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.
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. |
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 | ||
| 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 | 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 | ||
| Singularity | vendor | Command Line | See Apptainer | |
| Tensorflow | vendor | Command Line | ||
| zlib | vendor | Command Line | ||
| OpenCL | vendor | Command Line | ||
| 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 |
| | not installed | Commercial | Command Line | Intel Compiler Suite |
| | not installed | Commercial | Command Line | Intel Compiler Suite |
| | 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 | BOLT-LMM | |
| 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 | ||
| | vendor | Command Line | Obsolete - do not use. Use the module load Miniforge module instead. |
|
| 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 | ||
| | not installed | Commercial | Command Line | COMSOL |
| 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 |
| | not installed | Commercial | Desktop GUI | COMSOL |
| StarCCM+ | vendor | Desktop GUI | ||
| OpenMS | vendor | Command Line |
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 | Help | Link | 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 | link | Commercial - existing University license | shell | Keith Izod | Purchasing | NUIT ticket 2287405 | |
| gauss view | link | Commercial - existing University license | X11 / Open OnDemand | Keith Izod | Purchasing | NUIT ticket 2287405 | |
| 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 | link | Proprietary, permissive distribution: https://code.visualstudio.com/license | X11 / Open OnDemand | multiple users | Approved | Ticket raised with vendor 23341 | |
| Miniforge | Use module load Miniforge | link | Open Source | shell | multiple users | Approved | Installed |
| BCL Convert | link | Commercial | shell | Matthew Teasdale and other BSU users | Approved | ticket raised with vendor 23326 | |
| slurm-seff | SchedMD GitHub repository | Open Source | shell | Carol Booth | Approved | ticket raised with vendor 23342 | |
| imagemagick | System tool, no module needed | RedHat system package | Open Source | shell | Approved | Installed | |
| Stata MP 2 core | link | Commercial - existing University license for 2 core version | shell | multiple users in Business School | Investigating | NUIT tasks on SR2281701 | |
| Hypre | link | Open Source | shell | Francesco Zonta | Approved | Ticket raised with vendor 23340 | |
| htop | System tool, no module needed | RedHat system package | Open Source | shell | installed on login02, multiple users | Approved | Installed (login nodes only) |
| CASTEP / MPI | link | Cost-Free source code license | shell | Ioan Bogdan Magdau, Panagiotis Kourtis | Investigating | relies on lapack | |
| ORCA | link | Free for academic/personal use | shell | Multiple - alternative to Gaussian | Approved | Ticket raised with vendor 23327 | |
| Lapack | Lapack on Comet | link | Open Source | shell | multiple users | Approved | Ticket raised with vendor 23222 |
| Avogadro 1 & 2 | link | Open Source | X11 / Open OnDemand | Used alongside ORCA - alternative to Gauss View | Approved | Ticket raised with vendor 23332 | |
| ChimeraX | link | Free for academic, government, nonprofit, and personal use | X11 / Open OnDemand | Used alongside ORCA - alternative to Gauss View | Approved | Ticket raised with vendor 23332 | |
| seqkit | Investigating | ||||||
| bwa-mem2 | Investigating | ||||||
| bwa-meth | Investigating | ||||||
| Methyldackel | Investigating |