HPC Support - advanced:software

afni

Anonymous (anonymous@undisclosed.example.com) — 2026-03-26T20:27:57+00:00

AFNI AFNI is a software module available on Comet. AFNI overview To access AFNI on Comet, run module load AFNI. This will load the default version of AFNI. An overview of the module information is shown below (module -r spider ^AFNI$): If there are multiple versions of

ale

Anonymous (anonymous@undisclosed.example.com) — 2026-03-26T20:29:08+00:00

ALE ALE is a software module available on Comet. ALE overview To access ALE on Comet, run module load ALE. This will load the default version of ALE. An overview of the module information is shown below (module -r spider ^ALE$): If there are multiple versions of

ambermd

Anonymous (anonymous@undisclosed.example.com) — 2026-03-14T07:56:24+00:00

Amber MD From Ambermd.org: " Amber is a suite of biomolecular simulation programs. It began in the late 1970's, and is maintained by an active development community; see our history page and our contributors page for more information. The term “

ansys

Anonymous (anonymous@undisclosed.example.com) — 2026-04-30T09:23:41+00:00

ANSYS The documentation for the container-based 2025 R2 install of ANSYS is still under progress and requires further user feedback. This will replace the earlier ANSYS module after successful testing. " Ansys is a subsidiary of Siemens. Ansys software includes a suite of products for physics and engineering modelling using Finite Element Analysis (FEA) and Computational Fluid Dynamics (CFD). It is used to virtually test and analyze product performance in structural, fluid, thermal, and el…

ants

Anonymous (anonymous@undisclosed.example.com) — 2026-04-09T10:23:10+00:00

ANTS ANTS is a software module available on Comet. ANTS overview To access ANTS on Comet, run module load ANTS. This will load the default version of ANTS. An overview of the module information is shown below (module -r spider ^ANTS$): If there are multiple versions of

aocc

Anonymous (anonymous@undisclosed.example.com) — 2026-03-26T20:30:43+00:00

AOCC AOCC is a software module available on Comet. It provides the AMD Optimising Compiler Collection. AOCC overview To access AOCC on Comet, run module load AOCC. This will load the default version of AOCC. An overview of the module information is shown below (

apptainer

Anonymous (anonymous@undisclosed.example.com) — 2025-08-07T21:25:31+00:00

Apptainer * Category: Vendor provision * Access method: Loaded from Linux module software * License: Open Source * Command Line: Yes * Desktop GUI: Yes (no specific support for GUI, but can be used at the desktop without issue) Apptainer is a software container tool. It allows you to encapsulate an application and all the necessary supporting tools and libraries, enabling you to run the application without needing to locally install all of the supporting tools. You can move the cont…

arpack

Anonymous (anonymous@undisclosed.example.com) — 2026-04-09T10:25:12+00:00

arpack-ng arpack-ng is a software module available on Comet. arpack-ng overview To access arpack-ng on Comet, run module load arpack-ng. This will load the default version of arpack-ng. An overview of the module information is shown below (module -r spider ^arpack-ng$

avogadro

Anonymous (anonymous@undisclosed.example.com) — 2026-02-25T09:52:49+00:00

Avogadro 2 Avogadro 2 is a chemical editor and visualization application. It is a continuation of (and partial replacement of) Avogadro. * For further information: Running on Comet You can run Avogadro 2 on Comet by starting it from one of our

bclconvert

Anonymous (anonymous@undisclosed.example.com) — 2026-03-26T16:48:30+00:00

BCL_convert BCL_convert is a tool for working with data generated by Illumina sequencing instruments. It is also the replacement for bcl2fastq which is no longer updated or supported by Illumina. * For more information: Roadmap for BCL_convert

bgen

Anonymous (anonymous@undisclosed.example.com) — 2026-04-09T10:55:35+00:00

bgen bgen is a software module available on Comet. bgen overview To access bgen on Comet, run module load bgen. This will load the default version of bgen. An overview of the module information is shown below (module -r spider ^bgen$): If there are multiple versions of

bioapps

Anonymous (anonymous@undisclosed.example.com) — 2026-04-09T11:09:50+00:00

Bioapps Container This container is intended to collect most of the commonly used Bioinformatics software packages used on Rocket and Comet, and provide them in a single, easy to use format, without all of the complexity of many module load and module unload

biopython

Anonymous (anonymous@undisclosed.example.com) — 2026-04-09T10:56:49+00:00

Biopython Biopython is a software module available on Comet. Biopython overview To access Biopython on Comet, run module load Biopython. This will load the default version of Biopython. An overview of the module information is shown below (module -r spider ^Biopython$

blast

Anonymous (anonymous@undisclosed.example.com) — 2026-04-09T11:01:58+00:00

BLAST BLAST is a software module available on Comet. BLAST overview To access BLAST on Comet, run module load BLAST. This will load the default version of BLAST. An overview of the module information is shown below (module -r spider ^BLAST$):

blastplus

Anonymous (anonymous@undisclosed.example.com) — 2026-04-09T11:02:42+00:00

BLAST+ BLAST+ is a software module available on Comet. BLAST+ overview To access BLAST+ on Comet, run module load BLAST+. This will load the default version of BLAST+. An overview of the module information is shown below (module -r spider ^BLAST+$

bolt-lmm

Anonymous (anonymous@undisclosed.example.com) — 2026-02-02T16:12:01+00:00

Bolt-LMM " The BOLT-LMM algorithm computes statistics for testing association between phenotype and genotypes using a linear mixed model" Available from: * Installing from source Latest source code may be downloaded from: - this also includes a pre-built binary, but we have found it difficult to get this to run on Comet, as it appears to be li…

boltlmm

Anonymous (anonymous@undisclosed.example.com) — 2026-02-19T16:55:26+00:00

BOLT-LMM " The BOLT-LMM algorithm computes statistics for testing association between phenotype and genotypes using a linear mixed model " * For further information: ---------- Running on Comet The existing binaries of BOLT-LMM (as available at:

