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
COMSOL Multiphysics not installed Commercial Command Line COMSOL
COMSOL Multiphysics not installed Commercial Desktop GUI COMSOL
Intel Compiler Suite not installed Commercial Command Line Intel Compiler Suite
Intel Math Kernel Libraries not installed Commercial Command Line Intel Compiler Suite
Intel MPI Libraries not installed Commercial Command Line Intel Compiler Suite
Abaqus vendor Command Line Abaqus
AFNI vendor Command Line AFNI
ALE vendor Command Line ALE
Amber MD RSE Command Line and Desktop GUI Please see Amber MD
Ambertools RSE Command Line and Desktop GUI Please see Amber MD
AMD Optimizing Compiler vendor Command Line AOCC
AMD Optimizing Compiler Libraries vendor Command Line AOCC
Ansys RSE Commercial Command Line and Desktop GUI ANSYS 2025 R2 and above are now provided by the ANSYS container environment
ANTS vendor Command Line Please see ANTS
APBS RSE Command Line Please see Amber MD
Apptainer vendor Command Line Apptainer is our recommended container tool for Comet. Also consider browsing our Containers guide.
ARP/wARP RSE Command Line Please see CCP-EM Suite container
ARPACK vendor Command Line Please see ARPACK-NG
Avogadro 2 vendor Desktop GUI Please see Avogadro 2
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 Please see BGEN
bgenix vendor Command Line Please see bgenix
Bioconda vendor Command Line See the alternative Miniforge
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.
Biopython vendor Command Line Please see Biopython
BLAS vendor Command Line Please see OpenBLAS or LAPACK
BLAST vendor Command Line Please see BLAST
BLAST+ vendor Command Line Please see BLAST+
BOLT-LMM vendor Command Line BOLT-LMM Help, BOLT-LMM compile issues
Boost vendor Command Line Please see boost
Bowtie2 vendor Command Line Please see Bioapps
BUGS vendor Command Line Please see BUGS
BWA vendor Command Line Please see Bioapps
canu assemblers vendor Command Line Please see canu assemblersx
CASTEP RSE Command Line Please see CASTEP
CCP-EM Suite RSE Command Line See CCP-EM Suite.
CCP-EM v1 RSE Non-commercial, academic use Command Line Please see CCP-EM Suite container
CCP-EM v2 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
CDO vendor Command Line Please see CDO
CellBender vendor Command Line Please see CellBender
CheckMySequence, DoubleHelix, FindMySequence RSE Command Line Please see CCP-EM Suite container
ChimeraX vendor Desktop GUI Please see ChimeraX
cmake vendor Command Line cmake
CNVKit vendor Command Line Please see CNVKit
Code_Saturne vendor Command Line Please see Code Saturne
Conda vendor Command Line See the alternative Miniforge
Convert3D vendor Command Line Please see Convert 3D
CP2K vendor Command Line Please see CP2K
CryoDRGN RSE Command Line Please see CCP-EM Suite container
CryoSparc vendor Desktop GUI
CTFFind 4 RSE Command Line Please see CCP-EM Suite container
Cufflinks vendor Command Line Please see Cufflinks
cutadapt vendor Command Line Please see Cutadapt
DBD-csv vendor Command Line Please see DBD-CSV
DBD-mysql vendor Command Line Please see DBD-MySQL
DBD-sqlite vendor Command Line Please see DBD-SQLite
DEXSeq RSE Command Line Please see Bioapps
diamond vendor Command Line Please see diamond
Disambiguate vendor Command Line Please see Disambiguate
Docker vendor Command Line See our Docker guide in our container tools section
Doppio RSE Non-commercial, academic use Desktop GUI See CCP-EM Suite container]. | | Dorado | vendor | | Command Line | Please see [[:advanced:software:dorado|Dorado
Eigen vendor Command Line Please see Eigen
EMDA RSE Command Line Please see CCP-EM Suite container
EMDB Validation Analysis RSE Command Line Please see CCP-EM Suite container
FastQC vendor Desktop GUI Please see FastQC
FFTW vendor Command Line Please see FFTW and FFTW.MPI
flye vendor Command Line Please see flye
Freesurfer vendor Desktop GUI Please see Freesurfer
FSL vendor Desktop GUI FSL
GATK vendor Command Line Please see GATK
Gaussian vendor Commercial Command Line Please see Gaussian / GaussView
GaussView vendor Commercial Desktop GUI Please see Gaussian / GaussView
Generic Mapping Tools vendor Command Line Please see Generic Mapping Tools
Gmsh vendor Desktop GUI Please see Gmsh
GNU g++ vendor Command Line GCC
GNU gcc vendor Command Line GCC
GNU gfortran vendor Command Line GCC
GNU gnuplot vendor Command Line Please see gnuplot
gprMax vendor Command Line Please see gprMax
GRASS vendor Desktop GUI Please see GRASS
Gromacs vendor Command Line gromacs / CUDA / OpenCL
Guppy vendor Command Line See Guppy.
Hail vendor Command Line Please see Hail
HDF5 vendor Command Line Please see HDF5
HISAT2 vendor Command Line Please see Bioapps
HTSeq vendor Command Line Please see Bioapps
HTSlib vendor Command Line Available standalone, see HTSlib - also installed within Bioapps container for any tools requiring it.
Hybracter vendor Command Line Please see Hybracter
ISSM / Ice Sheet and Sea Level System Model vendor Command Line Please see Ice Sheet and Sea Level System Model
JAGS vendor Command Line Please see JAGS
JARS vendor Command Line Please see JARS
Java vendor Command Line Please see Java
jmol vendor Desktop GUI Please see jmol
Julia vendor Command Line Please see Julia
Jupyter Lab vendor Desktop GUI Jupyter
LAMMPS vendor Command Line Please see LAMMPS
last vendor Command Line Please see last
ldsc vendor Command Line Please see ldsc
libncurses vendor Command Line ncurses
libXmu vendor Command Line Included in the module load X11 environment - see also X11 Desktop
Linux X11 desktop vendor Desktop GUI Please see X11 Desktop
Locscale RSE Command Line Please see CCP-EM Suite container
