Running SUMO on UGent HPC - Revision history

Javdrher: /* Testing on the HPC infracture */

2014-03-17T15:14:50Z

Testing on the HPC infracture

← Older revision		Revision as of 15:14, 17 March 2014
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	* Log on to HPC and request for some worker nodes (see the HPC wiki for more information), for example this command will request the HPC for an interactive session:		* Log on to HPC and request for some worker nodes (see the HPC wiki for more information), for example this command will request the HPC for an interactive session:
	qsub -I		qsub -I
	* Wait for the session to be started. In the terminal, change directory to where the compiled SUMO Toolbox is located (by default this is ~~SUMORoot~~/csumo)		* Wait for the session to be started. In the terminal, change directory to where the compiled SUMO Toolbox is located (by default this is dist/csumo-toolbox)
	* Set the MCRROOT environmental variable to point to the MCR root, e.g:		* Set the MCRROOT environmental variable to point to the MCR root, e.g:
	export MCRROOT=/apps/gent/gengar/harpertown/software/MATLAB/MCR_2011a/v715		export MCRROOT=/apps/gent/gengar/harpertown/software/MATLAB/MCR_2011a/v715

Javdrher: /* Testing on the HPC infracture */

2014-03-17T15:14:34Z

Testing on the HPC infracture

← Older revision		Revision as of 15:14, 17 March 2014
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	* Set the MCRROOT environmental variable to point to the MCR root, e.g:		* Set the MCRROOT environmental variable to point to the MCR root, e.g:
	export MCRROOT=/apps/gent/gengar/harpertown/software/MATLAB/MCR_2011a/v715		export MCRROOT=/apps/gent/gengar/harpertown/software/MATLAB/MCR_2011a/v715
	* Try to run ~~the~~ a configuration xml-file using:		* Try to run a configuration xml-file using:
	./run_go.sh $MCRROOT pathToYourConfig/yourConfig.xml		./run_go.sh $MCRROOT pathToYourConfig/yourConfig.xml

Javdrher: /* Testing on the HPC infracture */

2014-03-17T15:14:16Z

Testing on the HPC infracture

← Older revision		Revision as of 15:14, 17 March 2014
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	./run_go.sh $MCRROOT pathToYourConfig/yourConfig.xml		./run_go.sh $MCRROOT pathToYourConfig/yourConfig.xml

	'''Only use this method for testing! Submit jobs for the real work (see below)'''		'''Only use this method for testing! Submit jobs for the real work (see below).'''

	== Submit SUMO jobs ==		== Submit SUMO jobs ==

Javdrher: /* Testing on the HPC infracture */

2014-03-17T15:14:08Z

Testing on the HPC infracture

← Older revision		Revision as of 15:14, 17 March 2014
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	./run_go.sh $MCRROOT pathToYourConfig/yourConfig.xml		./run_go.sh $MCRROOT pathToYourConfig/yourConfig.xml

	'''Only use this method for testing!'''		'''Only use this method for testing! Submit jobs for the real work (see below)'''

	== Submit SUMO jobs ==		== Submit SUMO jobs ==

Javdrher: /* Running an example on the HPC infracture */

2014-03-17T15:13:46Z

Running an example on the HPC infracture

← Older revision		Revision as of 15:13, 17 March 2014
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	* Compile the SUMO Toolbox for ''standalone'' use by typing into terminal the following command: <code>make dist-csumo</code>		* Compile the SUMO Toolbox for ''standalone'' use by typing into terminal the following command: <code>make dist-csumo</code>

	== ~~Running an example~~ on the HPC infracture ==		== Testing on the HPC infracture ==
	You can only run matlab code that was included in the mcc options. To run the standalone version of the toolbox, use the <code>run_go.sh</code> bash script which takes two arguments the MCR root and your configuration file. Note: make sure you test your configuration file extensively both locally and on the debug queue of the HPC to avoid wasting your HPC resources as the infrastructure can be very busy at times.		You can only run matlab code that was included in the mcc options. To run the standalone version of the toolbox, use the <code>run_go.sh</code> bash script which takes two arguments the MCR root and your configuration file. Note: make sure you test your configuration file extensively both locally and on the debug queue of the HPC to avoid wasting your HPC resources as the infrastructure can be very busy at times.


