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	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+/2.7.1	https://www.ncbi.nlm.nih.gov/books/NBK279690/	-	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
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