MACS2 vendor Command Line Please see MACS2
Mamba vendor Command Line See the alternative Miniforge
Matlab vendor Commercial Command Line Matlab
Matlab vendor Commercial Desktop GUI Matlab
matplotlib vendor Command Line Please see matplotlib
MBX RSE Command Line Please see Amber MD
megan vendor Command Line Please see megan
merlin vendor Command Line Now installed. See Merlin.
MetalCoord RSE Command Line Please see CCP-EM Suite container
metaSPAdes vendor Command Line Parts of the SPAdes toolkit - please see SPAdes
METIS vendor Command Line Please see METIS
Model Angelo RSE Command Line See CCP-EM Suite.
Modeller (Salilabs) RSE Non-commercial, academic use Command Line Please see CCP-EM Suite container
Mono vendor Command Line Please see Mono
Mrtrix vendor Desktop GUI Please see Mrtrix
MultiQC vendor Command Line Please see MultiQC
MUMPS vendor Command Line Please see MUMPS
MuSpAn self install Command Line Please see the MuSpAn install guide
NBO vendor Command Line Please see NBO
Nektar++ vendor Command Line Please see Nektar++
Netcdf-c vendor Command Line Please see NetCDF-C
Netcdf-fortran vendor Command Line Please see NetCDF-Fortran
Nextflow vendor Command Line Please see Netxtflow
numpy vendor Command Line numpy
Nvidia CUDA SDK vendor Command Line CUDA SDK
Nvidia HPC SDK vendor Command Line HPC SDK
OpenBLAS vendor Command Line Please see OpenBLAS
OpenCascade CE vendor Command Line Please see OpenCascade CE
OpenCL vendor Command Line OpenCL
OpenFOAM vendor Command Line Please see OpenFOAM
OpenGeoSys vendor Command Line Please see OpenGeoSys
OpenGL (MESA) vendor Desktop GUI MESA
OpenGL (Nvidia) vendor Desktop GUI VirtualGL / Nvidia OpenGL
OpenMP vendor Command Line Please see OpenMP
OpenMPI vendor Command Line Please see OpenMPI
OpenMS vendor Command Line Now installed. See OpenMS.
OpenSeesPy vendor Command Line Please see OpenSeesPy
OpenSSL vendor Command Line Please see OpenSSL
ORCA vendor Command Line Please see Orca
parallel vendor Command Line Please see Parallel
Paraview vendor Command Line and Desktop GUI Please see Paraview
Perl vendor Command Line Please see Perl
pgap RSE Command Line Please see pgap
Picard vendor Command Line Please see Bioapps
PISM vendor Command Line Please see PISM
Plink vendor Command Line Please see Plink
PLUMED RSE Command Line Please see Amber MD
Podman vendor Command Line Podman is one of the supporter container tools on Comet. Also consider browsing our Containers guide.
PRSice vendor Command Line Please see PRSice
PTSCOTCH vendor Command Line PT-SCOTCH refers to SCOTCH when running in parallel mode
Pysam vendor Command Line Please see PySAM
Python vendor Command Line Please see Python
Python JAX vendor Command Line Please see Python JAX|
Python OpenTURNS vendor Command Line Please see Python OpenTURNS
Python RAY vendor Command Line Please see Python RAY
PyTorch vendor Command Line PyTorch
QCTOOL vendor Command Line Please see OCTOOL
quantum-espresso vendor Command Line Please see Quantum Espresso|
R vendor Command Line R
R Studio vendor Desktop GUI R Studio
R.avaflow vendor Desktop GUI Please see R.avaflow
R.keras vendor Command Line Please see R.keras
R.piecewiseSEM vendor Command Line Please see R.Piecewise SEM
R.stan vendor Command Line Please see R.Stan - also Stan
Regenie vendor Command Line See Regenie.
Relion RSE Command Line See CCP-EM Suite.
Relion RSE Desktop GUI Please see CCP-EM Suite container
Remora vendor Command Line Please see Remora
Rerio vendor Command Line Please see Rerio
Resmap RSE Command Line Please see CCP-EM Suite container
RIBFIND RSE Command Line Please see CCP-EM Suite container
SAIGE vendor Command Line Please see SAIGE
Salmon vendor Command Line Please see Salmon
Sambamba vendor Command Line Please see Bioapps
Samtools vendor Command Line Please see Bioapps
SCOTCH vendor Command Line Please see SCOTCH
Singularity vendor Command Line The functionality of Singularity has been replaced by Apptainer on Comet. Also consider browsing our Containers guide.
SMINA vendor Command Line Please see SMINA
Snakemake vendor Command Line Please see Snakemake
SPAdes vendor Command Line Please see SPAdes
Stan vendor Command Line Please see Stan
STAR vendor Command Line Please see STAR
StarCCM+ vendor Command Line + Desktop GUI StarCCM+
Stata/MP vendor Command Line Please see StataMP
StringTie vendor Command Line Please see Bioapps
Subread vendor Command Line Please see Subread
Suitesparse RSE Command Line Please see Amber MD
Szip vendor Command Line Please see SZip
tabix vendor Command Line Please see tabix
TEMPy RSE Command Line Please see CCP-EM Suite container
TEMPy-REFF RSE Command Line Please see CCP-EM Suite container
Tensorflow vendor Command Line Tensorflow
Tetgen vendor Command Line Please see Tetgen
TinyXML vendor Command Line Please see TinyXML
Topaz RSE Command Line Please see CCP-EM Suite container
Tophat / Tophat 2 RSE Command Line Please see Bioapps
Torchani RSE Command Line Please see Amber MD
Triangle vendor Command Line Please see Triangle
Tricycler vendor Command Line Please see Tricycler
Trim Galore vendor Command Line Please see Trim Galore
UCSF Motioncor 3 RSE Command Line Please see CCP-EM Suite container
Unicycler vendor Command Line Please see Unicycler
VCFTools vendor Command Line Please see VCF Tools
VEP vendor Command Line Please see VEP
VINA vendor Command Line Please see VINA
VirtualGL vendor Desktop GUI VirtualGL / Nvidia OpenGL
Visual Studio Code / VSCode vendor Desktop GUI Please see VSCode
vLLM RSE Command Line Please see vLLM
Vtk vendor Command Line Please see VTK
XengSort vendor Command Line Please see XengSort
xmds vendor Command Line Please see xmds
zlib vendor Command Line zlib

