HPC Cluster Software Resources - Revision history

Admin at 13:35, 29 May 2024

2024-05-29T13:35:50Z

← Older revision		Revision as of 13:35, 29 May 2024
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	For more information on working with Lmod modules on the ELSA cluster see the dedicated [[HPC_Cluster_Lmod\|ELSA Lmod tutorial]] page.		For more information on working with Lmod modules on the ELSA cluster see the dedicated [[HPC_Cluster_Lmod\|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. Use <code>module avail</code> to get the most updated list of available software packages.'''		'''Note: This software listing may be incomplete or contain software that is no longer available. It will be updated in the future. Use the''' <code>module avail</code> '''command to get the most updated list of available software packages.'''

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Admin at 13:35, 29 May 2024

2024-05-29T13:35:20Z

← Older revision		Revision as of 13:35, 29 May 2024
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	For more information on working with Lmod modules on the ELSA cluster see the dedicated [[HPC_Cluster_Lmod\|ELSA Lmod tutorial]] page.		For more information on working with Lmod modules on the ELSA cluster see the dedicated [[HPC_Cluster_Lmod\|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.'''		'''Note: This software listing may be incomplete or contain software that is no longer available. It will be updated in the future. Use <code>module avail</code> to get the most updated list of available software packages.'''

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Admin at 13:34, 29 May 2024

2024-05-29T13:34:22Z

← Older revision		Revision as of 13:34, 29 May 2024
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	For more information on working with Lmod modules on the ELSA cluster see the dedicated [[HPC_Cluster_Lmod\|ELSA Lmod tutorial]] page.		For more information on working with Lmod modules on the ELSA cluster see the dedicated [[HPC_Cluster_Lmod\|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.'''

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Admin at 12:17, 5 October 2023

2023-10-05T12:17:32Z

← Older revision		Revision as of 12:17, 5 October 2023
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	\| CIAO \|\| <code>module</code> \|\| TBD \|\| TBD		\| CIAO \|\| <code>module</code> \|\| TBD \|\| TBD
	\|-		\|-
	\| <br>cuda/8.0<br>cuda/9.2<br>~~cuda/10.0 \|\|~~ <code>module add cuda</code><br><code>module add cuda/8.0</code><br><code>module add cuda/9.2</code><br><code>module add cuda/10.0</code> \|\| https://docs.nvidia.com/cuda/ \|\| Default is CUDA 9.2 if using <code>module add cuda</code>		\| CUDA \|\| <code>module add cuda</code><br><code>module add cuda/8.0</code><br><code>module add cuda/10.1</code><br><code>module add cuda/10.2</code><br><code>module add cuda/11.4</code><br><code>module add cuda/11.7</code><br><code>module add cuda/11.8</code> \|\| https://docs.nvidia.com/cuda/ \|\| Default is CUDA 11.4 if using <code>module add cuda</code><p>CUDA 11.8 contains TensorRT 8.6.1.6 and cuDNN 8.9.5.29
	\|-
	~~\| cuDNN \|\|~~ <~~code~~>~~module add cudnn</code> \|\| https://docs~~.~~nvidia~~.~~com/deeplearning/sdk/cudnn-developer-guide/index~~.~~html \|\| -~~
	\|-		\|-
	\| ddcMD\|\| <code>module add ddcmd</code> \|\| https://github.com/LLNL/ddcMD \|\| A fully GPU-accelerated molecular dynamics program for the Martini force field		\| ddcMD\|\| <code>module add ddcmd</code> \|\| https://github.com/LLNL/ddcMD \|\| A fully GPU-accelerated molecular dynamics program for the Martini force field

Admin at 12:06, 5 October 2023

2023-10-05T12:06:33Z

← Older revision		Revision as of 12:06, 5 October 2023
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	\| ESPResSo \|\| <code>module add espresso</code> \|\| http://espressomd.org/wordpress/documentation/ \|\| Extensible Simulation Package for Research on Soft Matter		\| ESPResSo \|\| <code>module add espresso</code> \|\| http://espressomd.org/wordpress/documentation/ \|\| Extensible Simulation Package for Research on Soft Matter
			\|-
			\| FastQC \|\| <code>module add fastqc</code> \|\| TBD \|\| TBD
	\|-		\|-
	\| FASTX-Toolkit \|\| <code>module add fastx</code> \|\| http://hannonlab.cshl.edu/fastx_toolkit/commandline.html \|\| FASTQ/A short-reads pre-processing tools		\| FASTX-Toolkit \|\| <code>module add fastx</code> \|\| http://hannonlab.cshl.edu/fastx_toolkit/commandline.html \|\| FASTQ/A short-reads pre-processing tools

