====== Software List ====== 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**. ===== 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 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 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 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 from [[https://www.eessi.io/|EESSI]] | EESSI | Remotely installed | GCC, Matlab or Conda | Software is packaged and basic operation is tested by partners in the [[https://www.eessi.io/|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 [[https://nuservice.ncl.ac.uk|IT Service ticket system]], but may not be able to assist with every possible application. | * https://www.eessi.io - European Environment for Scientific Software Installations ===== Software Table ===== This software table describes the packages which are (or are intended to be) available on **Comet**. ^ Title ^ Category ^ License ^ Interface ^ Help ^ | AMD Optimizing Compiler | vendor | | Command Line | | | AMD Optimizing Compiler Libraries | vendor | | Command Line | | | cmake | vendor | | Command Line | | | Docker | vendor | | Command Line | | | 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]] | | Gromacs | vendor | | Command Line | | | libncurses | vendor | | Command Line | | | numpy | vendor | | Command Line | | | Nvidia CUDA SDK | vendor | | Command Line | | | Nvidia HPC SDK | vendor | | Command Line | | | OpenBLAS | vendor | | Command Line | | | OpenMP | vendor | | Command Line | | | OpenMPI | vendor | | Command Line | | | OpenSSL | vendor | | Command Line | | | Podman | vendor | | Command Line | | | Python | vendor | | Command Line | | | PyTorch | vendor | | Command Line | | | R | vendor | | Command Line | | | Singularity | vendor | | Command Line | | | Tensorflow | vendor | | Command Line | | | zlib | vendor | | Command Line | | | OpenCL | vendor | | Command Line | | | OpenGL (MESA) | vendor | | Desktop GUI | | | OpenGL (Nvidia) | vendor | | Desktop GUI | | | VirtualGL | vendor | | Desktop GUI | | | Ansys | vendor | Commercial | Command Line | [[:advanced:software:ansys|ANSYS]] | | Matlab | vendor | Commercial | Command Line | | | Jupyter Lab | vendor | | Desktop GUI | | | Linux X11 desktop | vendor | | Desktop GUI | | | R Studio | vendor | | Desktop GUI | | | Matlab | vendor | Commercial | Desktop GUI | | | Intel Compiler Suite | //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]] | | Intel Math Kernel Libraries | //not installed// | Commercial | Command Line | [[:advanced:software:intel|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 | | | 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 | | | Mamba | vendor | | Command Line | | | 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 | | | COMSOL Multiphysics | vendor | | Command Line | | | 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 | [[:advanced:software:ansys|ANSYS]] | | COMSOL Multiphysics | vendor | | Desktop GUI | | | StarCCM+ | vendor | | Desktop GUI | | | OpenMS | vendor | | Command Line | | ---- [[:advanced:software|Back to Advanced Software Topics]]