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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