====== Software List ====== This page documents the list of centrally provisioned software on **Comet**. * [[#Software Type|]] - Types of software and levels of support available * [[#Software List|]] - All of the software now installed on Comet * [[#Container List|]] - All of the pre-built container images available for use on Comet * [[#Software Requests|]] - Table of additional software requests ===== 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 , or use the [[https://nuservice.ncl.ac.uk|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 , or the normal [[https://nuservice.ncl.ac.uk|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 [[started:module_basics|module]] | vendor | Centrally installed | GCC, Matlab or Conda | Software which is loaded from a [[started:module_basics|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 , or the normal [[https://nuservice.ncl.ac.uk|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 | [[:advanced:software:comsol|COMSOL]] | | COMSOL Multiphysics | //not installed// | Commercial | Desktop GUI | [[:advanced:software:comsol|COMSOL]] | | Intel Compiler Suite | //not installed// | Commercial | Command Line | [[:advanced:software:intel|Intel Compiler Suite]] | | Intel Math Kernel Libraries | //not installed// | Commercial | Command Line | [[:advanced:software:intel|Intel Compiler Suite]] | | Intel MPI Libraries | //not installed// | Commercial | Command Line | [[:advanced:software:intel|Intel Compiler Suite]] | | Abaqus | vendor | | Command Line | [[:advanced:software:abaqus|Abaqus]] | | AFNI | vendor | | Command Line | [[:advanced:software:afni|AFNI]] | | ALE | vendor | | Command Line | [[:advanced:software:ale|ALE]] | | Amber MD | RSE | | Command Line **and** Desktop GUI | Please see [[:advanced:software:ambermd|Amber MD]] | | Ambertools | RSE | | Command Line **and** Desktop GUI | Please see [[:advanced:software:ambermd|Amber MD]] | | AMD Optimizing Compiler | vendor | | Command Line | [[:advanced:software:aocc|AOCC]] | | AMD Optimizing Compiler Libraries | vendor | | Command Line | [[:advanced:software:aocc|AOCC]] | | Ansys | RSE | Commercial | Command Line **and** Desktop GUI | ANSYS 2025 R2 and above are now provided by the [[[[:advanced:software:ansys|ANSYS]] container environment | | ANTS | vendor | | Command Line | Please see [[:advanced:software:ants|ANTS]] | | APBS | RSE | | Command Line | Please see [[:advanced:software:ambermd|Amber MD]] | | Apptainer | vendor | | Command Line | [[:advanced:software:apptainer|Apptainer]] is our recommended container tool for Comet. Also consider browsing our [[advanced:containers|Containers guide]]. | | ARP/wARP | RSE | | Command Line | Please see [[advanced:software:ccpemsuite|CCP-EM Suite container]] | | ARPACK | vendor | | Command Line | Please see [[:advanced:software:arpack|ARPACK-NG]] | | Avogadro 2 | vendor | | Desktop GUI | Please see [[advanced:software:avogadro|Avogadro 2]] | | BamUtil | vendor | | Command Line | Please see [[:advanced:software:bioapps|Bioapps]] | | BCFTools | vendor | | Command Line | Please see [[:advanced:software:bioapps|Bioapps]] | | bcl2fastq | vendor | | Command Line | Obsolete. Replaced by ''BCL_convert'' - see [[advanced:software:bclconvert|BCL_convert]] | | BEDTools | vendor | | Command Line | Please see [[:advanced:software:bioapps|Bioapps]] | | BGEN | vendor | | Command Line | Please see [[:advanced:software:bgen|BGEN]] | | bgenix | vendor | | Command Line | Please see [[:advanced:software:bgenix|bgenix]] | | Bioconda | vendor | | Command Line | See the alternative [[:advanced:software:miniforge|Miniforge]] | | Bioconductor | vendor | | Command Line | Most of Bioconductor is installed as part of the [[:advanced:software:bioapps|Bioapps]] container image. See that page for more details and a list of all installed libraries. | | Biopython | vendor | | Command Line | Please see [[:advanced:software:biopython|Biopython]] | | BLAS | vendor | | Command Line | Please see [[:advanced:software:openblas|OpenBLAS]] or [[:advanced:software:lapack|LAPACK]] | | BLAST | vendor | | Command Line | Please see [[:advanced:software:blast|BLAST]] | | BLAST+ | vendor | | Command Line | Please see [[:advanced:software:blastplus|BLAST+]] | | BOLT-LMM | vendor | | Command Line | [[advanced:software:boltlmm|BOLT-LMM Help]], [[:advanced:software:bolt-lmm|BOLT-LMM compile issues]] | | Boost | vendor | | Command Line | Please see [[:advanced:software:boost|boost]] | | Bowtie2 | vendor | | Command Line | Please see [[:advanced:software:bioapps|Bioapps]] | | BUGS | vendor | | Command Line | Please see [[:advanced:software:bugs|BUGS]] | | BWA | vendor | | Command Line | Please see [[:advanced:software:bioapps|Bioapps]] | | canu assemblers | vendor | | Command Line | Please see [[:advanced:software:canu_assemblers|canu assemblersx]] | | CASTEP | RSE | | Command Line | Please see [[advanced:software:castep|CASTEP]] | | CCP-EM Suite | RSE | | Command Line | See [[:advanced:software:ccpemsuite|CCP-EM Suite]]. | | CCP-EM v1 | RSE | Non-commercial, academic use | Command Line | Please see [[advanced:software:ccpemsuite|CCP-EM Suite container]] | | CCP-EM v2 | RSE | Non-commercial, academic use | Command Line | Please see [[advanced:software:ccpemsuite|CCP-EM Suite container]] | | CCP4 | RSE | | Command Line + Desktop GUI | Please see [[advanced:software:ccpemsuite|CCP-EM Suite container]] | | CDO | vendor | | Command Line | Please see [[advanced:software:cdo|CDO]] | | CellBender | vendor | | Command Line | Please see [[advanced:software:cellbender|CellBender]] | | CheckMySequence, DoubleHelix, FindMySequence | RSE | | Command Line | Please see [[advanced:software:ccpemsuite|CCP-EM Suite container]] | | ChimeraX | vendor | | Desktop GUI | Please see [[advanced:software:chimerax|ChimeraX]] | | cmake | vendor | | Command Line | [[:advanced:software:cmake|cmake]] | | CNVKit | vendor | | Command Line | Please see [[:advanced:software:cnvkit|CNVKit]] | | Code_Saturne | vendor | | Command Line | Please see [[:advanced:software:code_saturne|Code Saturne]] | | Conda | vendor | | Command Line | See the alternative [[:advanced:software:miniforge|Miniforge]] | | Convert3D | vendor | | Command Line | Please see [[:advanced:software:convert3d|Convert 3D]] | | CP2K | vendor | | Command Line | Please see [[:advanced:software:cp2k|CP2K]] | | CryoDRGN | RSE | | Command Line | Please see [[advanced:software:ccpemsuite|CCP-EM Suite container]] | | CryoSparc | vendor | | Desktop GUI | | | CTFFind 4 | RSE | | Command Line | Please see [[advanced:software:ccpemsuite|CCP-EM Suite container]] | | Cufflinks | vendor | | Command Line | Please see [[:advanced:software:cufflinks|Cufflinks]] | | cutadapt | vendor | | Command Line | Please see [[:advanced:software:cutadapt|Cutadapt]] | | DBD-csv | vendor | | Command Line | Please see [[:advanced:software:dbd_csv|DBD-CSV]] | | DBD-mysql | vendor | | Command Line | Please see [[:advanced:software:dbd_mysql|DBD-MySQL]] | | DBD-sqlite | vendor | | Command Line | Please see [[:advanced:software:dbd_sqlite|DBD-SQLite]] | | DEXSeq | RSE | | Command Line | Please see [[:advanced:software:bioapps|Bioapps]] | | diamond | vendor | | Command Line | Please see [[:advanced:software:diamond|diamond]] | | Disambiguate | vendor | | Command Line | Please see [[:advanced:software:disambiguate|Disambiguate]] | | Docker | vendor | | Command Line | See our [[:advanced:docker|Docker]] guide in our container tools section | | Doppio | RSE | Non-commercial, academic use | Desktop GUI | See [[:advanced:software:ccpemsuite|CCP-EM Suite container]. | | Dorado | vendor | | Command Line | Please see [[:advanced:software:dorado|Dorado]] | | Eigen | vendor | | Command Line | Please see [[:advanced:software:eigen|Eigen]] | | EMDA | RSE | | Command Line | Please see [[advanced:software:ccpemsuite|CCP-EM Suite container]] | | EMDB Validation Analysis | RSE | | Command Line | Please see [[advanced:software:ccpemsuite|CCP-EM Suite container]] | | FastQC | vendor | | Desktop GUI | Please see [[:advanced:software:fastqc|FastQC]] | | FFTW | vendor | | Command Line | Please see [[:advanced:software:fftw|FFTW]] and [[:advanced:software:fftw_mpi|FFTW.MPI]] | | flye | vendor | | Command Line | Please see [[:advanced:software:flye|flye]] | | Freesurfer | vendor | | Desktop GUI | Please see [[:advanced:software:freesurfer|Freesurfer]] | | FSL | vendor | | Desktop GUI | [[:advanced:software:fsl|FSL]] | | GATK | vendor | | Command Line | Please see [[:advanced:software:gatk|GATK]] | | Gaussian | vendor | Commercial | Command Line | Please see [[:advanced:software:gaussian|Gaussian / GaussView]] | | GaussView | vendor | Commercial | Desktop GUI | Please see [[:advanced:software:gaussian|Gaussian / GaussView]] | | Generic Mapping Tools | vendor | | Command Line | Please see [[:advanced:software:generic_mapping_tools|Generic Mapping Tools]] | | Gmsh | vendor | | Desktop GUI | Please see [[:advanced:software:gmsh|Gmsh]] | | GNU g++ | vendor | | Command Line | [[:advanced:software:gcc|GCC]] | | GNU gcc | vendor | | Command Line | [[:advanced:software:gcc|GCC]] | | GNU gfortran | vendor | | Command Line | [[:advanced:software:gcc|GCC]] | | GNU gnuplot | vendor | | Command Line | Please see [[:advanced:software:gnuplot|gnuplot]] | | gprMax | vendor | | Command Line | Please see [[:advanced:software:gprmax|gprMax]] | | GRASS | vendor | | Desktop GUI | Please see [[:advanced:software:grass|GRASS]] | | Gromacs | vendor | | Command Line | [[:advanced:software:gromacs|gromacs / CUDA / OpenCL]] | | Guppy | vendor | | Command Line | See [[:advanced:software:ontguppy|Guppy]]. | | Hail | vendor | | Command Line | Please see [[:advanced:software:hail|Hail]] | | HDF5 | vendor | | Command Line | Please see [[:advanced:software:hdf5|HDF5]] | | HISAT2 | vendor | | Command Line | Please see [[:advanced:software:bioapps|Bioapps]] | | HTSeq | vendor | | Command Line | Please see [[:advanced:software:bioapps|Bioapps]] | | HTSlib | vendor | | Command Line | Available standalone, see [[:advanced:software:htslib|HTSlib]] - also installed within [[:advanced:software:bioapps|Bioapps container]] for any tools requiring it. | | Hybracter | vendor | | Command Line | Please see [[:advanced:software:hybracter|Hybracter]] | | ISSM / Ice Sheet and Sea Level System Model | vendor | | Command Line | Please see [[:advanced:software:issm|Ice Sheet and Sea Level System Model]] | | JAGS | vendor | | Command Line | Please see [[:advanced:software:jags|JAGS]] | | JARS | vendor | | Command Line | Please see [[:advanced:software:jars|JARS]] | | Java | vendor | | Command Line | Please see [[:advanced:software:java|Java]] | | jmol | vendor | | Desktop GUI | Please see [[:advanced:software:jmol|jmol]] | | Julia | vendor | | Command Line | Please see [[:advanced:software:julia|Julia]] | | Jupyter Lab | vendor | | Desktop GUI | [[:advanced:software:jupyter|Jupyter]] | | LAMMPS | vendor | | Command Line | Please see [[:advanced:software:lammps|LAMMPS]] | | last | vendor | | Command Line | Please see [[:advanced:software:last|last]] | | ldsc | vendor | | Command Line | Please see [[:advanced:software:ldsc|ldsc]] | | libncurses | vendor | | Command Line | [[:advanced:software:ncurses|ncurses]] | | libXmu | vendor | | Command Line | Included in the ''module load X11'' environment - see also [[:advanced:software:x11|X11 Desktop]] | | Linux X11 desktop | vendor | | Desktop GUI | Please see [[:advanced:software:x11|X11 Desktop]] | | Locscale | RSE | | Command Line | Please see [[advanced:software:ccpemsuite|CCP-EM Suite container]] | | MACS2 | vendor | | Command Line | Please see [[:advanced:software:macs2|MACS2]] | | Mamba | vendor | | Command Line | See the alternative [[:advanced:software:miniforge|Miniforge]] | | Matlab | vendor | Commercial | Command Line | [[:advanced:software:matlab|Matlab]] | | Matlab | vendor | Commercial | Desktop GUI | [[:advanced:software:matlab|Matlab]] | | matplotlib | vendor | | Command Line | Please see [[:advanced:software:matplotlib|matplotlib]] | | MBX | RSE | | Command Line | Please see [[:advanced:software:ambermd|Amber MD]] | | megan | vendor | | Command Line | Please see [[:advanced:software:megan|megan]] | | merlin | vendor | | Command Line | Now installed. See [[:advanced:software:merlin|Merlin]]. | | MetalCoord | RSE | | Command Line | Please see [[advanced:software:ccpemsuite|CCP-EM Suite container]] | | metaSPAdes | vendor | | Command Line | Parts of the SPAdes toolkit - please see [[:advanced:software:spades|SPAdes]] | | METIS | vendor | | Command Line | Please see [[:advanced:software:metis|METIS]] | | Model Angelo | RSE | | Command Line | See [[:advanced:software:ccpemsuite|CCP-EM Suite]]. | | Modeller (Salilabs) | RSE | Non-commercial, academic use | Command Line | Please see [[advanced:software:ccpemsuite|CCP-EM Suite container]] | | Mono | vendor | | Command Line | Please see [[:advanced:software:mono|Mono]] | | Mrtrix | vendor | | Desktop GUI | Please see [[:advanced:software:mrtrix|Mrtrix]] | | MultiQC | vendor | | Command Line | Please see [[:advanced:software:multiqc|MultiQC]] | | MUMPS | vendor | | Command Line | Please see [[:advanced:software:mumps|MUMPS]] | | MuSpAn | self install | | Command Line | Please see the [[:advanced:software:muspan|MuSpAn]] install guide | | NBO | vendor | | Command Line | Please see [[:advanced:software:nbo|NBO]] | | Nektar++ | vendor | | Command Line | Please see [[:advanced:software:nektar|Nektar++]] | | Netcdf-c | vendor | | Command Line | Please see [[:advanced:software:netcdf-c|NetCDF-C]] | | Netcdf-fortran | vendor | | Command Line | Please see [[:advanced:software:netcdf-fortran|NetCDF-Fortran]] | | Nextflow | vendor | | Command Line | Please see [[:advanced:software:nextflow|Netxtflow]] | | numpy | vendor | | Command Line | [[:advanced:software:numpy|numpy]] | | Nvidia CUDA SDK | vendor | | Command Line | [[:advanced:software:cuda|CUDA SDK]] | | Nvidia HPC SDK | vendor | | Command Line | [[:advanced:software:nvhpc|HPC SDK]] | | OpenBLAS | vendor | | Command Line | Please see [[:advanced:software:openblas|OpenBLAS]] | | OpenCascade CE | vendor | | Command Line | Please see [[:advanced:software:opencascade_ce|OpenCascade CE]] | | OpenCL | vendor | | Command Line | [[:advanced:software:opencl|OpenCL]] | | OpenFOAM | vendor | | Command Line | Please see [[:advanced:software:openfoam|OpenFOAM]] | | OpenGeoSys | vendor | | Command Line | Please see [[:advanced:software:ogs|OpenGeoSys]] | | OpenGL (MESA) | vendor | | Desktop GUI | [[:advanced:software:mesa|MESA]] | | OpenGL (Nvidia) | vendor | | Desktop GUI | [[:advanced:software:virtualgl|VirtualGL / Nvidia OpenGL]] | | OpenMP | vendor | | Command Line | Please see [[:advanced:software:openmp|OpenMP]] | | OpenMPI | vendor | | Command Line | Please see [[:advanced:software:openmpi|OpenMPI]] | | OpenMS | vendor | | Command Line | Now installed. See [[:advanced:software:openms|OpenMS]]. | | OpenSeesPy | vendor | | Command Line | Please see [[:advanced:software:openseespy|OpenSeesPy]] | | OpenSSL | vendor | | Command Line | Please see [[:advanced:software:openssl|OpenSSL]] | | ORCA | vendor | | Command Line | Please see [[:advanced:software:orca|Orca]] | | parallel | vendor | | Command Line | Please see [[:advanced:software:parallel|Parallel]] | | Paraview | vendor | | Command Line **and** Desktop GUI | Please see [[:advanced:software:paraview|Paraview]] | | Perl | vendor | | Command Line | Please see [[:advanced:software:perl|Perl]] | | pgap | RSE | | Command Line | Please see [[:advanced:software:pgap|pgap]] | | Picard | vendor | | Command Line | Please see [[:advanced:software:bioapps|Bioapps]] | | PISM | vendor | | Command Line | Please see [[:advanced:software:pism|PISM]] | | Plink | vendor | | Command Line | Please see [[:advanced:software:plink|Plink]] | | PLUMED | RSE | | Command Line | Please see [[:advanced:software:ambermd|Amber MD]] | | Podman | vendor | | Command Line | [[:advanced:software:podman|Podman]] is one of the supporter container tools on Comet. Also consider browsing our [[advanced:containers|Containers guide]]. | | PRSice | vendor | | Command Line | Please see [[:advanced:software:prsice|PRSice]] | | PTSCOTCH | vendor | | Command Line | PT-SCOTCH refers to [[:advanced:software:ptscotch|SCOTCH]] when running in parallel mode | | Pysam | vendor | | Command Line | Please see [[:advanced:software:pysam|PySAM]] | | Python | vendor | | Command Line | Please see [[:advanced:software:python|Python]] | | Python JAX | vendor | | Command Line | Please see [[:advanced:software:python_jax|Python JAX|]] | | Python OpenTURNS | vendor | | Command Line | Please see [[:advanced:software:python_openturns|Python OpenTURNS]] | | Python RAY | vendor | | Command Line | Please see [[:advanced:software:python_ray|Python RAY]] | | PyTorch | vendor | | Command Line | [[:advanced:software:pytorch|PyTorch]] | | QCTOOL | vendor | | Command Line | Please see [[:advanced:software:octool|OCTOOL]] | | quantum-espresso | vendor | | Command Line | Please see [[:advanced:software:quantum_espresso|Quantum Espresso|]] | | R | vendor | | Command Line | [[:advanced:software:r|R]] | | R Studio | vendor | | Desktop GUI | [[:advanced:software:rstudio|R Studio]] | | R.avaflow | vendor | | Desktop GUI | Please see [[:advanced:software:r_avaflow|R.avaflow]] | | R.keras | vendor | | Command Line | Please see [[:advanced:software:r_keras|R.keras]] | | R.piecewiseSEM | vendor | | Command Line | Please see [[:advanced:software:r_piecewisesem|R.Piecewise SEM]] | | R.stan | vendor | | Command Line | Please see [[:advanced:software:r_stan|R.Stan]] - also [[:advanced:software:stan|Stan]] | | Regenie | vendor | | Command Line | See [[:advanced:software:regenie|Regenie]]. | | Relion | RSE | | Command Line | See [[:advanced:software:ccpemsuite|CCP-EM Suite]]. | | Relion | RSE | | Desktop GUI | Please see [[advanced:software:ccpemsuite|CCP-EM Suite container]] | | Remora | vendor | | Command Line | Please see [[:advanced:software:remora|Remora]] | | Rerio | vendor | | Command Line | Please see [[:advanced:software:rerio|Rerio]] | | Resmap | RSE | | Command Line | Please see [[advanced:software:ccpemsuite|CCP-EM Suite container]] | | RIBFIND | RSE | | Command Line | Please see [[advanced:software:ccpemsuite|CCP-EM Suite container]] | | SAIGE | vendor | | Command Line | Please see [[:advanced:software:saige|SAIGE]] | | Salmon | vendor | | Command Line | Please see [[:advanced:software:salmon|Salmon]] | | Sambamba | vendor | | Command Line | Please see [[:advanced:software:bioapps|Bioapps]] | | Samtools | vendor | | Command Line | Please see [[:advanced:software:bioapps|Bioapps]] | | SCOTCH | vendor | | Command Line | Please see [[:advanced:software:ptscotch|SCOTCH]] | | Singularity | vendor | | Command Line | The functionality of Singularity has been replaced by [[:advanced:software:apptainer|Apptainer]] on Comet. Also consider browsing our [[advanced:containers|Containers guide]]. | | SMINA | vendor | | Command Line | Please see [[:advanced:software:smina|SMINA]] | | Snakemake | vendor | | Command Line | Please see [[:advanced:software:snakemake|Snakemake]] | | SPAdes | vendor | | Command Line | Please see [[:advanced:software:spades|SPAdes]] | | Stan | vendor | | Command Line | Please see [[:advanced:software:stan|Stan]] | | STAR | vendor | | Command Line | Please see [[:advanced:software:star|STAR]] | | StarCCM+ | vendor | | Command Line + Desktop GUI | [[:advanced:software:starccm|StarCCM+]] | | Stata/MP | vendor | | Command Line | Please see [[:advanced:statamp|StataMP]] | | StringTie | vendor | | Command Line | Please see [[:advanced:software:bioapps|Bioapps]] | | Subread | vendor | | Command Line | Please see [[:advanced:software:subread|Subread]] | | Suitesparse | RSE | | Command Line | Please see [[:advanced:software:ambermd|Amber MD]] | | Szip | vendor | | Command Line | Please see [[:advanced:software:szip|SZip]] | | tabix | vendor | | Command Line | Please see [[:advanced:software:tabix|tabix]] | | TEMPy | RSE | | Command Line | Please see [[advanced:software:ccpemsuite|CCP-EM Suite container]] | | TEMPy-REFF | RSE | | Command Line | Please see [[advanced:software:ccpemsuite|CCP-EM Suite container]] | | Tensorflow | vendor | | Command Line | [[:advanced:software:tensorflow|Tensorflow]] | | Tetgen | vendor | | Command Line | Please see [[:advanced:software:tetgen|Tetgen]] | | TinyXML | vendor | | Command Line | Please see [[:advanced:software:tinyxml|TinyXML]] | | Topaz | RSE | | Command Line | Please see [[advanced:software:ccpemsuite|CCP-EM Suite container]] | | Tophat / Tophat 2 | RSE | | Command Line | Please see [[:advanced:software:bioapps|Bioapps]] | | Torchani | RSE | | Command Line | Please see [[:advanced:software:ambermd|Amber MD]] | | Triangle | vendor | | Command Line | Please see [[:advanced:software:triangle|Triangle]] | | Tricycler | vendor | | Command Line | Please see [[:advanced:software:tricycler|Tricycler]] | | Trim Galore | vendor | | Command Line | Please see [[:advanced:software:trim_galor|Trim Galore]] | | UCSF Motioncor 3 | RSE | | Command Line | Please see [[advanced:software:ccpemsuite|CCP-EM Suite container]] | | Unicycler | vendor | | Command Line | Please see [[:advanced:software:unicycler|Unicycler]] | | VCFTools | vendor | | Command Line | Please see [[:advanced:software:vcftools|VCF Tools]] | | VEP | vendor | | Command Line | Please see [[:advanced:software:vep|VEP]] | | VINA | vendor | | Command Line | Please see [[:advanced:software:vina|VINA]] | | VirtualGL | vendor | | Desktop GUI | [[:advanced:software:virtualgl|VirtualGL / Nvidia OpenGL]] | | Visual Studio Code / VSCode | vendor | | Desktop GUI | Please see [[:advanced:vs_code|VSCode]] | | vLLM | RSE | | Command Line | Please see [[:advanced:software:vllm|vLLM]] | | Vtk | vendor | | Command Line | Please see [[:advanced:software:vtk|VTK]] | | XengSort | vendor | | Command Line | Please see [[:advanced:software:xengsort|XengSort]] | | xmds | vendor | | Command Line | Please see [[:advanced:software:xmds|xmds]] | | zlib | vendor | | Command Line | [[:advanced:software:zlib|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 ^ | [[:advanced:software:castep|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. | | [[:advanced:dnascent|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. | | [[:advanced:software:bioapps|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. | | [[:advanced:software:fsl|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. | | [[:advanced:software:cnvkit|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. | | [[:advanced:software:ambermd|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. | | [[:advanced:comfyui|ComfyUI]] | N/A | | A build recipe and instructions are provided to build this on a per-user basis. | | [[:advanced:samplecontainers|Ubuntu LTS]] | N/A | 120 MB | Sample Ubuntu LTS container recipe. | | [[:advanced:samplecontainers|Ubuntu LTS + development tools]] | N/A | 350 MB | Sample Ubuntu LTS container recipe with standard C, C++, Fortran and Python development tools. | | [[:advanced:samplecontainers|Nvidia CUDA/CUDNN]] | N/A | 5.9 GB | Sample Nvidia CUDA/CUDNN container recipe built on Ubuntu LTS. | | [[:advanced:software:ccpemsuite|CCP-EM Suite]] | ''/nobackup/shared/containers/ccpemsuite.2026.03.sif'' | 42 GB | CCP-EM, CCPEM2, CCP4, Doppio, Relion 5 and //other//, related