boost

Anonymous (anonymous@undisclosed.example.com) — 2026-04-09T11:03:40+00:00

Boost Boost is a software module available on Comet. Boost overview To access Boost on Comet, run module load Boost. This will load the default version of Boost. An overview of the module information is shown below (module -r spider ^Boost$):

canu_assemblers

Anonymous (anonymous@undisclosed.example.com) — 2026-04-09T11:04:37+00:00

canu canu is a software module available on Comet. canu overview To access canu on Comet, run module load canu. This will load the default version of canu. An overview of the module information is shown below (module -r spider ^canu$): If there are multiple versions of

castep

Anonymous (anonymous@undisclosed.example.com) — 2026-04-09T09:08:10+00:00

CASTEP " CASTEP is a leading code for calculating the properties of materials from first principles. Using density functional theory, it can simulate a wide range of properties of materials proprieties including energetics, structure at the atomic level, vibrational properties, electronic response properties etc. In particular it has a wide range of spectroscopic features that link directly to experiment, such as infra-red and Raman spectroscopies, NMR, and core level spectra.

ccpemsuite

Anonymous (anonymous@undisclosed.example.com) — 2026-03-25T17:24:10+00:00

CCP-EM Suite ... and related tools " CCPEM - Collaborative Computational Project for Electron cryo-Microscopy" CCPEM, Doppio, Relion and other tools are often used together. We are providing these tools in a single, self-contained container runtime environment for the users of our Comet HPC facility. This wiki page demonstrates how to find and use this software on Comet.

cdo

Anonymous (anonymous@undisclosed.example.com) — 2026-04-09T11:05:24+00:00

CDO CDO is a software module available on Comet. CDO overview To access CDO on Comet, run module load CDO. This will load the default version of CDO. An overview of the module information is shown below (module -r spider ^CDO$): If there are multiple versions of

cellbender

Anonymous (anonymous@undisclosed.example.com) — 2026-04-09T11:06:08+00:00

cellbender-env cellbender-env is a software module available on Comet. cellbender-env overview To access cellbender-env on Comet, run module load cellbender-env. This will load the default version of cellbender-env. An overview of the module information is shown below (

chimerax

Anonymous (anonymous@undisclosed.example.com) — 2026-02-19T15:11:47+00:00

ChimeraX " UCSF ChimeraX (or simply ChimeraX) is the next-generation molecular visualization program from the Resource for Biocomputing, Visualization, and Informatics (RBVI), following UCSF Chimera. " * See Running on Comet You can run ChimeraX on Comet by starting it from an

cmake

Anonymous (anonymous@undisclosed.example.com) — 2026-03-26T20:49:41+00:00

cmake cmake is a software module available on Comet. cmake overview To access cmake on Comet, run module load cmake. This will load the default version of cmake. An overview of the module information is shown below (module -r spider ^cmake$):

cnvkit

Anonymous (anonymous@undisclosed.example.com) — 2026-03-14T07:56:51+00:00

CNVKit " A command-line toolkit and Python library for detecting copy number variants and alterations genome-wide from high-throughput sequencing." * For more information see: ---------- CNVKit on Comet We have installed CNVKit using the published Docker container:

code_saturne

Anonymous (anonymous@undisclosed.example.com) — 2026-04-09T11:07:15+00:00

code-saturne code-saturne is a software module available on Comet. code-saturne overview To access code-saturne on Comet, run module load code-saturne. This will load the default version of code-saturne. An overview of the module information is shown below (

comsol

Anonymous (anonymous@undisclosed.example.com) — 2025-07-11T12:02:48+00:00

COMSOL Multiphysics COMSOL was going to be made available on the Comet HPC facility as commissioned in 2025, but changes to the University license mean that we are no longer able to offer this software. ---------- Back to Advanced Software list

cp2k

Anonymous (anonymous@undisclosed.example.com) — 2026-04-09T11:11:33+00:00

CP2K CP2K is a software module available on Comet. CP2K overview To access CP2K on Comet, run module load CP2K. This will load the default version of CP2K. An overview of the module information is shown below (module -r spider ^CP2K$): If there are multiple versions of

cuda

Anonymous (anonymous@undisclosed.example.com) — 2025-12-15T09:20:31+00:00

Nvidia CUDA SDK * Category: Vendor provision * Access method: Loaded from Linux module software * License: Nvidia license * Command Line: Yes * Desktop GUI: No The Nvidia CUDA SDK provided specialist software, libraries and functions for GPU compute using the Nvidia GPU architecture. For official documentation see:

cufflinks

Anonymous (anonymous@undisclosed.example.com) — 2026-04-09T11:12:14+00:00

Cufflinks Cufflinks is a software module available on Comet. Cufflinks overview To access Cufflinks on Comet, run module load Cufflinks. This will load the default version of Cufflinks. An overview of the module information is shown below (module -r spider ^Cufflinks$

cutadapt

Anonymous (anonymous@undisclosed.example.com) — 2026-04-09T11:12:59+00:00

cutadapt cutadapt is a software module available on Comet. cutadapt overview To access cutadapt on Comet, run module load cutadapt. This will load the default version of cutadapt. An overview of the module information is shown below (module -r spider ^cutadapt$

dbd_csv

Anonymous (anonymous@undisclosed.example.com) — 2026-04-09T11:15:06+00:00

DBD::CSV DBD::CSV is a software module available on Comet. DBD::CSV overview To access DBD::CSV on Comet, run module load DBD::CSV. This will load the default version of DBD::CSV. An overview of the module information is shown below (module -r spider ^DBD::CSV$

dbd_mysql

Anonymous (anonymous@undisclosed.example.com) — 2026-04-09T11:16:01+00:00

DBD-mysql DBD-mysql is a software module available on Comet. DBD-mysql overview To access DBD-mysql on Comet, run module load DBD-mysql. This will load the default version of DBD-mysql. An overview of the module information is shown below (module -r spider ^DBD-mysql$

dbd_sqlite

Anonymous (anonymous@undisclosed.example.com) — 2026-04-09T11:16:35+00:00

DBD::SQLite DBD::SQLite is a software module available on Comet. DBD::SQLite overview To access DBD::SQLite on Comet, run module load DBD::SQLite. This will load the default version of DBD::SQLite. An overview of the module information is shown below (

