Applications - Revision history

James at 17:55, 18 November 2022

2022-11-18T17:55:24Z

← Older revision		Revision as of 17:55, 18 November 2022
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	\|ABINIT		\|ABINIT
	\|8.2.2		\|8.2.2
	\|		\|9.6.2
	\|		\|
	\|-		\|-
	\|ASE		\|ASE
	\|3.18.0		\|3.18.0
	\|		\|Git commit f785806
	\|		\|Python 3.6+, NumPy, SciPy
			Optional: Matplotlib, tkinter, Flask
	\|-		\|-
	\|G-PhoCS		\|G-PhoCS
	\|1.3		\|1.3
	\|		\|1.3
	\|		\|
	\|-		\|-
	\|GMP		\|GMP
	\|6.1.2~~-GCCcore-~~6.~~4.0/ 7.3.0/ 8~~.2.0		\|6.1.2
	\|		\|6.1.2
	\|		\|
	\|-		\|-
	\|GPAW		\|GPAW
	\|19.8.1		\|19.8.1
	\|		\|22.8
	\|		\|
	\|-		\|-
	\|Gerris		\|Gerris
	\|20131206		\|20131206
	\|		\|20131206
	\|		\|
	\|-		\|-
	\|HDF5		\|HDF5
	\|1.8.17/1.10.1		\|1.8.17/1.10.1
	\|		\|1.13.3
	\|		\|
	\|-		\|-
	\|LAME		\|LAME
	\|3.100		\|3.100
	\|		\|3.100
	\|		\|
	\|-		\|-
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	\|abyss		\|abyss
	\|1.3.7 / 1.5.7		\|1.3.7 / 1.5.7
	\|		\|2.3.5
	\|		\|
	\|-		\|-
	\|adcirc		\|adcirc
	\|50_99_07		\|50_99_07
	\|		\|167f586
	\|		\|
	\|-		\|-
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	\|anvio		\|anvio
	\|2.0.2		\|2.0.2
	\|		\|7.1
	\|		\|
	\|-		\|-
	\|armadillo		\|armadillo
	\|9.2.7 / 9.200.7		\|9.2.7 / 9.200.7
	\|		\|11.4.x
	\|		\|
	\|-		\|-
	\|arpack		\|arpack
	\|3.1.5		\|3.1.5
	\|		\|Now maintained at arpack-ng
	\|		\|
	\|-		\|-
	\|augustus		\|augustus
	\|3.2.2		\|3.2.2
	\|		\|3.5.0
	\|		\|
	\|-		\|-
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	\|autodock_vina		\|autodock_vina
	\|1.1.2		\|1.1.2
	\|		\|1.2.0
	\|		\|
	\|-		\|-

James at 15:49, 18 November 2022

2022-11-18T15:49:59Z

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James at 18:56, 7 November 2022

2022-11-07T18:56:18Z

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James at 18:41, 7 November 2022

2022-11-07T18:41:53Z

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James at 18:40, 7 November 2022

2022-11-07T18:40:08Z

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James at 18:39, 7 November 2022

2022-11-07T18:39:30Z

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James at 18:11, 7 November 2022

2022-11-07T18:11:53Z

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James at 18:11, 7 November 2022

2022-11-07T18:11:07Z

← Older revision		Revision as of 18:11, 7 November 2022
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	<div class="noautonum">__NOTOC__</div>		<div class="noautonum">
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			!Application
			!Installed Version
			!Current Version
			!Dependencies
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			__NOTOC__</div>
	'''This is an index of available applications sorted by their academic relevance, as well as alphabetically.'''		'''This is an index of available applications sorted by their academic relevance, as well as alphabetically.'''

James: Text replacement - "[pP][bB][sS]" to "SLURM"

2022-10-27T19:48:48Z

Text replacement - "[pP][bB][sS]" to "SLURM"

← Older revision		Revision as of 19:48, 27 October 2022
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	'''<p style="font-size:15px;" >General Notes</p>'''		'''<p style="font-size:15px;" >General Notes</p>'''

	R language has become a de facto standard among statisticians for the development of statistical software, and is widely used for statistical software development and data analysis. R is available on the following HPCC's servers: Karle, Penzias, Appel and Andy. Karle is the only machine where R can be used without submitting jobs to ~~PBS~~ manager. On all other systems users must submit their R jobs via ~~PBS~~ batch scheduler.		R language has become a de facto standard among statisticians for the development of statistical software, and is widely used for statistical software development and data analysis. R is available on the following HPCC's servers: Karle, Penzias, Appel and Andy. Karle is the only machine where R can be used without submitting jobs to SLURM manager. On all other systems users must submit their R jobs via SLURM batch scheduler.
	More information about our installation can be found here [[R]]		More information about our installation can be found here [[R]]
	</div>		</div>
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	Clemens Lakner, Paul van der Mark, John P Huelsenbeck, Bret Larget, and Fredrik Ronquist. Efficiency of Markov chain Monte Carlo tree proposals in Bayesian phylogenetics. Systematic biology, 57(1):86--103, February 2008.		Clemens Lakner, Paul van der Mark, John P Huelsenbeck, Bret Larget, and Fredrik Ronquist. Efficiency of Markov chain Monte Carlo tree proposals in Bayesian phylogenetics. Systematic biology, 57(1):86--103, February 2008.

	'''Use:''' The example ~~PBS~~ script to run the FDPPDIV on PENZIAS is given below		'''Use:''' The example SLURM script to run the FDPPDIV on PENZIAS is given below

	<pre>		<pre>
	#!/bin/bash		#!/bin/bash
	#~~PBS~~ -q production		#SLURM -q production
	#~~PBS~~ -N <name_of_job>		#SLURM -N <name_of_job>
	#~~PBS~~ -l select=1:ncpus=2		#SLURM -l select=1:ncpus=2
	#~~PBS~~ -l place=free		#SLURM -l place=free
	#~~PBS~~ -V		#SLURM -V

	# You must explicitly change to the working directory in ~~PBS~~		# You must explicitly change to the working directory in SLURM
	cd $~~PBS_O_WORKDIR~~		cd $SLURM_O_WORKDIR

	mpirun -np 2 exabayes <input_file> > output_file		mpirun -np 2 exabayes <input_file> > output_file
Line 2,051:		Line 2,051:
	'''<p style="font-size:15px;" >General Notes</p>'''		'''<p style="font-size:15px;" >General Notes</p>'''

	R language has become a de facto standard among statisticians for the development of statistical software, and is widely used for statistical software development and data analysis. R is available on the following HPCC's servers: Karle, Penzias, Appel and Andy. Karle is the only machine where R can be used without submitting jobs to ~~PBS~~ manager. On all other systems users must submit their R jobs via ~~PBS~~ batch scheduler.		R language has become a de facto standard among statisticians for the development of statistical software, and is widely used for statistical software development and data analysis. R is available on the following HPCC's servers: Karle, Penzias, Appel and Andy. Karle is the only machine where R can be used without submitting jobs to SLURM manager. On all other systems users must submit their R jobs via SLURM batch scheduler.
	More information about our installation can be found here [[R]]		More information about our installation can be found here [[R]]
	</div>		</div>

James: Created page with "
NOTOC
'''This is an index of available applications sorted by their academic relevance, as well as alphabetically.''' For information about using modules to run your applications go to Using Modules To Run Your Applications.
== Computational Physics and Computational Chemistry == Applications in this section use classical mechanics, quantum mechanics and thermodynamics and are applied in..."

2022-10-17T17:01:40Z

Created page with "<div class="noautonum">__NOTOC__</div> '''This is an index of available applications sorted by their academic relevance, as well as alphabetically.''' For information about using modules to run your applications go to Using Modules To Run Your Applications. <div class= "mw-collapsible mw-collapsed"> == Computational Physics and Computational Chemistry == Applications in this section use classical mechanics, quantum mechanics and thermodynamics and are applied in..."

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