tools. | | [[:advanced:software:ogs|OpenGeoSys]] | ''/nobackup/shared/containers/ogs.2026.03.sif'' | 1 GB | OpenGeoSys Python environment, including Jupyter Lab for running OGS notebooks. | | [[:advanced:software:issm|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. | | [[:advanced:software:ldsc|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. | | [[:advanced:software:freesurfer|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. | | [[:advanced:software:vllm|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. | | [[:advanced:software:ansys|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. [[hpc.researchcomputing@newcastle.ac.uk|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 | | [[:advanced:software:gaussian|Gaussian]] | Use ''module load Gaussian'' | [[https://gaussian.com/gaussian16/|link]] | Commercial - existing University license | shell | Keith Izod, Jack Hemingway, Nick Walker, Sam Power | Purchased | Installed | | [[:advanced:software:gaussian|GaussView]] | Use ''module load GaussianView'' | [[https://gaussian.com/gaussview6/|link]] | Commercial - existing University license | X11 / Open OnDemand | Keith Izod, Jack Hemingway, Nick Walker, Sam Power | Purchased | Installed | | [[:advanced:software:gromacs|gromacs / CUDA]] | Use ''module load GROMACS/2026-cuda'' | [[https://manual.gromacs.org/current/install-guide/index.html|link]] | Open Source | shell | Finlay Clark | Approved | Installed | | [[:advanced:software:gromacs|gromacs / OpenCL]] | Use ''module load GROMACS/2026-opencl'' | [[https://manual.gromacs.org/current/install-guide/index.html|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 | | [[:advanced:vs_code|VSCode]] | Use ''module load VSCode'' - or launch from the Open OnDemand desktop menu | [[https://code.visualstudio.com/|link]] | Proprietary, permissive distribution: https://code.visualstudio.com/license | X11 / Open OnDemand | multiple users | Approved | Installed | | [[:advanced:software:miniforge|Miniforge]] | Use ''module load Miniforge'' | [[https://conda-forge.org/|link]] | Open Source | shell | multiple users | Approved | Installed | | [[:advanced:software:bclconvert|BCL Convert]] | Use ''module load BCL-Convert'' - start with ''bcl-convert''. Also see [[:advanced:software:bioapps|Bioapps]] | [[https://emea.support.illumina.com/sequencing/sequencing_software/bcl-convert/downloads.html|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 | | [[:advanced:statamp|Stata MP 2 core]] | Use ''module load Stata'' | [[https://www.stata.com/statamp/|link]] | Commercial - existing University license for 2 core version | shell | multiple users in Business School | Approved | Installed | | [[:advanced:software:hypre|Hypre]] | Use ''module load Hypre'' | [[https://computing.llnl.gov/projects/hypre-scalable-linear-solvers-multigrid-methods|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 | | [[:advanced:software:castep|CASTEP]] | Installed as a container - see our [[:advanced:software:castep|CASTEP]] guide | [[https://www.castep.org/get_castep|link]] | Cost-Free source code license | shell | Ioan Bogdan Magdau, Panagiotis Kourtis, Alex Christison | Approved | Installed | | ORCA | Use ''module load Orca'' | [[https://www.faccts.de/orca/|link]] | Free for academic/personal use | shell | Multiple - alternative to Gaussian | Approved | Installed | | [[:advanced:software:lapack|LAPACK]] | Use ''module load LAPACK/3.12.0'' | [[https://github.com/Reference-LAPACK/lapack|link]] | Open Source | shell | multiple users | Approved | Installed | | [[:advanced:software:avogadro|Avogadro 1 & 2]] | Use ''module load Avogadro'' - only usable on Open OnDemand GPU desktops | [[https://www.openchemistry.org/downloads/|link]] | Open Source | X11 / Open OnDemand | Used alongside ORCA - alternative to Gauss View | Approved | Installed | | [[:advanced:software:chimerax|ChimeraX]] | Use ''module load ChimeraX'' - only usable