HPC Cluster Software Resources: Difference between revisions
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| Omnia || <code>module add omnia</code> || https://github.com/omnia-md/omnia-md || High performance, high usability toolkits for predictive biomolecular simulation | | Omnia || <code>module add omnia</code> || https://github.com/omnia-md/omnia-md || High performance, high usability toolkits for predictive biomolecular simulation | ||
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| ParaView || <code>module add paraview</code> || https://www.paraview.org/documentation/ || Open-source, multi-platform data analysis and visualization application. | | ParaView || <code>module add paraview</code> || https://www.paraview.org/documentation/ || Open-source, multi-platform data analysis and visualization application. GUI accessed via [http://ondemand.hpc.tcnj.edu/ Open OnDemand] (under Interactive Apps) | ||
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| pNetCDF || <code>module add pnetcdf</code> || https://parallel-netcdf.github.io/wiki/Documentation.html || High-performance parallel I/O library for accessing the classic | | pNetCDF || <code>module add pnetcdf</code> || https://parallel-netcdf.github.io/wiki/Documentation.html || High-performance parallel I/O library for accessing the classic | ||
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| R || <code>module add R</code> || https://cran.r-project.org/manuals.html || Free software environment for statistical computing and graphics | | R || <code>module add R</code> || https://cran.r-project.org/manuals.html || Free software environment for statistical computing and graphics | ||
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| RStudio Server || <code>module add rstudio_singularity</code> || https://resources.rstudio.com/ || Integrated development environment (IDE) for R. | | RStudio Server || <code>module add rstudio_singularity</code> || https://resources.rstudio.com/ || Integrated development environment (IDE) for R. Web front-end accessed via [http://ondemand.hpc.tcnj.edu/ Open OnDemand] (under Interactive Apps) | ||
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| SageMath || <code>module add sagemath</code> || Example || Example | | SageMath || <code>module add sagemath</code> || Example || Example |
Revision as of 18:38, 21 May 2019
Application Name | Module Command | Application Website/Docs | Notes |
---|---|---|---|
Amber | module add amber |
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 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. OpenJDK is installed in the OS by default so no module is needed. |
Jellyfish | module add jellyfish |
http://www.genome.umd.edu/docs/JellyfishUserGuide.pdf | Fast, parallel k-mer counting for DNA |
Julia | module add julia |
https://docs.julialang.org/en/v1/ | Julia programming language |
LAMMPS | module add lammps |
https://lammps.sandia.gov/doc/Manual.html | Molecular dynamics simulator |
Mathematica | module add mathematica |
Example | Example |
Matlab | module add matlab |
Example | Example |
MOPAC | module add mopac |
http://openmopac.net/manual/ | General-purpose semiempirical molecular orbital package. Primarily used from within the WebMO (http://webmo.hpc.tcnj.edu) system |
MPMC | module add mpmc |
https://github.com/mpmccode/mpmc/wiki | Massively parallel monte carlo |
MrBayes | module add mrbayes |
http://nbisweden.github.io/MrBayes/manual.html | Program for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models |
NetPBM | module add netpbm |
http://netpbm.sourceforge.net/doc/ | Toolkit for manipulation of graphic images, including conversion of images between a variety of different formats |
NWChem | CPU - module add nwchem GPU - module add nwchem-cuda |
https://github.com/nwchemgit/nwchem/wiki | Open source high-performance computational chemistry |
Omnia | module add omnia |
https://github.com/omnia-md/omnia-md | High performance, high usability toolkits for predictive biomolecular simulation |
ParaView | module add paraview |
https://www.paraview.org/documentation/ | Open-source, multi-platform data analysis and visualization application. GUI accessed via Open OnDemand (under Interactive Apps) |
pNetCDF | module add pnetcdf |
https://parallel-netcdf.github.io/wiki/Documentation.html | High-performance parallel I/O library for accessing the classic
Unidata's NetCDF files, specifically the CDF 1, 2, and 5 formats |
PRINSEQ | module add prinseq |
http://prinseq.sourceforge.net/manual.html | Filter, reformat, or trim your genomic and metagenomic sequence data |
Python | module add python |
https://www.python.org/doc/ | Programming language that lets you work more quickly and integrate your systems more effectively |
R | module add R |
https://cran.r-project.org/manuals.html | Free software environment for statistical computing and graphics |
RStudio Server | module add rstudio_singularity |
https://resources.rstudio.com/ | Integrated development environment (IDE) for R. Web front-end accessed via Open OnDemand (under Interactive Apps) |
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 |