	* Log on to HPC and request for some worker nodes (see the HPC wiki for more information), for example this command will request the HPC for ~~node in the debug queue~~:		* Log on to HPC and request for some worker nodes (see the HPC wiki for more information), for example this command will request the HPC for an interactive session:
	qsub -I		qsub -I
	* In the terminal, change directory to where the compiled SUMO Toolbox is located (by default this is SUMORoot/csumo)		* Wait for the session to be started. In the terminal, change directory to where the compiled SUMO Toolbox is located (by default this is SUMORoot/csumo)
	* Set the MCRROOT environmental variable to point to the MCR root, e.g:		* Set the MCRROOT environmental variable to point to the MCR root, e.g:
	export MCRROOT=/apps/gent/gengar/harpertown/software/MATLAB/MCR_2011a/v715		export MCRROOT=/apps/gent/gengar/harpertown/software/MATLAB/MCR_2011a/v715
	* ~~Run~~ the a configuration xml-file using:		* Try to run the a configuration xml-file using:
	./run_go.sh $MCRROOT pathToYourConfig/yourConfig.xml		./run_go.sh $MCRROOT pathToYourConfig/yourConfig.xml

			'''Only use this method for testing!'''

	== Submit SUMO jobs ==		== Submit SUMO jobs ==

Javdrher: /* Compiling a standalone copy of the SUMO Toolbox for use on the HPC */

2014-03-17T15:12:19Z

Compiling a standalone copy of the SUMO Toolbox for use on the HPC

← Older revision		Revision as of 15:12, 17 March 2014
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	By default the examples directory is not included in the compiled version of the toolbox and you probably want to add your example to the mcc options. To make a standalone SUMO Toolbox version, type in make-csumo. The steps you need to follow are summarized below.		By default the examples directory is not included in the compiled version of the toolbox and you probably want to add your example to the mcc options. To make a standalone SUMO Toolbox version, type in make-csumo. The steps you need to follow are summarized below.

	Currently, compiled MATLAB code can be ran on haunter, gastly (recommended) and gengar. All other clusters (including the default delcatty) do not have MCR installed. Also, remember that the checkpointing framework (for jobs > 72 hours) does not work with MATLAB. SUMO Runs can take no more than 72 hours.		Currently, compiled MATLAB code can be ran on haunter, gastly (recommended) and gengar. All other clusters (including the default delcatty) do not have MCR installed. Also, remember that the checkpointing framework (for jobs > 72 hours) does not work with MATLAB. SUMO Runs can take no more than 72 hours. Therefor, include only one run (with no repeat) in your configs, and submit multiple jobs to repeat experiments (for example using array jobs).

	* Log on to the HPC		* Log on to the HPC

Javdrher: /* Submit SUMO jobs */

2014-03-17T15:10:30Z

Submit SUMO jobs

← Older revision		Revision as of 15:10, 17 March 2014
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	./$script ${EBROOTMATLAB} $opts > ~/${PBS_JOBNAME}.log 2> ~/${PBS_JOBNAME}.err		./$script ${EBROOTMATLAB} $opts > ~/${PBS_JOBNAME}.log 2> ~/${PBS_JOBNAME}.err
	</source>		</source>
	Ideally, configure output to be stored on the local disc of the node to avoid network overhead (although this is currently not possible as environment variables are unavailable in the XML!). Another alternative is $VSC_SCRATCH (fast access network storage). <code>echo ${VSC_SCRATCH}</code> provides the absolute path which can be used in the config.		Ideally, configure output to be stored on the local disc of the node to avoid network overhead (although this is currently not possible as environment variables are unavailable in the XML!). Another alternative is $VSC_SCRATCH (fast access network storage). <code>echo ${VSC_SCRATCH}</code> provides the absolute path which can be used in the config. Do not claim many cores: the advantage of multicore computing in MATLAB is quite limited, 1 or 2 should be ok. This has the additional advantage of being placed on nodes which are only partially filled.

