HPC Cluster Software Resources: Difference between revisions

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| Amber16<br>Amber18 || <code>module add amber/16</code><br><code>module add amber/18</code> || http://ambermd.org/Manuals.php || Amber is a suite of biomolecular simulation programs
| Amber16<br>Amber18 || <code>module add amber/16</code><br><code>module add amber/18</code> || http://ambermd.org/Manuals.php || Amber is a suite of biomolecular simulation programs
|-
|-
| Athena || <code>module add athena/4.2</code> || https://princetonuniversity.github.io/Athena-Cversion/ || Athena is a grid-based code for astrophysical magnetohydrodynamics (MHD)
| Athena || <code>module add athena</code> || https://princetonuniversity.github.io/Athena-Cversion/ || Athena is a grid-based code for astrophysical magnetohydrodynamics (MHD)
|-
|-
| Athena++ || <code>module add athena++/1.0</code> || https://princetonuniversity.github.io/athena/ || Athena++ is a complete re-write of the Athena astrophysical magnetohydrodynamics (MHD) code in C++
| Athena++ || <code>module add athena++</code> || https://princetonuniversity.github.io/athena/ || Athena++ is a complete re-write of the Athena astrophysical magnetohydrodynamics (MHD) code in C++
|-
|-
| Blast+ || <code>module add blast+/2.7.1</code> || https://www.ncbi.nlm.nih.gov/books/NBK279690/ || Basic Local Alignment Search Tool
| Blast+ || <code>module add blast+</code> || https://www.ncbi.nlm.nih.gov/books/NBK279690/ || Basic Local Alignment Search Tool
|-
|-
| Cassandra || <code>module add cassandra/1.2</code> || https://cassandra.nd.edu/index.php/documentation || Cassandra is an open source Monte Carlo package
| Cassandra || <code>module add cassandra</code> || https://cassandra.nd.edu/index.php/documentation || Cassandra is an open source Monte Carlo package
|-
|-
| cuda/8.0<br>cuda/9.2<br>cuda/10.0 || <code>module add cuda/8.0</code><br><code>module add cuda/9.2</code><br><code>module add cuda/10.0</code> || https://docs.nvidia.com/cuda/ || Default is CUDA 9.2 if using <code>module add cuda</code>
| cuda/8.0<br>cuda/9.2<br>cuda/10.0 || <code>module add cuda/8.0</code><br><code>module add cuda/9.2</code><br><code>module add cuda/10.0</code> || https://docs.nvidia.com/cuda/ || Default is CUDA 9.2 if using <code>module add cuda</code>
|-
|-
| cuDNN || <code>module add cudnn/5.05</code><br><code>module add cudnn/5.1.10</code><br><code>module add cudnn/6.0.21</code> || https://docs.nvidia.com/deeplearning/sdk/cudnn-developer-guide/index.html || -
| cuDNN || <code>module add cudnn</code> || https://docs.nvidia.com/deeplearning/sdk/cudnn-developer-guide/index.html || -
|-
|-
| ELSA Tutorial || <code>module add elsa-tutorial/1.0</code> || TBA || Used with ELSA SLURM tutorial
| ELSA Tutorial || <code>module add elsa-tutorial</code> || TBA || Used with ELSA SLURM tutorial
|-
|-
| ESPResSo || <code>module add espresso/3.3.1</code> || http://espressomd.org/wordpress/documentation/ || Extensible Simulation Package for Research on Soft Matter
| ESPResSo || <code>module add espresso</code> || http://espressomd.org/wordpress/documentation/ || Extensible Simulation Package for Research on Soft Matter
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|-
| FASTX-Toolkit || <code>module add fastx/0.0.14</code> || http://hannonlab.cshl.edu/fastx_toolkit/commandline.html || FASTQ/A short-reads pre-processing tools
| FASTX-Toolkit || <code>module add fastx</code> || http://hannonlab.cshl.edu/fastx_toolkit/commandline.html || FASTQ/A short-reads pre-processing tools
|-
|-
| FFmpeg || <code>module add ffmpeg/2.8</code> || https://ffmpeg.org/ffmpeg.html || ffmpeg is a very fast video and audio converter
| FFmpeg || <code>module add ffmpeg</code> || https://ffmpeg.org/ffmpeg.html || ffmpeg is a very fast video and audio converter
|-
|-
| Garli || <code>module add garli/2.01</code> || Website no longer accessible || Genetic Algorithm for Rapid Likelihood Inference
| Garli || <code>module add garli</code> || Website no longer accessible || Genetic Algorithm for Rapid Likelihood Inference
|-
|-
| Gaussian || <code>module add gaussian/16</code> || http://gaussian.com/man/ || Electronic structure modeling
| Gaussian || <code>module add gaussian</code> || http://gaussian.com/man/ || Electronic structure modeling
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|-
| GNUplot || <code>module add gnuplot/5.0.6</code> || http://www.gnuplot.info/documentation.html || Portable command-line driven graphing utility
| GNUplot || <code>module add gnuplot</code> || http://www.gnuplot.info/documentation.html || Portable command-line driven graphing utility
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|-
| Go || <code>module add go/1.11</code> || https://golang.org/doc/ || Go programming language
| Go || <code>module add go</code> || https://golang.org/doc/ || Go programming language
