Configure GotCloud - Revision history

Mktrost at 13:39, 16 October 2014

2014-10-16T13:39:45Z

← Older revision		Revision as of 09:39, 16 October 2014
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	* MOSIX		* MOSIX
	* SGE (Sun Grid Engine)		* SGE (Sun Grid Engine)
			** Used by StarCluster
	* SLURM		* SLURM
			* PBS (Portable Batch System)

	You can specify the type of cluster with the option '''-batchtype'''. In addition you can pass options		You can specify the type of cluster with the option '''-batchtype'''. In addition you can pass options
	to that cluster system with the option '''-batchopt'''.		to that cluster system with the option '''-batchopt'''.
			* Alternatively, you can set them using BATCH_TYPE and BATCH_OPTS in the configuration file.
	For example, here are examples of invocations of the aligner using these batch systems:		For example, here are examples of invocations of the aligner using these batch systems:

Mktrost at 19:24, 2 August 2013

2013-08-02T19:24:13Z

← Older revision		Revision as of 15:24, 2 August 2013
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	<code>		<code>
	'''~~gen_biopipeline.pl~~ -conf ~/testalign.conf -out ~/outtest -batchtype slurm -batchopts "--mem 8g"'''		'''gotcloud align -conf ~/testalign.conf -out ~/outtest -batchtype slurm -batchopts "--mem 8g"'''

	'''~~gen_biopipeline.pl~~ -conf ~/testalign.conf -out ~/outtest -batchtype mosix -batchopts "-b"'''		'''gotcloud align -conf ~/testalign.conf -out ~/outtest -batchtype mosix -batchopts "-b"'''
	'''~~gen_biopipeline.pl~~ -conf ~/testalign.conf -out ~/outtest -batchtype mosix -batchopts "-15,16,17"'''		'''gotcloud align -conf ~/testalign.conf -out ~/outtest -batchtype mosix -batchopts "-15,16,17"'''

	'''~~gen_biopipeline.pl~~ -conf ~/testalign.conf -out ~/outtest -batchtype sge'''		'''gotcloud align -conf ~/testalign.conf -out ~/outtest -batchtype sge'''
	</code>		</code>

Terry Gliedt at 19:22, 19 February 2013

2013-02-19T19:22:01Z

← Older revision		Revision as of 15:22, 19 February 2013
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	some things you'll want to know about to make using GotCloud as simple to use as possible.		some things you'll want to know about to make using GotCloud as simple to use as possible.

	'''Configure ~~For~~ Your Batch Environment'''		'''Configure Your Batch Environment'''

	GotCloud supports two options to allow you to submit the work from the aligner and umake		GotCloud supports two options to allow you to submit the work from the aligner and umake

Terry Gliedt at 19:21, 19 February 2013

2013-02-19T19:21:43Z

← Older revision		Revision as of 15:21, 19 February 2013
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	You will not need to set or know about most of the settings, however, there are		You will not need to set or know about most of the settings, however, there are
	some things you'll want to know about to make using GotCloud as simple to use as possible.		some things you'll want to know about to make using GotCloud as simple to use as possible.

			'''Configure For Your Batch Environment'''

			GotCloud supports two options to allow you to submit the work from the aligner and umake
			to run on your local cluster.
			There are many different types of clusters and the details of their interfaces vary for each installation.
			As distributed GotCloud contacts support for these:

			* MOSIX
			* SGE (Sun Grid Engine)
			* SLURM

			You can specify the type of cluster with the option '''-batchtype'''. In addition you can pass options
			to that cluster system with the option '''-batchopt'''.
			For example, here are examples of invocations of the aligner using these batch systems:

			<code>
			'''gen_biopipeline.pl -conf ~/testalign.conf -out ~/outtest -batchtype slurm -batchopts "--mem 8g"'''

			'''gen_biopipeline.pl -conf ~/testalign.conf -out ~/outtest -batchtype mosix -batchopts "-b"'''
			'''gen_biopipeline.pl -conf ~/testalign.conf -out ~/outtest -batchtype mosix -batchopts "-15,16,17"'''

			'''gen_biopipeline.pl -conf ~/testalign.conf -out ~/outtest -batchtype sge'''
			</code>

			The interface to actually submit a job to a cluster is coded in '''scripts/runcluster.pl'''
			(probably installed in ''/usr/local/gotcloud'').
			You may need to (and should) modify this code to work with your particular cluster system,
			whether it be to handle options in some manner or add an entirely new batchtype.

Terry Gliedt: Created page with ''''Configure GotCloud''' Back to parent: GotCloud The GotCloud software relies on configuration files to make it as flexible as possible. You will not need to set or know…'

2013-02-19T15:03:10Z

Created page with ''''Configure GotCloud''' Back to parent: GotCloud The GotCloud software relies on configuration files to make it as flexible as possible. You will not need to set or know…'

New page

'''Configure GotCloud'''

Back to parent: [[GotCloud]]

The GotCloud software relies on configuration files to make it as flexible as possible.
You will not need to set or know about most of the settings, however, there are
some things you'll want to know about to make using GotCloud as simple to use as possible.