Admin at 12:05, 20 September 2023

2023-09-20T12:05:50Z

← Older revision		Revision as of 12:05, 20 September 2023
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	\| LAMMPS \|\| <code>module add lammps</code> \|\| https://lammps.sandia.gov/doc/Manual.html \|\| Molecular dynamics simulator		\| LAMMPS \|\| <code>module add lammps</code> \|\| https://lammps.sandia.gov/doc/Manual.html \|\| Molecular dynamics simulator
	\|-		\|-
	\| mafft\|\| <code>module add ~~mathematica~~</code> \|\| https://mafft.cbrc.jp/alignment/software/ \|\| MAFFT is a program used to create multiple sequence alignments of amino acid or nucleotide sequences		\| mafft\|\| <code>module add mafft</code> \|\| https://mafft.cbrc.jp/alignment/software/ \|\| MAFFT is a program used to create multiple sequence alignments of amino acid or nucleotide sequences
	\|-		\|-
	\| Mathematica \|\| <code>module add ~~mafft~~</code> \|\| https://reference.wolfram.com/language/?source=nav \|\| Single integrated, continually expanding system that covers the breadth and depth of technical computing. GUI accessed via [http://ondemand.hpc.tcnj.edu/ Open OnDemand] (under Interactive Apps)		\| Mathematica \|\| <code>module add mathematica</code> \|\| https://reference.wolfram.com/language/?source=nav \|\| Single integrated, continually expanding system that covers the breadth and depth of technical computing. GUI accessed via [http://ondemand.hpc.tcnj.edu/ Open OnDemand] (under Interactive Apps)
	\|-		\|-
	\| Matlab \|\| <code>module add matlab</code> \|\| 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 [http://ondemand.hpc.tcnj.edu/ Open OnDemand] (under Interactive Apps) mathematics directly		\| Matlab \|\| <code>module add matlab</code> \|\| 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 [http://ondemand.hpc.tcnj.edu/ Open OnDemand] (under Interactive Apps) mathematics directly