diamond

Anonymous (anonymous@undisclosed.example.com) — 2026-04-09T11:17:34+00:00

DIAMOND DIAMOND is a software module available on Comet. DIAMOND overview To access DIAMOND on Comet, run module load DIAMOND. This will load the default version of DIAMOND. An overview of the module information is shown below (module -r spider ^DIAMOND$

disambiguate

Anonymous (anonymous@undisclosed.example.com) — 2026-04-09T11:18:16+00:00

disambiguate-env disambiguate-env is a software module available on Comet. disambiguate-env overview To access disambiguate-env on Comet, run module load disambiguate-env. This will load the default version of disambiguate-env. An overview of the module information is shown below (

dorado

Anonymous (anonymous@undisclosed.example.com) — 2026-04-09T11:19:10+00:00

Dorado Dorado is a software module available on Comet. Dorado overview To access Dorado on Comet, run module load Dorado. This will load the default version of Dorado. An overview of the module information is shown below (module -r spider ^Dorado$

eigen

Anonymous (anonymous@undisclosed.example.com) — 2026-04-09T11:20:19+00:00

Eigen Eigen is a software module available on Comet. Eigen overview To access Eigen on Comet, run module load Eigen. This will load the default version of Eigen. An overview of the module information is shown below (module -r spider ^Eigen$):

fastqc

Anonymous (anonymous@undisclosed.example.com) — 2026-04-09T11:23:47+00:00

FastQC FastQC is a software module available on Comet. FastQC overview To access FastQC on Comet, run module load FastQC. This will load the default version of FastQC. An overview of the module information is shown below (module -r spider ^FastQC$

fftw_mpi

Anonymous (anonymous@undisclosed.example.com) — 2026-04-09T11:26:23+00:00

FFTW.MPI FFTW.MPI is a software module available on Comet. FFTW.MPI overview To access FFTW.MPI on Comet, run module load FFTW.MPI. This will load the default version of FFTW.MPI. An overview of the module information is shown below (module -r spider ^FFTW.MPI$

fftw

Anonymous (anonymous@undisclosed.example.com) — 2026-04-09T11:25:54+00:00

FFTW FFTW is a software module available on Comet. Important! Depending on your use case you may also need to look at FFTW.MPI. FFTW overview To access FFTW on Comet, run module load FFTW. This will load the default version of FFTW. An overview of the module information is shown below (

flye

Anonymous (anonymous@undisclosed.example.com) — 2026-04-09T11:27:21+00:00

Flye Flye is a software module available on Comet. Flye overview To access Flye on Comet, run module load Flye. This will load the default version of Flye. An overview of the module information is shown below (module -r spider ^Flye$): If there are multiple versions of

freesurfer

Anonymous (anonymous@undisclosed.example.com) — 2026-04-21T13:52:26+00:00

Freesurfer " FreeSurfer is a software package for the analysis and visualization of structural and functional neuroimaging data from cross-sectional or longitudinal studies. It is developed by the Laboratory for Computational Neuroimaging at the Athinoula A. Martinos Center for Biomedical Imaging. FreeSurfer is the structural MRI analysis software of choice for the

fsl

Anonymous (anonymous@undisclosed.example.com) — 2026-03-02T20:30:11+00:00

FSL " FSL is a comprehensive library of analysis tools for FMRI, MRI and diffusion brain imaging data. It runs on macOS (Intel and Apple Silicon), Linux, and Windows (via the Windows Subsystem for Linux), and is very easy to install. Most of the tools can be run both from the command line and as GUIs (

gatk

Anonymous (anonymous@undisclosed.example.com) — 2026-04-09T11:28:04+00:00

GATK GATK is a software module available on Comet. GATK overview To access GATK on Comet, run module load GATK. This will load the default version of GATK. An overview of the module information is shown below (module -r spider ^GATK$): If there are multiple versions of

gaussian

Anonymous (anonymous@undisclosed.example.com) — 2026-03-18T10:09:19+00:00

Gaussian / GaussView " Gaussian 16 is the latest in the Gaussian series of programs. It provides state-of-the-art capabilities for electronic structure modeling. Gaussian 16 is licensed for a wide variety of computer systems. All versions of Gaussian 16 contain every scientific/modeling feature, and none imposes any artificial limitations on calculations other than your computing resources and patience.

gcc

Anonymous (anonymous@undisclosed.example.com) — 2026-03-26T20:54:28+00:00

GCC GCC is a software module available on Comet. GCC overview To access GCC on Comet, run module load GCC. This will load the default version of GCC. An overview of the module information is shown below (module -r spider ^GCC$): If there are multiple versions of

generic_mapping_tools

Anonymous (anonymous@undisclosed.example.com) — 2026-04-09T11:29:16+00:00

GMT GMT is a software module available on Comet. GMT overview To access GMT on Comet, run module load GMT. This will load the default version of GMT. An overview of the module information is shown below (module -r spider ^GMT$): If there are multiple versions of

gmsh

Anonymous (anonymous@undisclosed.example.com) — 2026-04-09T11:30:12+00:00

gnuplot gnuplot is a software module available on Comet. gnuplot overview To access gnuplot on Comet, run module load gnuplot. This will load the default version of gnuplot. An overview of the module information is shown below (module -r spider ^gnuplot$

gnuplot

Anonymous (anonymous@undisclosed.example.com) — 2026-04-09T11:30:47+00:00

gprmax

Anonymous (anonymous@undisclosed.example.com) — 2026-04-09T11:31:34+00:00

gprMax-env gprMax-env is a software module available on Comet. gprMax-env overview To access gprMax-env on Comet, run module load gprMax-env. This will load the default version of gprMax-env. An overview of the module information is shown below (

gromacs

Anonymous (anonymous@undisclosed.example.com) — 2026-02-19T16:39:45+00:00

Gromacs " A free and open-source software suite for high-performance molecular dynamics and output analysis." * For more information: Running on Comet The standard version of Gromacs can run on any CPU node of Comet. Load the standard version of Gromacs as follows:

hail

Anonymous (anonymous@undisclosed.example.com) — 2026-04-09T11:32:37+00:00

hail-env hail-env is a software module available on Comet. hail-env overview To access hail-env on Comet, run module load hail-env. This will load the default version of hail-env. An overview of the module information is shown below (module -r spider ^hail-env$

hdf5

Anonymous (anonymous@undisclosed.example.com) — 2026-04-09T11:36:53+00:00

hdf5 hdf5 is a software module available on Comet. If you are intending to use HDF5 within R, be aware that due to practical limits of the size of the library path not all module library paths are added by default. If you are compiling R libraries which need HDF5, then you will need to extend your

htslib

Anonymous (anonymous@undisclosed.example.com) — 2026-04-09T11:38:24+00:00

HTSlib HTSlib is a software module available on Comet. HTSlib overview To access HTSlib on Comet, run module load HTSlib. This will load the default version of HTSlib. An overview of the module information is shown below (module -r spider ^HTSlib$

hybracter

Anonymous (anonymous@undisclosed.example.com) — 2026-04-09T11:40:11+00:00

hybracter-env hybracter-env is a software module available on Comet. hybracter-env overview To access hybracter-env on Comet, run module load hybracter-env. This will load the default version of hybracter-env. An overview of the module information is shown below (

hypre

Anonymous (anonymous@undisclosed.example.com) — 2026-02-20T10:14:30+00:00

Hypre " Hypre, a software library of high performance preconditioners and solvers for the solution of large, sparse linear systems of equations on massively parallel computers" * For more information: Running on Comet The Hypre library is added to the

intel

Anonymous (anonymous@undisclosed.example.com) — 2025-04-07T15:12:38+00:00

Intel Compiler Suite * Category: NOT INSTALLED * Access method: NOT INSTALLED The Intel Compiler Suite was a software module which was available on previous University HPC facilities (Rocket). It was loaded via the module load intel command and provided the following functions:

issm

Anonymous (anonymous@undisclosed.example.com) — 2026-03-24T20:20:30+00:00

Ice Sheet & Sea Level System Model " ISSM is open source and is funded by the NASA Cryosphere, IceBridge Research and MAP (Modeling Analysis and Prediction) programs, JPL R&TD (Research, Technology and Development) and the National Science Foundation.

jags

Anonymous (anonymous@undisclosed.example.com) — 2026-04-09T11:46:56+00:00

JAGS JAGS is a software module available on Comet. JAGS overview To access JAGS on Comet, run module load JAGS. This will load the default version of JAGS. An overview of the module information is shown below (module -r spider ^JAGS$): If there are multiple versions of

java

Anonymous (anonymous@undisclosed.example.com) — 2026-04-09T11:48:43+00:00

Java Java is a software module available on Comet. Java overview To access Java on Comet, run module load Java. This will load the default version of Java. An overview of the module information is shown below (module -r spider ^Java$): If there are multiple versions of

julia

Anonymous (anonymous@undisclosed.example.com) — 2026-04-09T11:49:36+00:00

Julia Julia is a software module available on Comet. Julia overview To access Julia on Comet, run module load Julia. This will load the default version of Julia. An overview of the module information is shown below (module -r spider ^Julia$):

jupyter

Anonymous (anonymous@undisclosed.example.com) — 2025-09-01T13:52:19+00:00

Jupyter Lab * Category: Vendor provision * Access method: Loaded from Linux module software * License: Open Source * Command Line: No * Desktop GUI: Yes (via Open OnDemand) Running Versions Loading N/A - command line use of Jupyter is not supported. Please use the published Jupyter application in the Open OnDemand dashboard.

lammps

Anonymous (anonymous@undisclosed.example.com) — 2026-04-09T11:50:20+00:00

lammps lammps is a software module available on Comet. lammps overview To access lammps on Comet, run module load lammps. This will load the default version of lammps. An overview of the module information is shown below (module -r spider ^lammps$

lapack

Anonymous (anonymous@undisclosed.example.com) — 2026-02-20T14:32:49+00:00

LAPACK " LAPACK is a library of Fortran subroutines for solving the most commonly occurring problems in numerical linear algebra." * See: It is important to note that the BLAS functions included in LAPACK (libblas.so and liblapack.so) are distinct

last

Anonymous (anonymous@undisclosed.example.com) — 2026-04-09T11:51:07+00:00

last last is a software module available on Comet. last overview To access last on Comet, run module load last. This will load the default version of last. An overview of the module information is shown below (module -r spider ^last$): If there are multiple versions of

ldsc

Anonymous (anonymous@undisclosed.example.com) — 2026-04-09T09:49:29+00:00

ldsc " ldsc is a command line tool for estimating heritability and genetic correlation from GWAS summary statistics. ldsc also computes LD Scores." The original version of ldsc was available from , this no longer works on any modern versions of Python.

macs2

Anonymous (anonymous@undisclosed.example.com) — 2026-04-09T11:54:59+00:00

MACS2-env MACS2-env is a software module available on Comet. MACS2-env overview To access MACS2-env on Comet, run module load MACS2-env. This will load the default version of MACS2-env. An overview of the module information is shown below (module -r spider ^MACS2-env$

matlab

Anonymous (anonymous@undisclosed.example.com) — 2026-05-06T12:00:30+00:00

Matlab * Category: Vendor provision * Access method: Loaded from Linux module software * License: University Campus license, centrally managed * Command Line: Yes * Desktop GUI: Yes (via Open OnDemand) Running Versions * Matlab 2026a * Matlab 2024a

matplotlib

Anonymous (anonymous@undisclosed.example.com) — 2026-04-09T11:55:41+00:00

matplotlib matplotlib is a software module available on Comet. matplotlib overview To access matplotlib on Comet, run module load matplotlib. This will load the default version of matplotlib. An overview of the module information is shown below (

