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.
Note: This software listing may be incomplete or contain software that is no longer available. It will be updated in the future.
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 |
Alphafold2 | module |
TBD | TBD |
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++ |
Autodock Vina | module |
TBD | TBD |
Blast+ | module add blast+ |
https://www.ncbi.nlm.nih.gov/books/NBK279690/ | Basic Local Alignment Search Tool |
Blender | module |
TBD | TBD |
Cassandra | module add cassandra |
https://cassandra.nd.edu/index.php/documentation | Cassandra is an open source Monte Carlo package |
ChimeraX | module |
TBD | TBD |
CIAO | module |
TBD | TBD |
CUDA | module add cuda module add cuda/8.0 module add cuda/10.1 module add cuda/10.2 module add cuda/11.4 module add cuda/11.7 module add cuda/11.8 |
https://docs.nvidia.com/cuda/ | Default is CUDA 11.4 if using module add cuda CUDA 11.8 contains TensorRT 8.6.1.6 and cuDNN 8.9.5.29 |
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 |
FastQC | module add fastqc |
TBD | TBD |
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) |
GipsyX | module |
TBD | TBD |
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 mafft |
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 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 |
MGLtools | module |
TBD | TBD |
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 |
MSconvert | module |
TBD | TBD |
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 |
OpenMM | module |
TBD | TBD |
OpenMS | module |
TBD | TBD |
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) |
Partitionfinder | module |
TBD | TBD |
PAUP | module |
TBD | TBD |
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 |
Pride PPP-AR | module |
TBD | TBD |
PRINSEQ | module add prinseq |
http://prinseq.sourceforge.net/manual.html | Filter, reformat, or trim your genomic and metagenomic sequence data |
PWiz | module |
TBD | TBD |
Pylith | module |
TBD | TBD |
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 |