on Open OnDemand desktops (preferably GPU) | [[https://www.rbvi.ucsf.edu/chimerax/download.html|link]] | Free for academic, government, nonprofit, and personal use | X11 / Open OnDemand | Used alongside ORCA - alternative to Gauss View | Approved | Installed | | [[:advanced:software:bioapps|seqkit]] | Please see [[:advanced:software:bioapps|Bioapps]] | | Open Source | shell | Common bioinformatics tools - requested by many users. Existing versions in modules have conflicting dependencies. | Approved | Installed via container | | [[:advanced:software:bioapps|bwa-mem2]] | Please see [[:advanced:software:bioapps|Bioapps]] | | Open Source | shell | Common bioinformatics tools - requested by many users. Existing versions in modules have conflicting dependencies. | Approved | Installed via container | | [[:advanced:software:bioapps|bwa-meth]] | Please see [[:advanced:software:bioapps|Bioapps]] | | Open Source | shell | Common bioinformatics tools - requested by many users. Existing versions in modules have conflicting dependencies. | Approved | Installed via container | | [[:advanced:software:bioapps|Methyldackel]] | Please see [[:advanced:software:bioapps|Bioapps]] | | Open Source | shell | Common bioinformatics tools - requested by many users. Existing versions in modules have conflicting dependencies. | Approved | Installed via container | | [[:advanced:software:bioapps|DEXSeq]] | Please see [[:advanced:software:bioapps|Bioapps]] | [[https://bioconductor.org/packages/release/bioc/html/DEXSeq.html|link]] | Open Source | shell | Ogo Ajayi | Approved | Installed via container | | [[:advanced:software:ambermd|AmberMD]] | Please see [[:advanced:software:ambermd|Amber MD]] | [[https://ambermd.org/GetAmber.php|link]] | Open Source | shell | Shangyuwen Yang | Approved | Installed via container | | [[:advanced:software:muspan|MuSpAn]] | Please see [[:advanced:software:muspan|MuSpAn]] | [[https://www.muspan.co.uk/|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 | | [[:advanced:rclone|RClone]] | System tool, no module needed | RedHat system package | Open Source | shell | Michael Beaty | Approved | Installed | | [[:advanced:software:nextflow|Nextflow]] | | [[https://www.nextflow.io/|Link]] | Open Source | shell / service | Jordan Cuff, Monika Gonka, Ahlam Alqahtani | Investigating | | | Globus connect personal | | [[https://docs.globus.org/globus-connect-personal/install/linux/|link]] | | shell / X11 | multiple users | | | | Globus cli | | [[https://docs.globus.org/cli/quickstart/|link]] | | shell | multiple users | | | | [[:advanced:software:bioapps|Tophat]] | Please see [[:advanced:software:bioapps|Bioapps]] | [[https://github.com/DaehwanKimLab/tophat|link]] | Open Source | shell | Ogo Ajayi | Approved | Installed via container | | [[:advanced:software:freesurfer|Freesurfer]] | | [[https://surfer.nmr.mgh.harvard.edu/fswiki/rel7downloads|link]] | Open Source | | Karoline Leiberg | Approved | Installed via container | | [[:advanced:software:vllm|vLLM]] | Please see [[:advanced:software:vllm|vLLM]] | [[https://vllm.ai/|link]] | Open Source | shell | Jiajie Luo | Approved | Installed via container | | [[:advanced:matlab|Matlab 2026a]] | Update module to latest University version | | University License | shell / X11 | | Approved | Installed | | [[:advanced:software:sas|SAS]] | | [[https://www.sas.com/en_gb|link]] | University License | shell / X11 | Steven Wang, Dexter Canoy, Misty Troutt, Hemant Patle, John Casement | Investigating | | | [[:advanced:software:convert3d|Convert3D]] | | [[https://www.itksnap.org/pmwiki/pmwiki.php?n=Convert3D.Convert3D|link]] | Open Source | shell | Gerard Hall | Investigating | | | [[:advanced:software:gipsyx|GipsyX]] | | [[https://gipsyx.jpl.nasa.gov/index.php?page=software|link]] | Restricted License | shell / X11 | Peter Clarke | Investigating | | ---- [[:advanced:software|Back to Advanced Software Topics]]