Admin at 16:17, 2 March 2023

2023-03-02T16:17:43Z

← Older revision		Revision as of 16:17, 2 March 2023
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	\|-		\|-
	\| ABySS\|\| <code>module add abyss</code> \|\| https://docs.anaconda.com/anaconda/ \|\| ABySS is a de novo sequence assembler intended for short paired-end reads and large genomes		\| ABySS\|\| <code>module add abyss</code> \|\| https://docs.anaconda.com/anaconda/ \|\| ABySS is a de novo sequence assembler intended for short paired-end reads and large genomes
			\|-
			\| Alphafold2 \|\| <code>module</code> \|\| TBD \|\| TBD
	\|-		\|-
	\| Amber \|\| <code>module add amber</code> \|\| http://ambermd.org/Manuals.php \|\| Amber is a suite of biomolecular simulation programs		\| Amber \|\| <code>module add amber</code> \|\| http://ambermd.org/Manuals.php \|\| Amber is a suite of biomolecular simulation programs
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	\|-		\|-
	\| Athena++ \|\| <code>module add athena++</code> \|\| https://princetonuniversity.github.io/athena/ \|\| Athena++ is a complete re-write of the Athena astrophysical magnetohydrodynamics (MHD) code in C++		\| Athena++ \|\| <code>module add athena++</code> \|\| https://princetonuniversity.github.io/athena/ \|\| Athena++ is a complete re-write of the Athena astrophysical magnetohydrodynamics (MHD) code in C++
			\|-
			\| Autodock Vina \|\| <code>module</code> \|\| TBD \|\| TBD
	\|-		\|-
	\| Blast+ \|\| <code>module add blast+</code> \|\| https://www.ncbi.nlm.nih.gov/books/NBK279690/ \|\| Basic Local Alignment Search Tool		\| Blast+ \|\| <code>module add blast+</code> \|\| https://www.ncbi.nlm.nih.gov/books/NBK279690/ \|\| Basic Local Alignment Search Tool
			\|-
			\| Blender \|\| <code>module</code> \|\| TBD \|\| TBD
	\|-		\|-
	\| Cassandra \|\| <code>module add cassandra</code> \|\| https://cassandra.nd.edu/index.php/documentation \|\| Cassandra is an open source Monte Carlo package		\| Cassandra \|\| <code>module add cassandra</code> \|\| https://cassandra.nd.edu/index.php/documentation \|\| Cassandra is an open source Monte Carlo package
			\|-
			\| ChimeraX \|\| <code>module</code> \|\| TBD \|\| TBD
			\|-
			\| CIAO \|\| <code>module</code> \|\| TBD \|\| TBD
	\|-		\|-
	\| <br>cuda/8.0<br>cuda/9.2<br>cuda/10.0 \|\| <code>module add cuda</code><br><code>module add cuda/8.0</code><br><code>module add cuda/9.2</code><br><code>module add cuda/10.0</code> \|\| https://docs.nvidia.com/cuda/ \|\| Default is CUDA 9.2 if using <code>module add cuda</code>		\| <br>cuda/8.0<br>cuda/9.2<br>cuda/10.0 \|\| <code>module add cuda</code><br><code>module add cuda/8.0</code><br><code>module add cuda/9.2</code><br><code>module add cuda/10.0</code> \|\| https://docs.nvidia.com/cuda/ \|\| Default is CUDA 9.2 if using <code>module add cuda</code>
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	\| 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 [http://ondemand.hpc.tcnj.edu/ Open OnDemand] (under Interactive Apps)		\| 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 [http://ondemand.hpc.tcnj.edu/ Open OnDemand] (under Interactive Apps)
			\|-
			\| GipsyX \|\| <code>module</code> \|\| TBD \|\| TBD
	\|-		\|-
	\| GMT\|\| <code>module add gmt</code> \|\| 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		\| GMT\|\| <code>module add gmt</code> \|\| 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
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	\|-		\|-
	\| Matlab \|\| <code>module add matlab</code> \|\| 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 [http://ondemand.hpc.tcnj.edu/ Open OnDemand] (under Interactive Apps) mathematics directly		\| Matlab \|\| <code>module add matlab</code> \|\| 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 [http://ondemand.hpc.tcnj.edu/ Open OnDemand] (under Interactive Apps) mathematics directly
			\|-
			\| MGLtools \|\| <code>module</code> \|\| TBD \|\| TBD
	\|-		\|-
	\| MOPAC \|\| <code>module add mopac</code> \|\| http://openmopac.net/manual/ \|\| General-purpose semiempirical molecular orbital package. Primarily used from within the WebMO (http://webmo.hpc.tcnj.edu) system		\| MOPAC \|\| <code>module add mopac</code> \|\| http://openmopac.net/manual/ \|\| General-purpose semiempirical molecular orbital package. Primarily used from within the WebMO (http://webmo.hpc.tcnj.edu) system
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	\| MrBayes \|\| <code>module add mrbayes</code> \|\| http://nbisweden.github.io/MrBayes/manual.html \|\| Program for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models		\| MrBayes \|\| <code>module add mrbayes</code> \|\| http://nbisweden.github.io/MrBayes/manual.html \|\| Program for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models
			\|-
			\| MSconvert \|\| <code>module</code> \|\| TBD \|\| TBD
	\|-		\|-
	\| MUSCLE\|\| <code>module add muscle</code> \|\| 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		\| MUSCLE\|\| <code>module add muscle</code> \|\| 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
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	\| Omnia \|\| <code>module add omnia</code> \|\| https://github.com/omnia-md/omnia-md \|\| High performance, high usability toolkits for predictive biomolecular simulation		\| Omnia \|\| <code>module add omnia</code> \|\| https://github.com/omnia-md/omnia-md \|\| High performance, high usability toolkits for predictive biomolecular simulation
			\|-
			\| OpenMM \|\| <code>module</code> \|\| TBD \|\| TBD
			\|-
			\| OpenMS \|\| <code>module</code> \|\| TBD \|\| TBD
	\|-		\|-
	\| Open OnDemand \|\| http://ondemand.hpc.tcnj.edu \|\| [http://docs.hpc.tcnj.edu/index.php/HPC_Cluster_Getting_Started#Open_OnDemand 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		\| Open OnDemand \|\| http://ondemand.hpc.tcnj.edu \|\| [http://docs.hpc.tcnj.edu/index.php/HPC_Cluster_Getting_Started#Open_OnDemand 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 \|\| <code>module add paraview</code> \|\| https://www.paraview.org/documentation/ \|\| Open-source, multi-platform data analysis and visualization application. GUI accessed via [http://ondemand.hpc.tcnj.edu/ Open OnDemand] (under Interactive Apps)		\| ParaView \|\| <code>module add paraview</code> \|\| https://www.paraview.org/documentation/ \|\| Open-source, multi-platform data analysis and visualization application. GUI accessed via [http://ondemand.hpc.tcnj.edu/ Open OnDemand] (under Interactive Apps)
			\|-
			\| Partitionfinder \|\| <code>module</code> \|\| TBD \|\| TBD
			\|-
			\| PAUP \|\| <code>module</code> \|\| TBD \|\| TBD
	\|-		\|-
	\| pNetCDF \|\| <code>module add pnetcdf</code> \|\| https://parallel-netcdf.github.io/wiki/Documentation.html \|\| High-performance parallel I/O library for accessing the classic		\| pNetCDF \|\| <code>module add pnetcdf</code> \|\| 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		Unidata's NetCDF files, specifically the CDF 1, 2, and 5 formats
			\|-
			\| Pride PPP-AR \|\| <code>module</code> \|\| TBD \|\| TBD
	\|-		\|-
	\| PRINSEQ \|\| <code>module add prinseq</code> \|\| http://prinseq.sourceforge.net/manual.html \|\| Filter, reformat, or trim your genomic and metagenomic sequence data		\| PRINSEQ \|\| <code>module add prinseq</code> \|\| http://prinseq.sourceforge.net/manual.html \|\| Filter, reformat, or trim your genomic and metagenomic sequence data
			\|-
			\| PWiz \|\| <code>module</code> \|\| TBD \|\| TBD
			\|-
			\| Pylith \|\| <code>module</code> \|\| TBD \|\| TBD
	\|-		\|-
	\| Python \|\| <code>module add python</code> \|\| https://www.python.org/doc/ \|\| Programming language that lets you work more quickly and integrate your systems more effectively		\| Python \|\| <code>module add python</code> \|\| https://www.python.org/doc/ \|\| Programming language that lets you work more quickly and integrate your systems more effectively

