Parallel Cluster Guides - Revision history

Iryu: /* Run several single-cpu jobs in MC2 */

2012-05-01T23:12:18Z

Run several single-cpu jobs in MC2

← Older revision		Revision as of 23:12, 1 May 2012
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	, you can use the following file.		, you can use the following file.

	<blockquote style="background: white; border: 0; padding: 1em; width: 750px;"><pre>		<blockquote style="background: white; border: 0; padding: 1em; width: 750px;"><pre>
	#!/bin/bash		#!/bin/bash
Line 313:		Line 312:

	wait		wait


	</pre></blockquote>		</pre></blockquote>


	The only difference is to put ampersand sign(&) in the end of the command line.		The only difference is to put ampersand sign(&) in the end of the command line.

Iryu: /* run ParaDiS in MC2 */

2012-05-01T23:11:41Z

run ParaDiS in MC2

← Older revision		Revision as of 23:11, 1 May 2012
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	</pre></blockquote>		</pre></blockquote>

			=== Run several single-cpu jobs in MC2 ===

			If you want to run many jobs which all use just one cpu, we can use the following stop the calculation, we can do it by submitting the following file.
			For example, if you want to run two jobs whose command are

			bin/paradiscyl tests/CYL_TEST1.ctrl >& tests/CYL_TEST1.log
			bin/paradiscyl tests/CYL_TEST2.ctrl >& tests/CYL_TEST2.log

			, you can use the following file.

			<blockquote style="background: white; border: 0; padding: 1em; width: 750px;"><pre>
			#!/bin/bash

			### Job id
			#PBS -N CYL_TEST
			### #PBS -N fmm.8cpu

			#PBS -j oe

			### ppn : # of cpus / walltime = running time
			#PBS -l nodes=1:ppn=1,walltime=48:00:00
			#PBS -V

			### ---------------------------------------
			### BEGINNING OF EXECUTION
			### ---------------------------------------

			echo The master node of this job is `hostname`
			echo The working directory is `echo $PBS_O_WORKDIR`
			echo This job runs on the following nodes:
			echo `cat $PBS_NODEFILE`

			ncpu=`cat $PBS_NODEFILE \| wc -w`
			echo "Number of processors = $ncpu "

			### end of information preamble

			cd $PBS_O_WORKDIR

			echo $PWD

			cd $PBS_O_WORKDIR

			export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/home/iryu/Codes/fftw3_lib
			export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/lib64:/home/iryu/usr/lib

			### To see which compiler is being used.(You can see it from Job_id.oJOBNAME)
			###ldd bin/paradiscyl

			bin/paradiscyl tests/CYL_TEST1.ctrl >& tests/CYL_TEST1.log &
			bin/paradiscyl tests/CYL_TEST2.ctrl >& tests/CYL_TEST2.log &

			wait


			</pre></blockquote>


			The only difference is to put ampersand sign(&) in the end of the command line.

Iryu: /* In paradis.serial.run */

2011-11-21T18:54:56Z

In paradis.serial.run

← Older revision		Revision as of 18:54, 21 November 2011
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	Then, we need to turn off the x-window in "winDefaultsFile" which is specified in the ctrl file.		Then, we need to turn off the x-window in "winDefaultsFile" which is specified in the ctrl file.
	For example, if it is "inputs/paradis.xdefaults", modify this file as follows.		For example, if it is "inputs/paradis.xdefaults", modify this file as follows.If you don't have X-server in your computer, you need to do the same thing to run the simulation.
	enable_window = 0 # Toggle enabling/disabling simulation X-window.		enable_window = 0 # Toggle enabling/disabling simulation X-window.

Iryu: /* paradis.serial.run */

2011-11-17T18:28:45Z

paradis.serial.run

← Older revision		Revision as of 18:28, 17 November 2011
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	=== paradis.serial.run ===		=== paradis.serial.run ===
	<blockquote style="background: white; border: 0; padding: 1em; width: ~~700px~~;"><pre>		<blockquote style="background: white; border: 0; padding: 1em; width: 750px;"><pre>
	#!/bin/bash		#!/bin/bash

Iryu: /* check compilers */

2011-11-17T18:28:02Z

check compilers

← Older revision		Revision as of 18:28, 17 November 2011
Line 196:		Line 196:
	libintlc.so.5 => /share/apps/intel/lib/intel64/libintlc.so.5 (0x00002b38ef23a000)		libintlc.so.5 => /share/apps/intel/lib/intel64/libintlc.so.5 (0x00002b38ef23a000)

	If you have some problem to find ~~the~~ compiler, we need to add it in your user bash_profile.		If you have some problem to find proper compiler, we need to add it in your user bash_profile.
	To do that, check your bash_profile, as follows.		To do that, check your bash_profile, as follows.

