS Now installed. See OpenMS.

Software Title Follow-Ups

These titles were requested as part of the initial installation on Comet, but require additional work before they can be progressed.

Title Category License Interface Help
JARS
PISM
CryoSPARC

Container List

We sometimes choose to provide software via container environments either due to their complexity, need for additional libraries or dependencies that are difficult to manage via software module, or simply because the developer already provides a pre-built container.

These containers are available for your use on Comet, and we would strongly recommend that you use them in preference to building the software yourself, or requesting a central software module install. Click on the title to see further information on that container, including how to run the software.

In all cases the container can (and should) be run from where it currently sits in the /nobackup containers directory - you should not make duplicate copies of these container images.

Title / Wiki Page Container Location Size Description
CASTEP /nobackup/shared/containers/castep-25.12.sif 720 MB Includes the CASTEP application binaries and optimised libraries (LAPACK, OpenBLAS, FFTW3) compiled for the AMD Epyc CPU architecture used on Comet.
DNAscent /nobackup/shared/containers/mboemo_dnascent_dnascent.sif 5 GB Developer provided runtime image. Obtained from: https://cloud.sylabs.io/library/mboemo/dnascent/dnascent
R-GIS-Pipeline /nobackup/shared/containers/R-gis-pipeline.sif 800 MB A custom R GIS image with latest version of R, GCC, Abseil C++ libraries and a large number of custom R packages: tidyverse, terra, sf, matrix, lme4, openxsls, data.table … and more. All AMD Epyc CPU optimised.
Bioapps /nobackup/shared/containers/bioapps.2026.03.sif 1 GB Runtime container with an extensive collection of bioinformatics tools. Intended to be used in preference to the standalone software modules already installed on Comet. The tools used in this container are all AMD Epyc optimised and can be used regardless of any other software modules loaded at the same time - no need to load/unload software due to conflicting dependencies.
FSL /nobackup/shared/containers/fsl.6.0.7.19.sif 7.5 GB Runtime environment containing the FSL application and all optional components. Please read our documentation guide for assistance.
CNVKit /nobackup/shared/containers/cnvkit.0.9.13.sif 1.3 GB Uses the published Docker container from https://github.com/etal/cnvkit - converted to a local Apptainer image. Please read our documentation guide for assistance.
Amber MD /nobackup/shared/containers/ambermd.24.25.sif 10 GB Amber MD suite of biomolecular simulation tools. Available in both CPU and GPU accelerated versions.
ComfyUI N/A A build recipe and instructions are provided to build this on a per-user basis.
Ubuntu LTS N/A 120 MB Sample Ubuntu LTS container recipe.
Ubuntu LTS + development tools N/A 350 MB Sample Ubuntu LTS container recipe with standard C, C++, Fortran and Python development tools.
Nvidia CUDA/CUDNN N/A 5.9 GB Sample Nvidia CUDA/CUDNN container recipe built on Ubuntu LTS.
CCP-EM Suite /nobackup/shared/containers/ccpemsuite.2026.03.sif 42 GB CCP-EM, CCPEM2, CCP4, Doppio, Relion 5 and other, related tools.
OpenGeoSys /nobackup/shared/containers/ogs.2026.03.sif 1 GB OpenGeoSys Python environment, including Jupyter Lab for running OGS notebooks.
Ice Sheet and Sea Level System Model /nobackup/shared/containers/issm.2026.03.sif 3 GB ISSM is used in large scale ice flow modelling. This container image has ready-to-run ISSM binaries packaged with the required Python runtime needed to allow you to call ISSM functions in your own scripts.
ldsc /nobackup/shared/containers/ldsc.2026.03.sif 360 MB ldsc is a command line tool for estimating heritability and genetic correlation from GWAS summary statistics. ldsc also computes LD Scores. This container has a version of ldsc which is targetted for a specific Python version and has difficulty running with other versions of its dependencies.

Software Requests

Any additional software requests received since Comet was commissioned are recorded here. These will be taken to the Directors of the AHPC service, considered, prioritised and submitted to the our HPC vendor for installation and commissioning.