Admin at 13:39, 25 March 2021

2021-03-25T13:39:57Z

← Older revision		Revision as of 13:39, 25 March 2021
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	\| MUSCLE\|\| <code>module add muscle</code> \|\| 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		\| MUSCLE\|\| <code>module add muscle</code> \|\| 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\|\| <code>module add namd</code> \|\| https://www.ks.uiuc.edu/Research/namd/ \|\| NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems
	\|-		\|-
	\| NetPBM \|\| <code>module add netpbm</code> \|\| http://netpbm.sourceforge.net/doc/ \|\| Toolkit for manipulation of graphic images, including conversion of images between a variety of different formats		\| NetPBM \|\| <code>module add netpbm</code> \|\| http://netpbm.sourceforge.net/doc/ \|\| Toolkit for manipulation of graphic images, including conversion of images between a variety of different formats

Admin at 13:37, 25 March 2021

2021-03-25T13:37:14Z

← Older revision		Revision as of 13:37, 25 March 2021
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	\| 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 [http://ondemand.hpc.tcnj.edu/ Open OnDemand] (under Interactive Apps)		\| 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 [http://ondemand.hpc.tcnj.edu/ Open OnDemand] (under Interactive Apps)
			\|-
			\| GMT\|\| <code>module add gmt</code> \|\| 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 \|\| <code>module add gnuplot</code> \|\| http://www.gnuplot.info/documentation.html \|\| Portable command-line driven graphing utility		\| GNUplot \|\| <code>module add gnuplot</code> \|\| http://www.gnuplot.info/documentation.html \|\| Portable command-line driven graphing utility

Admin at 13:33, 25 March 2021

2021-03-25T13:33:04Z

← Older revision		Revision as of 13:33, 25 March 2021
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	\| cuDNN \|\| <code>module add cudnn</code> \|\| https://docs.nvidia.com/deeplearning/sdk/cudnn-developer-guide/index.html \|\| -		\| cuDNN \|\| <code>module add cudnn</code> \|\| https://docs.nvidia.com/deeplearning/sdk/cudnn-developer-guide/index.html \|\| -
	\|-		\|-
	\| ddcMD\|\| <code>module add ~~dccmd~~</code> \|\| https://github.com/LLNL/ddcMD \|\| A fully GPU-accelerated molecular dynamics program for the Martini force field		\| ddcMD\|\| <code>module add ddcmd</code> \|\| https://github.com/LLNL/ddcMD \|\| A fully GPU-accelerated molecular dynamics program for the Martini force field
	\|-		\|-
	\| ELSA Tutorial \|\| <code>module add elsa-tutorial</code> \|\| TBA \|\| Used with ELSA SLURM tutorial		\| ELSA Tutorial \|\| <code>module add elsa-tutorial</code> \|\| TBA \|\| Used with ELSA SLURM tutorial