megan

Anonymous (anonymous@undisclosed.example.com) — 2026-04-09T11:57:56+00:00

MEGAN MEGAN is a software module available on Comet. MEGAN overview To access MEGAN on Comet, run module load MEGAN. This will load the default version of MEGAN. An overview of the module information is shown below (module -r spider ^MEGAN$):

merlin

Anonymous (anonymous@undisclosed.example.com) — 2026-03-26T20:48:57+00:00

merlin merlin is a software module available on Comet. merlin overview To access merlin on Comet, run module load merlin. This will load the default version of merlin. An overview of the module information is shown below (module -r spider ^merlin$

mesa

Anonymous (anonymous@undisclosed.example.com) — 2025-09-01T14:23:11+00:00

MESA OpenGL * Category: Vendor provision * Access method: Loaded from Linux module software * License: Open Source * Command Line: No * Desktop GUI: Yes (via Open OnDemand) The MESA OpenGL module may be used on Open OnDemand desktop sessions to provide OpenGL functionality to Linux desktop applications. This allows applications to provide 3D rendering/display functionality even if you are not running on a GPU node.

metis

Anonymous (anonymous@undisclosed.example.com) — 2026-04-09T11:59:39+00:00

METIS METIS is a software module available on Comet. METIS overview To access METIS on Comet, run module load METIS. This will load the default version of METIS. An overview of the module information is shown below (module -r spider ^METIS$):

miniforge

Anonymous (anonymous@undisclosed.example.com) — 2026-02-19T16:31:09+00:00

Miniforge - Conda and Mamba The Miniforge tool provides access to versions of the conda and mamba utilities. These come pre-configured to use the open-source conda-forge community software channels. We reccomend the use of Miniforge in all cases where you need to create a conda or mamba environment.

mono

Anonymous (anonymous@undisclosed.example.com) — 2026-04-09T12:00:39+00:00

Mono Mono is a software module available on Comet. Mono overview To access Mono on Comet, run module load Mono. This will load the default version of Mono. An overview of the module information is shown below (module -r spider ^Mono$): If there are multiple versions of

multiqc

Anonymous (anonymous@undisclosed.example.com) — 2026-04-09T12:01:45+00:00

multiqc multiqc is a software module available on Comet. multiqc overview To access multiqc on Comet, run module load multiqc. This will load the default version of multiqc. An overview of the module information is shown below (module -r spider ^multiqc$

mumps

Anonymous (anonymous@undisclosed.example.com) — 2026-04-09T12:00:04+00:00

MUMPS MUMPS is a software module available on Comet. MUMPS overview To access MUMPS on Comet, run module load MUMPS. This will load the default version of MUMPS. An overview of the module information is shown below (module -r spider ^MUMPS$):

muspan

Anonymous (anonymous@undisclosed.example.com) — 2026-03-10T11:15:52+00:00

MuSpAn From : " MuSpAn is a multiscale spatial analysis toolbox for analysing complex imaging data. It uses cutting-edge mathematical and statistical approaches to data analysis to provide the most comprehensive spatial analysis available. MuSpAn is being continually expanded, with a team of quantitative researchers constantly developing new methodology to tackle problems in analysing spatial transcriptomics, multiplex immunohistochemistry, imaging mass cytometry a…

nbo

Anonymous (anonymous@undisclosed.example.com) — 2026-04-09T12:02:32+00:00

NBO NBO is a software module available on Comet. NBO overview To access NBO on Comet, run module load NBO. This will load the default version of NBO. An overview of the module information is shown below (module -r spider ^NBO$): If there are multiple versions of

ncurses

Anonymous (anonymous@undisclosed.example.com) — 2026-04-09T11:51:51+00:00

ncurses ncurses is a software module available on Comet. ncurses overview To access ncurses on Comet, run module load ncurses. This will load the default version of ncurses. An overview of the module information is shown below (module -r spider ^ncurses$

nektar

Anonymous (anonymous@undisclosed.example.com) — 2026-04-09T12:03:20+00:00

NEKTAR++ NEKTAR++ is a software module available on Comet. NEKTAR++ overview To access NEKTAR++ on Comet, run module load NEKTAR++. This will load the default version of NEKTAR++. An overview of the module information is shown below (module -r spider ^NEKTAR++$

netcdf-c

Anonymous (anonymous@undisclosed.example.com) — 2026-04-09T12:03:58+00:00

netcdf-c netcdf-c is a software module available on Comet. netcdf-c overview To access netcdf-c on Comet, run module load netcdf-c. This will load the default version of netcdf-c. An overview of the module information is shown below (module -r spider ^netcdf-c$

netcdf-fortran

Anonymous (anonymous@undisclosed.example.com) — 2026-04-09T12:04:25+00:00

netcdf-fortran netcdf-fortran is a software module available on Comet. netcdf-fortran overview To access netcdf-fortran on Comet, run module load netcdf-fortran. This will load the default version of netcdf-fortran. An overview of the module information is shown below (

numpy

Anonymous (anonymous@undisclosed.example.com) — 2026-04-09T10:26:39+00:00

numpy numpy is a software module available on Comet. numpy overview To access numpy on Comet, run module load numpy. This will load the default version of numpy. An overview of the module information is shown below (module -r spider ^numpy$):

nvhpc

Anonymous (anonymous@undisclosed.example.com) — 2025-12-15T09:17:45+00:00

Nvidia HPC SDK * Category: Vendor provision * Access method: Loaded from Linux module software * License: Nvidia license * Command Line: Yes * Desktop GUI: No The Nvidia HPC SDK provided specialist software, libraries and functions for HPC-related compute using the Nvidia GPU architecture. For official documentation see:

ogs

Anonymous (anonymous@undisclosed.example.com) — 2026-03-23T15:45:32+00:00

OpenGeoSys " OpenGeoSys (OGS) is a scientific open source project for the development of numerical methods for the simulation of thermo-hydro-mechanical-chemical (THMC) processes in porous and fractured media. Current version is OpenGeoSys-6 which is documented on this page. For information about OpenGeoSys-5, see its dedicated section. OGS has been successfully applied in the fields of regional, contaminant and coastal hydrology, fundamental and geothermal energy systems, geotechnical enginee…