	Do not claim many cores: the advantage of multicore computing in MATLAB is quite limited, 1 or 2 should be ok. This has the additional advantage of being placed on nodes which are only partially filled.

	To submit the job to the schedule:		To submit the job to the schedule:

Javdrher: /* Submit SUMO jobs */

2014-03-17T15:10:06Z

Submit SUMO jobs

← Older revision		Revision as of 15:10, 17 March 2014
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	Do not claim many cores: the advantage of multicore computing in MATLAB is quite limited, 1 or 2 should be ok. This has the additional advantage of being placed on nodes which are only partially filled.		Do not claim many cores: the advantage of multicore computing in MATLAB is quite limited, 1 or 2 should be ok. This has the additional advantage of being placed on nodes which are only partially filled.

			To submit the job to the schedule:
			qsub -q long run_script.sh

			To get an overview of all queues and their properties:
			qstat -q

			To get an overview of the status of your submitted jobs:
			qstat -u `whoami`

	For more advanced topics (such as array jobs), please refer to the HPC user wiki.		For more advanced topics (such as array jobs), please refer to the HPC user wiki.

Javdrher: /* Submit SUMO jobs */

2014-03-17T15:08:27Z

Submit SUMO jobs

← Older revision		Revision as of 15:08, 17 March 2014
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	Ideally, configure output to be stored on the local disc of the node to avoid network overhead (although this is currently not possible as environment variables are unavailable in the XML!). Another alternative is $VSC_SCRATCH (fast access network storage). <code>echo ${VSC_SCRATCH}</code> provides the absolute path which can be used in the config.		Ideally, configure output to be stored on the local disc of the node to avoid network overhead (although this is currently not possible as environment variables are unavailable in the XML!). Another alternative is $VSC_SCRATCH (fast access network storage). <code>echo ${VSC_SCRATCH}</code> provides the absolute path which can be used in the config.

	Do not claim many cores: the advantage of multicore computing in MATLAB is quite limited, 1 or 2 should be ok. This has the additional advantage of being placed on nodes which are only partially filled. For more advanced topics (such as array jobs), please refer to the HPC user wiki.		Do not claim many cores: the advantage of multicore computing in MATLAB is quite limited, 1 or 2 should be ok. This has the additional advantage of being placed on nodes which are only partially filled.

			For more advanced topics (such as array jobs), please refer to the HPC user wiki.

Javdrher: /* Submit SUMO jobs */

2014-03-17T15:07:56Z

Submit SUMO jobs

← Older revision		Revision as of 15:07, 17 March 2014
Line 108:		Line 108:
	Ideally, configure output to be stored on the local disc of the node to avoid network overhead (although this is currently not possible as environment variables are unavailable in the XML!). Another alternative is $VSC_SCRATCH (fast access network storage). <code>echo ${VSC_SCRATCH}</code> provides the absolute path which can be used in the config.		Ideally, configure output to be stored on the local disc of the node to avoid network overhead (although this is currently not possible as environment variables are unavailable in the XML!). Another alternative is $VSC_SCRATCH (fast access network storage). <code>echo ${VSC_SCRATCH}</code> provides the absolute path which can be used in the config.

	For more advanced topics (such as array jobs), please refer to the HPC user wiki.		Do not claim many cores: the advantage of multicore computing in MATLAB is quite limited, 1 or 2 should be ok. This has the additional advantage of being placed on nodes which are only partially filled. For more advanced topics (such as array jobs), please refer to the HPC user wiki.