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|-
| Gromacs || <code>module add gromacs/2018.3</code><br><code>module add gromacs+plumed/2018.4</code> || http://manual.gromacs.org/documentation/<br>https://www.plumed.org/doc-master/user-doc/html/index.html || Versatile package to perform molecular dynamics
| Gromacs || <code>module add gromacs</code><br><code>module add gromacs+plumed</code> || http://manual.gromacs.org/documentation/<br>https://www.plumed.org/doc-master/user-doc/html/index.html || Versatile package to perform molecular dynamics
|-
|-
| Hoomd-Blue || <code>module add hoomd-blue/2.1.6</code> || https://hoomd-blue.readthedocs.io/en/stable/ || General purpose particle simulation toolkit
| Hoomd-Blue || <code>module add hoomd-blue</code> || https://hoomd-blue.readthedocs.io/en/stable/ || General purpose particle simulation toolkit
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|-
| JDK || <code>module add jdk/1.8</code> || - || Java. Note: OpenJDK is recommended over this version (Oracle Java) due to licensing issues
| JDK || <code>module add jdk</code> || - || Java. Note: OpenJDK is recommended over this version (Oracle Java) due to licensing issues
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|-
| Jellyfish || <code>module add </code> || Example || Example
| Jellyfish || <code>module add jellyfish</code> || Example || Example
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|-
| Julia || <code>module add </code> || Example || Example
| Julia || <code>module add julia</code> || Example || Example
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|-
| LAMMPS || <code>module add </code> || Example || Example
| LAMMPS || <code>module add lammps</code> || Example || Example
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|-
| Mathematica || <code>module add </code> || Example || Example
| Mathematica || <code>module add mathematica</code> || Example || Example
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|-
| Matlab || <code>module add </code> || Example || Example
| Matlab || <code>module add matlab</code> || Example || Example
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| MOPAC || <code>module add </code> || Example || Example
| MOPAC || <code>module add mopac</code> || Example || Example
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| MPMC || <code>module add </code> || Example || Example
| MPMC || <code>module add mpmc</code> || Example || Example
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| MrBayes || <code>module add </code> || Example || Example
| MrBayes || <code>module add mrbayes</code> || Example || Example
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| NetPBM || <code>module add </code> || Example || Example
| NetPBM || <code>module add netpbm</code> || Example || Example
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| NWChem || Example || Example || Example
| NWChem || <code>module add nwchem</code><br><code>module add nwchem-cuda</code> || Example || Example
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|-
| Omnia || Example || Example || Example
| Omnia || <code>module add omnia</code> || Example || Example
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| ParaView || Example || Example || Example
| ParaView || <code>module add paraview</code> || Example || Example
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| pNetCDF || Example || Example || Example
| pNetCDF || <code>module add pnetcdf</code> || Example || Example
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| PrinSEQ || Example || Example || Example
| PrinSEQ || <code>module add prinseq</code> || Example || Example
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| Python || Example || Example || Example
| Python || <code>module add python</code> || Example || Example
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| R || Example || Example || Example
| R || <code>module add R</code> || Example || Example
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| RStudio || Example || Example || Example
| RStudio || <code>module add rstudio_singularity</code> || Example || Example
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| SageMath || Example || Example || Example
| SageMath || <code>module add sagemath</code> || Example || Example
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| SAS || Example || Example || Example
| SAS || <code>module add sas</code> || Example || Example
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| SOAPDenovo2 || Example || Example || Example
| SOAPDenovo2 || <code>module add soapdenovo2</code> || Example || Example
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| Sondovac || Example || Example || Example
| Sondovac || <code>module add sondovac</code> || Example || Example
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| SOP || Example || Example || Example
