HPC Cluster Software Resources

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The ELSA HPC cluster utilizes the Lmod environment module system. Lmod allows you to load and unload various environments to support multiple applications. It also allows you to select among different versions of an application depending on your requirements, e.g. load a Python 2.7.12 environment for application "A" and then load a Python 3.6.0 environment for application "B."

When working interactively at the Linux command-line (e.g. on a login node or dev node), you can run the module add module_name at the shell prompt to load a particular environment. You should also include the appropriate module add module_name command(s) in your SLURM submission script. Use the module avail command at the Linux shell prompt to list all available modules. If you do not specify the version number when adding a module, it will usually load the newest version unless otherwise noted, e.g. module add python is equivalent to module add python/3.6.0.

For more information on working with Lmod modules on the ELSA cluster see the dedicated ELSA Lmod tutorial page.

Application Name Module Command Application Website/Docs Notes
ABySS module add abyss https://docs.anaconda.com/anaconda/ ABySS is a de novo sequence assembler intended for short paired-end reads and large genomes
Amber module add amber http://ambermd.org/Manuals.php Amber is a suite of biomolecular simulation programs
anaconda module add anaconda3 https://docs.anaconda.com/anaconda/ Anaconda is a package manager, an environment manager, a Python/R data science distribution, and a collection of over 7,500+ open-source packages
ASTRAL module add astral https://github.com/smirarab/ASTRAL/blob/master/astral-tutorial.md ASTRAL is a java program for estimating a species tree given a set of unrooted gene trees
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 -
ddcMD module add ddcmd https://github.com/LLNL/ddcMD A fully GPU-accelerated molecular dynamics program for the Martini force field
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 https://molevol.mbl.edu/index.php/Garli_FAQ 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)
GMT module add gmt https://www.generic-mapping-tools.org/ GMT is an open-source collection of command-line tools for manipulating geographic and Cartesian data sets (including filtering, trend fitting, gridding, projecting, etc.) and producing high-quality illustrations ranging from simple x–y plots via contour maps to artificially illuminated surfaces and 3D perspective views
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
ISLE - http://stat.cmu.edu/isle/ A browser-based interactive statistics & data analysis platform. http://isle.hpc.tcnj.edu/
JDK module add jdk - Java. Note: OpenJDK is recommended over this version (Oracle Java) due to licensing issues.
JDK/OpenJDK module add jdk/13 https://openjdk.java.net/ OpenJDK. This overrides the built-in, older version provided with the OS.
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
mafft module add mathematica https://mafft.cbrc.jp/alignment/software/ MAFFT is a program used to create multiple sequence alignments of amino acid or nucleotide sequences
Mathematica module add mafft 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
MPSolve module add mpsolve https://numpi.dm.unipi.it/software/mpsolve MPSolve stands for Multiprecision Polynomial SOLVEr. It is a software that aims to provide an easy to use (hopefully) universal blackbox for solving polynomials and secular equations.
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
MUSCLE module add muscle https://www.drive5.com/muscle/manual/ MUSCLE is one of the best-performing multiple alignment programs according to published benchmark tests, with accuracy and speed that are consistently better than CLUSTALW
NAMD module add namd https://www.ks.uiuc.edu/Research/namd/ NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems
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 Getting started with 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
RAxML module add raxml https://cme.h-its.org/exelixis/web/software/raxml/index.html RAxML (Randomized Axelerated Maximum Likelihood) is a program for sequential and parallelMaximum Likelihood based inference of large phylogenetic trees
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
Torchvision module add python-vision https://github.com/pytorch/vision The Torchvision package consists of popular datasets, model architectures, and common image transformations for computer vision
Transcriptomics module add transcriptomics bowtie2 - http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml
fastqc - https://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/
hisat - http://www.ccb.jhu.edu/software/hisat/manual.shtml
hisat2 - https://ccb.jhu.edu/software/hisat2/manual.shtml
samtools/bcftools - http://www.htslib.org/doc/
STAR - https://github.com/alexdobin/STAR/tree/master/doc
stringtie - https://ccb.jhu.edu/software/stringtie/index.shtml?t=manual
tophat - https://ccb.jhu.edu/software/tophat/manual.shtml
Various tools to support transcriptomics
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. Includes POV-Ray