Iryu: /* In paradis.serial.run */

2011-11-17T18:27:10Z

In paradis.serial.run

← Older revision		Revision as of 18:27, 17 November 2011
Line 141:		Line 141:

	We can see that the first part ("bin/paradiscyl tests/CYL_test/CYL_T5_MC2/CYL_T4_MC2_3.ctrl") is exactly same as the command you use when you run a input file in your computer.After this simbol(" >&"), the name of log file is specified("tests/CYL_test/CYL_T4_MC2/CYL_T4_MC2_3.log")		We can see that the first part ("bin/paradiscyl tests/CYL_test/CYL_T5_MC2/CYL_T4_MC2_3.ctrl") is exactly same as the command you use when you run a input file in your computer.After this simbol(" >&"), the name of log file is specified("tests/CYL_test/CYL_T4_MC2/CYL_T4_MC2_3.log")

			Then, we need to turn off the x-window in "winDefaultsFile" which is specified in the ctrl file.
			For example, if it is "inputs/paradis.xdefaults", modify this file as follows.
			enable_window = 0 # Toggle enabling/disabling simulation X-window.

	=== submit paradis.serial.run ===		=== submit paradis.serial.run ===

Iryu: /* In paradis.serial.run */

2011-11-17T18:22:03Z

In paradis.serial.run

← Older revision		Revision as of 18:22, 17 November 2011
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	bin/paradiscyl tests/CYL_test/CYL_T5_MC2/CYL_T4_MC2_3.ctrl >& tests/CYL_test/CYL_T4_MC2/CYL_T4_MC2_3.log		bin/paradiscyl tests/CYL_test/CYL_T5_MC2/CYL_T4_MC2_3.ctrl >& tests/CYL_test/CYL_T4_MC2/CYL_T4_MC2_3.log

	We can see that the first part ("bin/paradiscyl tests/CYL_test/CYL_T5_MC2/CYL_T4_MC2_3.ctrl") is exactly same as the command you use when you run a input file in your computer.After this simbol(" >&"), the log file ~~name~~ is specified("tests/CYL_test/CYL_T4_MC2/CYL_T4_MC2_3.log")		We can see that the first part ("bin/paradiscyl tests/CYL_test/CYL_T5_MC2/CYL_T4_MC2_3.ctrl") is exactly same as the command you use when you run a input file in your computer.After this simbol(" >&"), the name of log file is specified("tests/CYL_test/CYL_T4_MC2/CYL_T4_MC2_3.log")

	=== submit paradis.serial.run ===		=== submit paradis.serial.run ===

Iryu: /* paradis.serial.run */

2011-11-07T20:19:13Z

paradis.serial.run

← Older revision		Revision as of 20:19, 7 November 2011
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	To run a ParaDiS input in mc2, we need to edit the following file("paradis.serial.run") and submit it.		To run a ParaDiS input in mc2, we need to edit the following file("paradis.serial.run") and submit it.

	=== paradis.serial.run ===		=== In paradis.serial.run ===
	First of all, we can specify the JOB NAME in "[[#paradis.serial.run\|paradis.serial.run]]", as follows		First of all, we can specify the JOB NAME in "[[#paradis.serial.run\|paradis.serial.run]]", as follows

Iryu: /* paradis.serial.run */

2011-11-07T20:18:54Z

paradis.serial.run

← Older revision		Revision as of 20:18, 7 November 2011
Line 129:		Line 129:

	=== paradis.serial.run ===		=== paradis.serial.run ===
	First of all, we can specify the JOB NAME in "[[#~~stitch~~\|paradis.serial.run]]", as follows		First of all, we can specify the JOB NAME in "[[#paradis.serial.run\|paradis.serial.run]]", as follows

	### Job id		### Job id

Iryu: /* paradis.serial.run */

2011-11-07T20:14:43Z

paradis.serial.run

← Older revision		Revision as of 20:14, 7 November 2011
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	=== paradis.serial.run ===		=== paradis.serial.run ===
	First of all, we can specify the JOB NAME in "[[paradis.serial.run]]", as follows		First of all, we can specify the JOB NAME in "[[#stitch\|paradis.serial.run]]", as follows

	### Job id		### Job id