| SOP || <code>module add sop-gpu</code> || Example || Example
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| Spades || Example || Example || Example
| Spades || <code>module add spades</code> || Example || Example
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| Swift || Example || Example || Example
| Swift || <code>module add swift</code> || Example || Example
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| Transcriptomics || Example || Example || Example
| Transcriptomics || <code>module add transcriptomics</code> || Example || Example
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| Trimmomatic || Example || Example || Example
| Trimmomatic || <code>module add trimmomatic</code> || Example || Example
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| Trinity || Example || Example || Example
| Trinity || <code>module add trinity</code> || Example || Example
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| VisIt || Example || Example || Example
| VisIt || <code>module add visit</code> || Example || Example
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| VMD || Example || Example || Example
| VMD || <code>module add vmd</code> || Example || Example
|}
|}

Revision as of 16:13, 21 May 2019

This page currently contains no content. (code411)

Application Name Module Command Application Website/Docs Notes
Amber16
Amber18		 module add amber/16
module add amber/18		 http://ambermd.org/Manuals.php Amber is a suite of biomolecular simulation programs
Athena module add athena https://princetonuniversity.github.io/Athena-Cversion/ Athena is a grid-based code for astrophysical magnetohydrodynamics (MHD)
Athena++ module add athena++ https://princetonuniversity.github.io/athena/ Athena++ is a complete re-write of the Athena astrophysical magnetohydrodynamics (MHD) code in C++
Blast+ module add blast+ https://www.ncbi.nlm.nih.gov/books/NBK279690/ Basic Local Alignment Search Tool
Cassandra module add cassandra https://cassandra.nd.edu/index.php/documentation Cassandra is an open source Monte Carlo package
cuda/8.0
cuda/9.2
cuda/10.0		 module add cuda/8.0
module add cuda/9.2
module add cuda/10.0		 https://docs.nvidia.com/cuda/ Default is CUDA 9.2 if using module add cuda
cuDNN module add cudnn https://docs.nvidia.com/deeplearning/sdk/cudnn-developer-guide/index.html -
ELSA Tutorial module add elsa-tutorial TBA Used with ELSA SLURM tutorial
ESPResSo module add espresso http://espressomd.org/wordpress/documentation/ Extensible Simulation Package for Research on Soft Matter
FASTX-Toolkit module add fastx http://hannonlab.cshl.edu/fastx_toolkit/commandline.html FASTQ/A short-reads pre-processing tools
FFmpeg module add ffmpeg https://ffmpeg.org/ffmpeg.html ffmpeg is a very fast video and audio converter
Garli module add garli Website no longer accessible Genetic Algorithm for Rapid Likelihood Inference
Gaussian module add gaussian http://gaussian.com/man/ Electronic structure modeling
GNUplot module add gnuplot http://www.gnuplot.info/documentation.html Portable command-line driven graphing utility
Go module add go https://golang.org/doc/ Go programming language
Gromacs module add gromacs
module add gromacs+plumed		 http://manual.gromacs.org/documentation/
https://www.plumed.org/doc-master/user-doc/html/index.html		 Versatile package to perform molecular dynamics
Hoomd-Blue module add hoomd-blue https://hoomd-blue.readthedocs.io/en/stable/ General purpose particle simulation toolkit
JDK module add jdk - Java. Note: OpenJDK is recommended over this version (Oracle Java) due to licensing issues
Jellyfish module add jellyfish Example Example
Julia module add julia Example Example
LAMMPS module add lammps Example Example
Mathematica module add mathematica Example Example
Matlab module add matlab Example Example
MOPAC module add mopac Example Example
MPMC module add mpmc Example Example
MrBayes module add mrbayes Example Example
NetPBM module add netpbm Example Example
NWChem module add nwchem
module add nwchem-cuda		 Example Example
Omnia module add omnia Example Example
ParaView module add paraview Example Example
pNetCDF module add pnetcdf Example Example
PrinSEQ module add prinseq Example Example
Python module add python Example Example
R module add R Example Example
RStudio module add rstudio_singularity Example Example
SageMath module add sagemath Example Example
SAS module add sas Example Example
SOAPDenovo2 module add soapdenovo2 Example Example
Sondovac module add sondovac Example Example
SOP module add sop-gpu Example Example
Spades module add spades Example Example
Swift module add swift Example Example
Transcriptomics module add transcriptomics Example Example
Trimmomatic module add trimmomatic Example Example
Trinity module add trinity Example Example
VisIt module add visit Example Example
VMD module add vmd Example Example
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