Title / Wiki Page Help Website License Interface Requested By Action Status
screen System tool, no module needed RedHat system package Open Source shell multiple users Approved Installed
tmux System tool, no module needed RedHat system package Open Source shell multiple users Approved Installed
Gaussian Use module load Gaussian link Commercial - existing University license shell Keith Izod, Jack Hemingway, Nick Walker, Sam Power Purchased Installed
GaussView Use module load GaussianView link Commercial - existing University license X11 / Open OnDemand Keith Izod, Jack Hemingway, Nick Walker, Sam Power Purchased Installed
gromacs / CUDA Use module load GROMACS/2026-cuda link Open Source shell Finlay Clark Approved Installed
gromacs / OpenCL Use module load GROMACS/2026-opencl link Open Source shell Finlay Clark Approved Installed
emacs System tool, no module needed RedHat system package Open Source shell multiple users Approved Installed
bc System tool, no module needed RedHat system package Open Source shell multiple users Approved Installed
VSCode Use module load VSCode - or launch from the Open OnDemand desktop menu link Proprietary, permissive distribution: https://code.visualstudio.com/license X11 / Open OnDemand multiple users Approved Installed
Miniforge Use module load Miniforge link Open Source shell multiple users Approved Installed
BCL Convert Use module load BCL-Convert - start with bcl-convert. Also see Bioapps link Commercial shell Matthew Teasdale and other BSU users Approved Installed
slurm-seff SchedMD GitHub repository Open Source shell Carol Booth Approved Installed
imagemagick System tool, no module needed RedHat system package Open Source shell Approved Installed
Stata MP 2 core Use module load Stata link Commercial - existing University license for 2 core version shell multiple users in Business School Approved Installed
Hypre Use module load Hypre link Open Source shell Francesco Zonta Approved Installed
htop System tool, no module needed Removed due to excess resource use compared to top. RedHat system package Open Source shell installed on login02, multiple users Approved Installed (login nodes only) Now removed
CASTEP Installed as a container - see our CASTEP guide link Cost-Free source code license shell Ioan Bogdan Magdau, Panagiotis Kourtis, Alex Christison Approved Installed
ORCA Use module load Orca link Free for academic/personal use shell Multiple - alternative to Gaussian Approved Installed
LAPACK Use module load LAPACK/3.12.0 link Open Source shell multiple users Approved Installed
Avogadro 1 & 2 Use module load Avogadro - only usable on Open OnDemand GPU desktops link Open Source X11 / Open OnDemand Used alongside ORCA - alternative to Gauss View Approved Installed
ChimeraX Use module load ChimeraX - only usable on Open OnDemand desktops (preferably GPU) link Free for academic, government, nonprofit, and personal use X11 / Open OnDemand Used alongside ORCA - alternative to Gauss View Approved Installed
seqkit Please see Bioapps Open Source shell Common bioinformatics tools - requested by many users. Existing versions in modules have conflicting dependencies. Approved Installed via container
bwa-mem2 Please see Bioapps Open Source shell Common bioinformatics tools - requested by many users. Existing versions in modules have conflicting dependencies. Approved Installed via container
bwa-meth Please see Bioapps Open Source shell Common bioinformatics tools - requested by many users. Existing versions in modules have conflicting dependencies. Approved Installed via container
Methyldackel Please see Bioapps Open Source shell Common bioinformatics tools - requested by many users. Existing versions in modules have conflicting dependencies. Approved Installed via container
DEXSeq Please see Bioapps link Open Source shell Ogo Ajayi Approved Installed via container
AmberMD Please see Amber MD link Open Source shell Shangyuwen Yang Approved Installed via container
MuSpAn Please see MuSpAn link Free Academic-use only license shell Craig Stamp Approved User Install
bash-completion System tool, no module needed RedHat system package Open Source shell Michael Beaty Approved Installed
csh System tool, no module needed RedHat system package Open Source shell Achraf Koulali Approved Installed
RClone System tool, no module needed RedHat system package Open Source shell Michael Beaty Approved Installed
Nextflow Link Open Source shell / service Jordan Cuff, Monika Gonka Investigating
Globus connect personal link shell / X11 multiple users
Globus cli link shell multiple users

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