Software Title Follow-Ups

These titles were requested as part of the initial installation on Comet, require additional work before they can be progressed or are currently missing due to other reasons.

Title Category License Interface Help
Abaqus
bgenix
BUGS
Convert3D
CryoSPARC
GRASS
JARS
jmol
Mrtrix
OpenCascade CE
octool
PISM
R.avaflow
R.piecewise SEM
Stan
Tetgen
Tricycler
VINA

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.
Freesurfer /nobackup/shared/containers/freesurfer.8.0.20.sif 10 GB Freesurfer is installed within a container as it has requirement for multiple system libraries which would otherwise need to be installed on each compute node. This container works in both command-line as well as X11/desktop mode.
vLLM /nobackup/shared/containers/vllm.0.19.1.sif 7 GB Container based install of the vLLM application plus Python, PyTorch and the vLLM examples.
ANSYS /nobackup/shared/containers/ansys.2025r2.sif 50 GB Later releases of ANSYS on Comet will be provisioned as container environments. This allows us to provide ANSYS on a supported Linux OS, iwth all of the dependencies needed by the ANSYS software without adding multiple, duplicate software modules across the entire system. ANSYS 2025 R2 and above also now works correctly in the graphical X11 Desktop environment provided by Open OnDemand.

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. Email the support team if you'd like to request software which is not listed on this page.

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, Ahlam Alqahtani Investigating
Globus connect personal link shell / X11 multiple users
Globus cli link shell multiple users
Tophat Please see Bioapps link Open Source shell Ogo Ajayi Approved Installed via container
Freesurfer link Open Source Karoline Leiberg Approved Installed via container
vLLM Please see vLLM link Open Source shell Jiajie Luo Approved Installed via container
Matlab 2026a Update module to latest University version University License shell / X11 Approved Installed
SAS link University License shell / X11 Steven Wang, Dexter Canoy, Misty Troutt, Hemant Patle, John Casement Investigating
Convert3D link Open Source shell Gerard Hall Investigating
GipsyX link Restricted License shell / X11 Peter Clarke Investigating

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