HPC Cluster Software Resources

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Application Name	Module Command	Application Website/Docs	Notes
Amber16 Amber18	module add amber/16 module add amber/18	http://ambermd.org/Manuals.php	Amber is a suite of biomolecular simulation programs
Athena	module add athena/4.2	https://princetonuniversity.github.io/Athena-Cversion/	Athena is a grid-based code for astrophysical magnetohydrodynamics (MHD)
Athena++	module add athena++/1.0	https://princetonuniversity.github.io/athena/	Athena++ is a complete re-write of the Athena astrophysical magnetohydrodynamics (MHD) code in C++
Blast+	module add blast+/2.7.1	https://www.ncbi.nlm.nih.gov/books/NBK279690/	Basic Local Alignment Search Tool
Cassandra	module add cassandra/1.2	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/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/5.05 module add cudnn/5.1.10 module add cudnn/6.0.21	https://docs.nvidia.com/deeplearning/sdk/cudnn-developer-guide/index.html	-
ELSA Tutorial	module add elsa-tutorial/1.0	TBA	Used with ELSA SLURM tutorial
ESPResSo	module add espresso/3.3.1	http://espressomd.org/wordpress/documentation/	Extensible Simulation Package for Research on Soft Matter
FASTX-Toolkit	module add fastx/0.0.14	http://hannonlab.cshl.edu/fastx_toolkit/commandline.html	FASTQ/A short-reads pre-processing tools
FFmpeg	module add ffmpeg/2.8	https://ffmpeg.org/ffmpeg.html	ffmpeg is a very fast video and audio converter
Garli	module add garli/2.01	Website no longer accessible	Genetic Algorithm for Rapid Likelihood Inference
Gaussian	module add gaussian/16	http://gaussian.com/man/	Electronic structure modeling
GNUplot	module add gnuplot/5.0.6	http://www.gnuplot.info/documentation.html	Portable command-line driven graphing utility
Go	module add go/1.11	https://golang.org/doc/	Go programming language
Gromacs	module add gromacs/2018.3 module add gromacs+plumed/2018.4	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/2.1.6	https://hoomd-blue.readthedocs.io/en/stable/	General purpose particle simulation toolkit
JDK	module add jdk/1.8	-	Java. Note: OpenJDK is recommended over this version (Oracle Java)
Jellyfish	Example	Example	Example
Julia	Example	Example	Example
LAMMPS	Example	Example	Example
Mathematica	Example	Example	Example
Matlab	Example	Example	Example
MOPAC	Example	Example	Example
MPMC	Example	Example	Example
MrBayes	Example	Example	Example
NetPBM	Example	Example	Example
NWChem	Example	Example	Example
Omnia	Example	Example	Example
ParaView	Example	Example	Example
pNetCDF	Example	Example	Example
PrinSEQ	Example	Example	Example
Python	Example	Example	Example
R	Example	Example	Example
RStudio	Example	Example	Example
SageMath	Example	Example	Example
SAS	Example	Example	Example
SOAPDenovo2	Example	Example	Example
Sondovac	Example	Example	Example
SOP	Example	Example	Example
Spades	Example	Example	Example
Swift	Example	Example	Example
Transcriptomics	Example	Example	Example
Trimmomatic	Example	Example	Example
Trinity	Example	Example	Example
VisIt	Example	Example	Example
VMD	Example	Example	Example