HPC Cluster Software Resources: Difference between revisions
Jump to navigation
Jump to search
No edit summary |
No edit summary |
||
Line 67: | Line 67: | ||
| 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 | ||
|- | |- | ||
| Open OnDemand || http://ondemand.hpc.tcnj.edu || [http://docs.hpc.tcnj.edu/index.php/HPC_Cluster_Getting_Started#Open_OnDemand TCNJ ELSA HPC OnDemand] || NSF-funded open-source HPC portal based on OSC’s original OnDemand portal. The goal of Open OnDemand is to provide an easy way for system administrators to provide web access to their HPC resources | | Open OnDemand || http://ondemand.hpc.tcnj.edu || [http://docs.hpc.tcnj.edu/index.php/HPC_Cluster_Getting_Started#Open_OnDemand TCNJ ELSA HPC Open OnDemand] || NSF-funded open-source HPC portal based on OSC’s original OnDemand portal. The goal of Open OnDemand is to provide an easy way for system administrators to provide web access to their HPC resources | ||
|- | |- | ||
| 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) | | 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) |
Revision as of 19:48, 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 |
GaussView | - | http://gaussian.com/wp-content/uploads/dl/gv6.pdf | Graphical interface used with Gaussian which aids in the creation of Gaussian input files, enables the user to run Gaussian calculations from a graphical interface without the need for using a command line instruction, and helps in the interpretation of Gaussian output. GUI accessed via Open OnDemand (under Interactive Apps) |
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 |
Jupyter Notebook | - | https://jupyter-notebook.readthedocs.io/en/stable/notebook.html | Open-source web application that allows you to create and share documents that contain live code, equations, visualizations and narrative text. Web interface accessed via Open OnDemand (under Interactive Apps) |
LAMMPS | module add lammps |
https://lammps.sandia.gov/doc/Manual.html | Molecular dynamics simulator |
Mathematica | module add mathematica |
https://reference.wolfram.com/language/?source=nav | Single integrated, continually expanding system that covers the breadth and depth of technical computing. GUI accessed via Open OnDemand (under Interactive Apps) |
Matlab | module add matlab |
https://www.mathworks.com/help/ | Desktop environment tuned for iterative analysis and design processes with a programming language that expresses matrix and array. GUI accessed via Open OnDemand (under Interactive Apps) mathematics directly |
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 |
Open OnDemand | http://ondemand.hpc.tcnj.edu | TCNJ ELSA HPC Open OnDemand | NSF-funded open-source HPC portal based on OSC’s original OnDemand portal. The goal of Open OnDemand is to provide an easy way for system administrators to provide web access to their HPC resources |
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 | - | https://resources.rstudio.com/ | Integrated development environment (IDE) for R. Web front-end accessed via Open OnDemand (under Interactive Apps) |
SageMath | module add sagemath |
http://doc.sagemath.org/ | Free open-source mathematics software system. Web version accessed via Jupyter Notebook in Open OnDemand (under Interactive Apps) |
SAS | module add sas |
SAS docs | Open analytics platform accessible from the interface or coding language of your choice |
SOAPDenovo2 | module add soapdenovo2 |
https://github.com/aquaskyline/SOAPdenovo2#how-to-use-it | Novel short-read assembly method that can build a de novo draft assembly for the human-sized genomes. The program is specially designed to assemble Illumina GA short reads. It creates new opportunities for building reference sequences and carrying out accurate analyses of unexplored genomes in a cost effective way |
Sondovac | module add sondovac |
https://github.com/V-Z/sondovac/wiki/Documentation | Script to create orthologous low-copy nuclear probes from
transcriptome and genome skim data for target enrichment |
SOP-GPU | module add sop-gpu |
https://sop-gpu.readthedocs.io/en/latest/ | Self Orginized Polymer Model fully implemented on a GPU. A scientific software package designed to perform Langevin Dynamics Simulations of the mechanical or thermal unfolding, and mechanical pulling/indentation of large biomolecular systems in the experimental subsecond (millisecond-to-second) timescale |
SPAdes | module add spades |
https://github.com/ablab/spades | St. Petersburg genome assembler – is an assembly toolkit containing various assembly pipelines |
Swift | module add swift |
http://swift-lang.org/docs/index.php | Simple tool for fast, easy scripting on big machines |
Transcriptomics | module add transcriptomics |
Example | Example |
Trimmomatic | module add trimmomatic |
http://www.usadellab.org/cms/index.php?page=trimmomatic http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/TrimmomaticManual_V0.32.pdf |
Flexible read trimming tool for Illumina NGS data |
Trinity | module add trinity |
https://github.com/trinityrnaseq/trinityrnaseq/wiki/Running-Trinity | Assembles transcript sequences from Illumina RNA-Seq data |
VisIt | module add visit |
https://wci.llnl.gov/simulation/computer-codes/visit/manuals | Open Source, interactive, scalable, visualization, animation and analysis tool |
VMD | module add vmd |
https://www.ks.uiuc.edu/Research/vmd/current/docs.html | Molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting |