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

2022-10-27T20:12:45Z

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

← Older revision		Revision as of 20:12, 27 October 2022
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	</pre>		</pre>

	Once the head or login node enviroment variables are properly set, one can create a ~~PBS~~ script		Once the head or login node enviroment variables are properly set, one can create a SLURM script
	to run an Mathematica job on a compute node and ensure that the head or login node environment		to run an Mathematica job on a compute node and ensure that the head or login node environment
	just set is passed on to the compute nodes by using the "#~~PBS~~ -V" option inside you ~~PBS~~ script:		just set is passed on to the compute nodes by using the "#SLURM -V" option inside you SLURM script:

	<pre>		<pre>
	#!/bin/bash		#!/bin/bash
	#~~PBS~~ -N mmat8_serial1		#SLURM -N mmat8_serial1
	#~~PBS~~ -q production		#SLURM -q production
	#~~PBS~~ -l select=1:ncpus=1:mem=1920mb		#SLURM -l select=1:ncpus=1:mem=1920mb
	#~~PBS~~ -l place=free		#SLURM -l place=free
	#~~PBS~~ -V		#SLURM -V

	# Find out name of master execution host (compute node)		# Find out name of master execution host (compute node)
	echo -n ">>>> ~~PBS~~ Master compute node is: "		echo -n ">>>> SLURM Master compute node is: "
	hostname		hostname

	# 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

	# Just point to the serial executable to run		# Just point to the serial executable to run
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	Since the PATH variable in the login environment is now includes the location of the Mathematica		Since the PATH variable in the login environment is now includes the location of the Mathematica
	executable and the "#~~PBS~~ -V" option ensures that this is passed to the compute node that the		executable and the "#SLURM -V" option ensures that this is passed to the compute node that the
	job is run on, the last line of the ~~PBS~~ script will be executed without environment-related problems.		job is run on, the last line of the SLURM script will be executed without environment-related problems.
	</div>		</div>
	</div>		</div>
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	22) xtpe-mc8		22) xtpe-mc8
	23) cray-mpich2/5.5.3		23) cray-mpich2/5.5.3
	24) ~~pbs~~/11.3.0.121723		24) SLURM/11.3.0.121723
	</pre>		</pre>

	From the list, we see that the Cray Programming Environment ("PrgEnv-cray/4.0.46") and the Cray Compiler		From the list, we see that the Cray Programming Environment ("PrgEnv-cray/4.0.46") and the Cray Compiler
	environment are loaded ("cce/8.0.7") by default among other things (~~PBS~~, MPICH, etc.). To unload these		environment are loaded ("cce/8.0.7") by default among other things (SLURM, MPICH, etc.). To unload these
	Cray modules and load in the Portland Group (PGI) equivalents we need to know the names of the PGI		Cray modules and load in the Portland Group (PGI) equivalents we need to know the names of the PGI
	modules. The "module avail" command will tell us this:		modules. The "module avail" command will tell us this:
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	.		.
	------------------------------------------------ /opt/modulefiles -----------------------------------------------------		------------------------------------------------ /opt/modulefiles -----------------------------------------------------
	Base-opts/1.0.2-1.0400.31284.2.2.gem(default) gcc/4.1.2 ~~pbs~~/11.2.0.113417		Base-opts/1.0.2-1.0400.31284.2.2.gem(default) gcc/4.1.2 SLURM/11.2.0.113417
	PrgEnv-cray/3.1.61 gcc/4.2.4 ~~pbs~~/11.3.0.121723(default)		PrgEnv-cray/3.1.61 gcc/4.2.4 SLURM/11.3.0.121723(default)
	PrgEnv-cray/4.0.46(default) gcc/4.4.2 petsc/3.1.08		PrgEnv-cray/4.0.46(default) gcc/4.4.2 petsc/3.1.08
	PrgEnv-gnu/3.1.61 gcc/4.4.4 petsc/3.1.09		PrgEnv-gnu/3.1.61 gcc/4.4.4 petsc/3.1.09
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	fftw/2.1.5.3 pathscale/4.0.12.1(default) xt-papi/4.2.0		fftw/2.1.5.3 pathscale/4.0.12.1(default) xt-papi/4.2.0
	fftw/3.2.2.1(default) pathscale/4.0.9 xt-papi/4.3.0(default)		fftw/3.2.2.1(default) pathscale/4.0.9 xt-papi/4.3.0(default)
	fftw/3.3.0.1 ~~pbs~~/11.1.0.111761		fftw/3.3.0.1 SLURM/11.1.0.111761
	</pre>		</pre>

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	14) xtpe-mc8		14) xtpe-mc8
	15) cray-mpich2/5.5.3		15) cray-mpich2/5.5.3
	16) ~~pbs~~/11.3.0.121723		16) SLURM/11.3.0.121723
	17) xt-libsci/11.1.00		17) xt-libsci/11.1.00
	18) pmi/3.0.0-1.0000.8661.28.2807.gem		18) pmi/3.0.0-1.0000.8661.28.2807.gem
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	Unless otherwise noted, all applications built locally were built using our default		Unless otherwise noted, all applications built locally were built using our default
	Intel-OpenMPI applications stack. Furthermore, the ~~PBS~~ Pro job submission scripts		Intel-OpenMPI applications stack. Furthermore, the SLURM Pro job submission scripts
	below are promised to work (at the time this section of the Wiki was written), but the		below are promised to work (at the time this section of the Wiki was written), but the
	number of processors (cores), memory, and process placement defined in the		number of processors (cores), memory, and process placement defined in the
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	The user should use their knowledge of the application, the system, and the benefit		The user should use their knowledge of the application, the system, and the benefit
	of their experience to choose the optimal combination of processors and memory		of their experience to choose the optimal combination of processors and memory
	for their scripts. Details on how to make full use of the ~~PBS~~ Pro job submission		for their scripts. Details on how to make full use of the SLURM Pro job submission
	options are covered in the ~~PBS~~ Pro section below.		options are covered in the SLURM Pro section below.

	=== ADCIRC ===		=== ADCIRC ===
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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
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	====General Notes====		====General Notes====

	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 "= Using Modules to Run your Applications =
Modules is a software package that provides for the fast and convenient management of the components of a user's environment via '''modulefiles'''. When executed by the module command each module file fully configures the environment for its associated application or application group.
The modules configuration language allows for t..."

2022-10-17T17:45:38Z

Created page with "= Using Modules to Run your Applications = <div class="toccolours mw-collapsible mw-collapsed"> Modules is a software package that provides for the fast and convenient management of the components of a user's environment via '''modulefiles'''. When executed by the module command each module file fully configures the environment for its associated application or application group. <div class="mw-collapsible-content"> The modules configuration language allows for t..."

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