ontguppy

Anonymous (anonymous@undisclosed.example.com) — 2026-03-26T20:48:05+00:00

ont-guppy ont-guppy is a software module available on Comet. ont-guppy overview To access ont-guppy on Comet, run module load ont-guppy. This will load the default version of ont-guppy. An overview of the module information is shown below (module -r spider ^ont-guppy$

openblas

Anonymous (anonymous@undisclosed.example.com) — 2026-04-09T11:00:07+00:00

OpenBLAS OpenBLAS is a software module available on Comet. Important! Note that libblas is also provided by LAPACK. You should choose the correct BLAS library based on the requirements of your other applications. OpenBLAS overview To access OpenBLAS on Comet, run

opencl

Anonymous (anonymous@undisclosed.example.com) — 2026-03-26T20:51:06+00:00

OpenCL OpenCL is a software module available on Comet. OpenCL overview To access OpenCL on Comet, run module load OpenCL. This will load the default version of OpenCL. An overview of the module information is shown below (module -r spider ^OpenCL$

openfoam

Anonymous (anonymous@undisclosed.example.com) — 2026-04-09T12:08:55+00:00

OpenFOAM OpenFOAM is a software module available on Comet. OpenFOAM overview To access OpenFOAM on Comet, run module load OpenFOAM. This will load the default version of OpenFOAM. An overview of the module information is shown below (module -r spider ^OpenFOAM$

openmp

Anonymous (anonymous@undisclosed.example.com) — 2026-04-09T12:15:11+00:00

OpenMP Unlike other software, OpenMP is not a module on Comet. Instead OpenMP is part of GCC. To use OpenMP functionality in your code and link in the GNU OpenMP runtime components, compile your code by adding the following flag to gcc: -fopenmp. The runtime OpenMP library (

openmpi

Anonymous (anonymous@undisclosed.example.com) — 2026-04-09T12:09:40+00:00

OpenMPI OpenMPI is a software module available on Comet. OpenMPI overview To access OpenMPI on Comet, run module load OpenMPI. This will load the default version of OpenMPI. An overview of the module information is shown below (module -r spider ^OpenMPI$

openms

Anonymous (anonymous@undisclosed.example.com) — 2026-03-26T20:52:07+00:00

openms openms is a software module available on Comet. openms overview To access openms on Comet, run module load openms. This will load the default version of openms. An overview of the module information is shown below (module -r spider ^openms$

openseespy

Anonymous (anonymous@undisclosed.example.com) — 2026-04-09T12:23:08+00:00

openseespy-env openseespy-env is a software module available on Comet. openseespy-env overview To access openseespy-env on Comet, run module load openseespy-env. This will load the default version of openseespy-env. An overview of the module information is shown below (

openssl

Anonymous (anonymous@undisclosed.example.com) — 2026-04-09T12:23:41+00:00

openssl openssl is a software module available on Comet. openssl overview To access openssl on Comet, run module load openssl. This will load the default version of openssl. An overview of the module information is shown below (module -r spider ^openssl$

orca

Anonymous (anonymous@undisclosed.example.com) — 2026-04-09T12:24:35+00:00

Orca Orca is a software module available on Comet. Orca overview To access Orca on Comet, run module load Orca. This will load the default version of Orca. An overview of the module information is shown below (module -r spider ^Orca$): If there are multiple versions of

parallel

Anonymous (anonymous@undisclosed.example.com) — 2026-04-09T12:25:41+00:00

parallel parallel is a software module available on Comet. parallel overview To access parallel on Comet, run module load parallel. This will load the default version of parallel. An overview of the module information is shown below (module -r spider ^parallel$

paraview

Anonymous (anonymous@undisclosed.example.com) — 2026-04-09T12:31:06+00:00

ParaView ParaView is a software module available on Comet. To run the interactive/desktop version of ParaView you should first start our X11 Desktop session via the Open OnDemand service. Do not run ParaView via SSH + X11 - this is unsupported and is not an acceptable use of the login servers

perl

Anonymous (anonymous@undisclosed.example.com) — 2026-04-09T12:33:04+00:00

Perl Perl is a software module available on Comet. Perl overview To access Perl on Comet, run module load Perl. This will load the default version of Perl. An overview of the module information is shown below (module -r spider ^Perl$): If there are multiple versions of

pgap

Anonymous (anonymous@undisclosed.example.com) — 2026-04-09T12:34:19+00:00

pgap " NCBI Prokaryotic Genome Annotation Pipeline The NCBI Prokaryotic Genome Annotation Pipeline is designed to annotate bacterial and archaeal genomes (chromosomes and plasmids). Genome annotation is a multi-level process that includes prediction of protein-coding genes, as well as other functional genome units such as structural RNAs, tRNAs, small RNAs and pseudogenes.

plink

Anonymous (anonymous@undisclosed.example.com) — 2026-04-09T12:37:44+00:00

PLINK PLINK is a software module available on Comet. PLINK overview To access PLINK on Comet, run module load PLINK. This will load the default version of PLINK. An overview of the module information is shown below (module -r spider ^PLINK$):

podman

Anonymous (anonymous@undisclosed.example.com) — 2025-08-07T19:43:19+00:00

Podman * Category: Vendor provision * Access method: Loaded from Linux module software * License: Open Source * Command Line: Yes * Desktop GUI: Yes (no specific support for GUI, but can be used at the desktop without issue) Podman is a container technology toolset, similar to Docker, Apptainer and Singularity. In most tasks Podman offers more features and options than Apptainer/Singularity, but is also more complex to set up and use. We therefore recommend Podman to more experience…

prsice

Anonymous (anonymous@undisclosed.example.com) — 2026-04-09T12:39:15+00:00

PRSice PRSice is a software module available on Comet. PRSice overview To access PRSice on Comet, run module load PRSice. This will load the default version of PRSice. An overview of the module information is shown below (module -r spider ^PRSice$

ptscotch

Anonymous (anonymous@undisclosed.example.com) — 2026-04-09T12:42:25+00:00

SCOTCH SCOTCH is a software module available on Comet. SCOTCH overview To access SCOTCH on Comet, run module load SCOTCH. This will load the default version of SCOTCH. An overview of the module information is shown below (module -r spider ^SCOTCH$

