Difference between revisions of "HPC Installed Software"

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[[Software Update Log]]: Last updated 07/02/2020
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[[Software Update Log]]: Last updated 11/02/2020
  
 
'''Notes''':  
 
'''Notes''':  
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||[[MUMmer]]|| mummer || 4.0.0 || A system for rapidly aligning large DNA sequences to one another
 
||[[MUMmer]]|| mummer || 4.0.0 || A system for rapidly aligning large DNA sequences to one another
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|-
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||[[OpenFOAM]]|| openfoam-org || 6 || Open-source Field Operation And Manipulation.
 
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||[[PSMC]]|| psmc || 1.0 || Implementation of the Pairwise Sequentially Markovian Coalescent (PSMC) model
 
||[[PSMC]]|| psmc || 1.0 || Implementation of the Pairwise Sequentially Markovian Coalescent (PSMC) model

Revision as of 19:02, 11 February 2020

Software Update Log: Last updated 11/02/2020

Notes:

  • When loading a module we recommend always defining the version you require, and not relying on what you think the default version might be. See below on how to discover available versions.
  • You MUST NOT run software on the login nodes:
    • Either, create an interactive session using salloc
    • Or submit a job via sbatch
  • Also remember to prefix your commands that call your application with srun, other requested/allocated resources will not be released.

Installed HPC Software

Application Software Module Name Latest Version Software Description
Ansys Fluent ansys/fluent Currently not available
BarraCUDA barracuda 0.7.0 A sequence mapping software that utilizes GPUs
CGAL cgal 4.6.3 Computational Geometry Algorithms Library
Comsol comsol 5.3 Multiphysics general-purpose simulation software
DENISE (Black-Edition) denise 1.3 2D time-domain isotropic (visco)elastic FD modeling and full waveform inversion (FWI) code for P/SV-waves
DENISE-SH denise-sh 1.0 2D time-domain isotropic (visco)elastic FD modeling and full waveform inversion (FWI) code for SH-waves
Ensembl-Vep ensembl-vep 98.3 VEP determines the effect of your variants (SNPs, insertions, deletions, CNVs or structural variants) on genes, transcripts, and protein sequence, as well as regulatory regions.
FWT2D fwt2d 4.8 2D Full-Waveform Topography
Gaussian and GaussView gaussian 16 Electronic structure modeling
GPU-Blast gpu-blast 1.0 GPU accelerated version of NCBI-BLAST
JDK jdk 11.0.5 Java Development Kit
Kraken kraken 2.0.8 Kraken taxonomic sequence classification system
LAMMPS lammps 20190808 Molecular Dynamics Simulator
MLST mlst 2.0.4 Multi-Locus Sequence Typing
ModelTest modeltest 0.1.6 ModelTest-NG is a tool for selecting the best-fit model of evolution for DNA and protein alignments
MUMmer mummer 4.0.0 A system for rapidly aligning large DNA sequences to one another
OpenFOAM openfoam-org 6 Open-source Field Operation And Manipulation.
PSMC psmc 1.0 Implementation of the Pairwise Sequentially Markovian Coalescent (PSMC) model
QIIME qiime2 2019.10 Quantitative Insights Into Microbial Ecology (canonically pronounced chime)
R r 3.6.1 The R Project for Statistical Computing
RAY ray 2.3.1 Parallel genome assemblies for parallel DNA sequencing
ROHan rohan 1.0.0 Joint inference of Runs of Homozygosity and rates of heterozygosity
SAVA sava 1.0 3D seismic finite-difference modelling
VASP 5.4.4 The Vienna Ab initio Simulation Package: atomic scale materials modelling from first principles.

Which Software Version

To find the available versions for any software please use: module spider module-name
For example:

[username@tlog2 ~]$ module spider gaussian
---------------------------------------------------------------------------------------------------------------------------------
  gaussian:
---------------------------------------------------------------------------------------------------------------------------------
     Versions:
        gaussian/16.AVX.b01
        gaussian/16.AVX2.b01
        gaussian/103

From the presented list, can can then find details on a specific version:

[username@tlog2 ~]$ module spider gaussian/16.AVX2.b01
---------------------------------------------------------------------------------------------------------------------------------
  gaussian: gaussian/16.AVX2.b01
---------------------------------------------------------------------------------------------------------------------------------
    Properties:
      Chemistry related software

    This module can be loaded directly: module load gaussian/16.AVX2.b01


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