HPC Cluster Software Resources

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
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