pysam

Anonymous (anonymous@undisclosed.example.com) — 2026-04-09T13:23:15+00:00

Pysam Pysam is a software module available on Comet. Pysam overview To access Pysam on Comet, run module load Pysam. This will load the default version of Pysam. An overview of the module information is shown below (module -r spider ^Pysam$):

python_jax

Anonymous (anonymous@undisclosed.example.com) — 2026-04-09T13:26:57+00:00

jax-env jax-env is a software module available on Comet. jax-env overview To access jax-env on Comet, run module load jax-env. This will load the default version of jax-env. An overview of the module information is shown below (module -r spider ^jax-env$

python_openturns

Anonymous (anonymous@undisclosed.example.com) — 2026-04-09T13:27:35+00:00

openturns-env openturns-env is a software module available on Comet. openturns-env overview To access openturns-env on Comet, run module load openturns-env. This will load the default version of openturns-env. An overview of the module information is shown below (

python_ray

Anonymous (anonymous@undisclosed.example.com) — 2026-04-09T13:28:21+00:00

ray-env ray-env is a software module available on Comet. ray-env overview To access ray-env on Comet, run module load ray-env. This will load the default version of ray-env. An overview of the module information is shown below (module -r spider ^ray-env$

python

Anonymous (anonymous@undisclosed.example.com) — 2026-04-09T13:25:28+00:00

Python Python is a software module available on Comet. Other Python Guides * Installing additional Python modules Python overview To access Python on Comet, run module load Python. This will load the default version of Python. An overview of the module information is shown below (

pytorch

Anonymous (anonymous@undisclosed.example.com) — 2026-01-07T13:24:17+00:00

PyTorch PyTorch is available on Comet as the module pytorch-env. This loads a version of Python and the PyTorch module: If you require a version of PyTorch to work with a different version of Python, read the following section to see how to install a custom version.

quantum_espresso

Anonymous (anonymous@undisclosed.example.com) — 2026-04-09T13:30:18+00:00

QuantumESPRESSO QuantumESPRESSO is a software module available on Comet. QuantumESPRESSO overview To access QuantumESPRESSO on Comet, run module load QuantumESPRESSO. This will load the default version of QuantumESPRESSO. An overview of the module information is shown below (

r_keras

Anonymous (anonymous@undisclosed.example.com) — 2026-04-09T13:32:15+00:00

R-keras R-keras is a software module available on Comet. R-keras overview To access R-keras on Comet, run module load R-keras. This will load the default version of R-keras. An overview of the module information is shown below (module -r spider ^R-keras$

r_stan

Anonymous (anonymous@undisclosed.example.com) — 2026-04-09T13:39:00+00:00

R-stan R-stan is a software module available on Comet. R-stan overview To access R-stan on Comet, run module load R-stan. This will load the default version of R-stan. An overview of the module information is shown below (module -r spider ^R-stan$

r

Anonymous (anonymous@undisclosed.example.com) — 2026-03-26T20:33:39+00:00

R R is a software module available on Comet. R overview To access R on Comet, run module load R. This will load the default version of R. An overview of the module information is shown below (module -r spider ^R$): If there are multiple versions of

regenie

Anonymous (anonymous@undisclosed.example.com) — 2026-04-09T13:36:13+00:00

regenie regenie is a software module available on Comet. regenie overview To access regenie on Comet, run module load regenie. This will load the default version of regenie. An overview of the module information is shown below (module -r spider ^regenie$

remora

Anonymous (anonymous@undisclosed.example.com) — 2026-04-09T13:36:54+00:00

remora-env remora-env is a software module available on Comet. remora-env overview To access remora-env on Comet, run module load remora-env. This will load the default version of remora-env. An overview of the module information is shown below (

rerio

Anonymous (anonymous@undisclosed.example.com) — 2026-04-09T13:37:40+00:00

rerio rerio is a software module available on Comet. rerio overview To access rerio on Comet, run module load rerio. This will load the default version of rerio. An overview of the module information is shown below (module -r spider ^rerio$):

saige

Anonymous (anonymous@undisclosed.example.com) — 2026-03-26T15:45:15+00:00

SAIGE " SAIGE is an R package developed with Rcpp for genome-wide association tests in large-scale data sets and biobanks. " * For more information: * Source code: ---------- Running SAIGE on Comet We have installed SAIGE on Comet using the images published on

salmon

Anonymous (anonymous@undisclosed.example.com) — 2026-04-09T13:39:42+00:00

Salmon Salmon is a software module available on Comet. Salmon overview To access Salmon on Comet, run module load Salmon. This will load the default version of Salmon. An overview of the module information is shown below (module -r spider ^Salmon$

smina

Anonymous (anonymous@undisclosed.example.com) — 2026-04-09T13:43:37+00:00

SMINA SMINA is a software module available on Comet. SMINA overview To access SMINA on Comet, run module load SMINA. This will load the default version of SMINA. An overview of the module information is shown below (module -r spider ^SMINA$):

snakemake

Anonymous (anonymous@undisclosed.example.com) — 2026-04-09T13:44:18+00:00

snakemake snakemake is a software module available on Comet. snakemake overview To access snakemake on Comet, run module load snakemake. This will load the default version of snakemake. An overview of the module information is shown below (module -r spider ^snakemake$

spades

Anonymous (anonymous@undisclosed.example.com) — 2026-04-09T13:45:11+00:00

SPAdes SPAdes is a software module available on Comet. SPAdes overview To access SPAdes on Comet, run module load SPAdes. This will load the default version of SPAdes. An overview of the module information is shown below (module -r spider ^SPAdes$

star

Anonymous (anonymous@undisclosed.example.com) — 2026-04-09T13:50:05+00:00

STAR STAR is a software module available on Comet. STAR overview To access STAR on Comet, run module load STAR. This will load the default version of STAR. An overview of the module information is shown below (module -r spider ^STAR$): If there are multiple versions of

starccm

Anonymous (anonymous@undisclosed.example.com) — 2026-04-09T13:53:00+00:00

STAR-CCM+ Important! Most users of STAR-CCM+ are using a version installed in their group project directory. This documentation is only relevant to users running STAR-CCM+ from the module. Consult your project colleagues to understand which version of STAR-CCM+ you are expected to use.

