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

2022-10-27T19:31:20Z

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

← Older revision		Revision as of 19:31, 27 October 2022
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	</pre>		</pre>

	Running the fence lizard test case should take less than 15 minutes and will produce ~~PBS~~ output and error files beginning		Running the fence lizard test case should take less than 15 minutes and will produce SLURM output and error files beginning
	with the job name 'BPP2_serial'. The primary BPP2 application results will be written into the user-specified file at the end		with the job name 'BPP2_serial'. The primary BPP2 application results will be written into the user-specified file at the end
	of the BPP2 command line after the greater-than sign. Here it is named 'bpp2_ser.out'. The expression '2>&1' combines		of the BPP2 command line after the greater-than sign. Here it is named 'bpp2_ser.out'. The expression '2>&1' combines
	Unix standard output from the program with Unix standard error. Users should always explicitly specify the name of the		Unix standard output from the program with Unix standard error. Users should always explicitly specify the name of the
	application's output file in this way to ensure that it is written directly into the user's working directory which has much		application's output file in this way to ensure that it is written directly into the user's working directory which has much
	more disk space than the ~~PBS~~ spool directory on /var.		more disk space than the SLURM spool directory on /var.

	Details on the meaning of the ~~PBS~~ script are covered in the ~~PBS~~ section in Applications Enviroment [http://wiki.csi.cuny.edu/cunyhpc/index.php/Applications_Environment#Running_MET_at_Andy_with_SLURM]. The most important lines are the '#SBATCH --nodes=1 ncpus=1 mem=2880'. The first instructs ~~PBS~~ to select 1 resource 'chunk' with 1 processor (core) and 2,880 MBs		Details on the meaning of the SLURM script are covered in the SLURM section in Applications Enviroment [http://wiki.csi.cuny.edu/cunyhpc/index.php/Applications_Environment#Running_MET_at_Andy_with_SLURM]. The most important lines are the '#SBATCH --nodes=1 ncpus=1 mem=2880'. The first instructs SLURM to select 1 resource 'chunk' with 1 processor (core) and 2,880 MBs
	of memory in it for the job. The second instructs SLURM to place this job wherever the least used resources are found (freely).		of memory in it for the job. The second instructs SLURM to place this job wherever the least used resources are found (freely).
	The master compute node that ~~PBS~~ finally selects to run your job will be printed in the ~~PBS~~ output file by the 'hostname'		The master compute node that SLURM finally selects to run your job will be printed in the SLURM output file by the 'hostname'
	command.		command.

James: Created page with "At the CUNY HPC Center BPP2 is installed on Andy and Penzias. BPP2 is a serial code that takes its input from a simple text file provided on the command line. Below is an example SLURM script that will run the fence lizard test case provided with the distribution archive (/share/apps/bpp2/default/examples). To include all required environmental variables and the path to the BPP2 executable run the modules load command (the modules utility is discussed in detail above)..."

2022-10-17T17:28:15Z

Created page with "At the CUNY HPC Center BPP2 is installed on Andy and Penzias. BPP2 is a serial code that takes its input from a simple text file provided on the command line. Below is an example SLURM script that will run the fence lizard test case provided with the distribution archive (/share/apps/bpp2/default/examples). To include all required environmental variables and the path to the BPP2 executable run the modules load command (the modules utility is discussed in detail above)..."

New page

At the CUNY HPC Center BPP2 is installed on Andy and Penzias. BPP2 is a serial code that takes its input from a simple text
file provided on the command line. Below is an example SLURM script that will run the fence lizard test case provided with
the distribution archive (/share/apps/bpp2/default/examples).

To include all required environmental variables and the path to the BPP2 executable run the modules load command (the
modules utility is discussed in detail above):

<pre>
module load bpp2
</pre>

<pre>
#!/bin/bash
#SBATCH --partition production
#SBATCH --job-name BPP2_Serial
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --mem=2880

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

# You must explicitly change to the working directory in SLURM
cd $SLURM_SUMBIT_DIR

# Invoke the executable in command-line mode to run
echo ">>>> Begin BPP2 Serial Run ..."
bpp2 ./lizard.bpp.ctl > bpp2_ser.out 2>&1
echo ">>>> End BPP2 Serial Run ..."
</pre>

This script can be dropped in to a file (say bpp2.job) and started with the command:

<pre>
qsub bpp2.job
</pre>

Running the fence lizard test case should take less than 15 minutes and will produce PBS output and error files beginning
with the job name 'BPP2_serial'. The primary BPP2 application results will be written into the user-specified file at the end
of the BPP2 command line after the greater-than sign. Here it is named 'bpp2_ser.out'. The expression '2>&1' combines
Unix standard output from the program with Unix standard error. Users should always explicitly specify the name of the
application's output file in this way to ensure that it is written directly into the user's working directory which has much
more disk space than the PBS spool directory on /var.

Details on the meaning of the PBS script are covered in the PBS section in Applications Enviroment [http://wiki.csi.cuny.edu/cunyhpc/index.php/Applications_Environment#Running_MET_at_Andy_with_SLURM]. The most important lines are the '#SBATCH --nodes=1 ncpus=1 mem=2880'. The first instructs PBS to select 1 resource 'chunk' with 1 processor (core) and 2,880 MBs
of memory in it for the job. The second instructs SLURM to place this job wherever the least used resources are found (freely).
The master compute node that PBS finally selects to run your job will be printed in the PBS output file by the 'hostname'
command.

BPP2 - Revision history

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