subread

Anonymous (anonymous@undisclosed.example.com) — 2026-04-09T13:53:51+00:00

Subread Subread is a software module available on Comet. Subread overview To access Subread on Comet, run module load Subread. This will load the default version of Subread. An overview of the module information is shown below (module -r spider ^Subread$

szip

Anonymous (anonymous@undisclosed.example.com) — 2026-04-09T13:54:23+00:00

Szip Szip is a software module available on Comet. Szip overview To access Szip on Comet, run module load Szip. This will load the default version of Szip. An overview of the module information is shown below (module -r spider ^Szip$): If there are multiple versions of

tabix

Anonymous (anonymous@undisclosed.example.com) — 2026-04-09T13:54:53+00:00

tabix tabix is a software module available on Comet. tabix overview To access tabix on Comet, run module load tabix. This will load the default version of tabix. An overview of the module information is shown below (module -r spider ^tabix$):

tensorflow

Anonymous (anonymous@undisclosed.example.com) — 2026-04-09T13:56:06+00:00

tensorflow-env tensorflow-env is a software module available on Comet. tensorflow-env overview To access tensorflow-env on Comet, run module load tensorflow-env. This will load the default version of tensorflow-env. An overview of the module information is shown below (

tinyxml

Anonymous (anonymous@undisclosed.example.com) — 2026-04-09T13:56:38+00:00

TinyXML TinyXML is a software module available on Comet. TinyXML overview To access TinyXML on Comet, run module load TinyXML. This will load the default version of TinyXML. An overview of the module information is shown below (module -r spider ^TinyXML$

triangle

Anonymous (anonymous@undisclosed.example.com) — 2026-04-09T13:57:13+00:00

Triangle Triangle is a software module available on Comet. Triangle overview To access Triangle on Comet, run module load Triangle. This will load the default version of Triangle. An overview of the module information is shown below (module -r spider ^Triangle$

trim_galor

Anonymous (anonymous@undisclosed.example.com) — 2026-04-09T13:58:13+00:00

Trim_Galore Trim_Galore is a software module available on Comet. Trim_Galore overview To access Trim_Galore on Comet, run module load Trim_Galore. This will load the default version of Trim_Galore. An overview of the module information is shown below (

unicycler

Anonymous (anonymous@undisclosed.example.com) — 2026-04-09T14:01:26+00:00

Unicycler Unicycler is a software module available on Comet. Unicycler overview To access Unicycler on Comet, run module load Unicycler. This will load the default version of Unicycler. An overview of the module information is shown below (module -r spider ^Unicycler$

vcftools

Anonymous (anonymous@undisclosed.example.com) — 2026-04-09T14:02:07+00:00

VCFtools VCFtools is a software module available on Comet. VCFtools overview To access VCFtools on Comet, run module load VCFtools. This will load the default version of VCFtools. An overview of the module information is shown below (module -r spider ^VCFtools$

vep

Anonymous (anonymous@undisclosed.example.com) — 2026-04-09T14:02:44+00:00

VEP VEP is a software module available on Comet. VEP overview To access VEP on Comet, run module load VEP. This will load the default version of VEP. An overview of the module information is shown below (module -r spider ^VEP$): If there are multiple versions of

virtualgl

Anonymous (anonymous@undisclosed.example.com) — 2025-09-22T14:53:44+00:00

VirtualGL / Nvidia OpenGL * Category: Vendor provision * Access method: Loaded from Linux module software * License: Open Source * Command Line: No * Desktop GUI: Yes (via Open OnDemand) The VirtualGL module may be used on Open OnDemand desktop sessions to provide hardware accelerated OpenGL functionality to Linux desktop applications. This allows applications to provide 3D rendering/display functionality when running on a GPU node.

vllm

Anonymous (anonymous@undisclosed.example.com) — 2026-04-20T08:06:45+00:00

vLLM " vLLM is a fast and easy-to-use library for LLM inference and serving. Originally developed in the Sky Computing Lab at UC Berkeley, vLLM has grown into one of the most active open-source AI projects built and maintained by a diverse community of many dozens of academic institutions and companies from over 2000 contributors.

vtk

Anonymous (anonymous@undisclosed.example.com) — 2026-04-09T14:05:36+00:00

VTK Important!! VTK is normally used by other applications within one of our X11 Linux Desktop sessions. Do not attempt to load/run VTK applications over SSH+X11 as this is unsupported and against the use policies of the login nodes. VTK is a software module available on

x11

Anonymous (anonymous@undisclosed.example.com) — 2026-04-27T14:24:12+00:00

Linux X11 Desktop * Category: Vendor provision * Access method: Accessed from Open OnDemand portal You don't need to manually load any modules to use the Linux desktop, instead this software is automatically loaded for you when you start an Open OnDemand desktop session.

xengsort

Anonymous (anonymous@undisclosed.example.com) — 2026-04-09T14:06:14+00:00

xengsort-env xengsort-env is a software module available on Comet. xengsort-env overview To access xengsort-env on Comet, run module load xengsort-env. This will load the default version of xengsort-env. An overview of the module information is shown below (

xmds

Anonymous (anonymous@undisclosed.example.com) — 2026-04-09T14:07:16+00:00

xmds xmds is a software module available on Comet. xmds overview To access xmds on Comet, run module load xmds. This will load the default version of xmds. An overview of the module information is shown below (module -r spider ^xmds$): If there are multiple versions of

zlib

Anonymous (anonymous@undisclosed.example.com) — 2026-03-26T20:41:33+00:00

zlib zlib is a software module available on Comet. zlib overview To access zlib on Comet, run module load zlib. This will load the default version of zlib. An overview of the module information is shown below (module -r spider ^zlib$): If there are multiple versions of