GotCloud: Configuration - Revision history

Mktrost at 22:53, 23 October 2014

2014-10-23T22:53:30Z

← Older revision		Revision as of 18:53, 23 October 2014
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	* Some settings can be defined both in the configuration file and on the GotCloud command-line		* Some settings can be defined both in the configuration file and on the GotCloud command-line
	** command-line options take priority over configuration file settings		** command-line options take priority over configuration file settings
			* A KEY can be used in another KEY's value by specifying $(KEY)
			** Example:
			**: <code>KEY1 = value1</code>
			**: <code>KEY2 = $(KEY1)/value2</code>
			*** When <code>KEY2</code> is used, it will be equal to: <code>value1/value2</code>

	====Output Directory====		====Output Directory====

Mktrost: /* Cluster Configuration */

2014-10-23T22:08:00Z

Cluster Configuration

← Older revision		Revision as of 18:08, 23 October 2014
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	====Cluster Configuration====		====Cluster Configuration====
	Regardless of the type of cluster system used, GotCloud will wait for each job to complete after launching it. GotCloud will ~~launch~~ the ~~maximum number of jobs in parallel~~, and ~~wait until one finishes before sending another job to the cluster system.~~		Regardless of the type of cluster system used, GotCloud will wait for each job to complete after launching it.
			* For any BATCH_TYPEs that run in batch mode, GotCloud generates a script that will wait until the step is complete before returning
			** In a sense, it "fakes" interactive mode for all batch types since it will not proceed until a command is finished
			* If you are at UM and are using flux, you can specify either <code>flux</code> or <code>pbs</code>

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Mktrost at 22:05, 23 October 2014

2014-10-23T22:05:58Z

← Older revision		Revision as of 18:05, 23 October 2014
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	====Reference/Resource Files====		====Reference/Resource Files====
	* See [[GotCloud: Genetic Reference and Resource Files]] for reference/resource file configuration settings		* See [[GotCloud: Genetic Reference and Resource Files]] for reference/resource file configuration settings


	====Cluster Configuration====		====Cluster Configuration====

Mktrost at 22:05, 23 October 2014

2014-10-23T22:05:44Z

← Older revision		Revision as of 18:05, 23 October 2014
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	** command-line options take priority over configuration file settings		** command-line options take priority over configuration file settings

			====Output Directory====
	~~'''~~Output Directory~~'''~~
	* The output directory is required for running GotCloud, so GotCloud knows where to write its output		* The output directory is required for running GotCloud, so GotCloud knows where to write its output
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	\|}		\|}

			====Reference/Resource Files====
	~~'''~~Reference/Resource Files~~'''~~
	* See [[GotCloud: Genetic Reference and Resource Files]] for reference/resource file configuration settings		* See [[GotCloud: Genetic Reference and Resource Files]] for reference/resource file configuration settings


	~~'''~~Cluster Configuration~~'''~~		====Cluster Configuration====
	Regardless of the type of cluster system used, GotCloud will wait for each job to complete after launching it. GotCloud will launch the maximum number of jobs in parallel, and wait until one finishes before sending another job to the cluster system.		Regardless of the type of cluster system used, GotCloud will wait for each job to complete after launching it. GotCloud will launch the maximum number of jobs in parallel, and wait until one finishes before sending another job to the cluster system.

Mktrost at 22:01, 23 October 2014

2014-10-23T22:01:40Z

← Older revision		Revision as of 18:01, 23 October 2014
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	\|OUT_DIR\|\|--outdir \|\| output directory		\|OUT_DIR\|\|--outdir \|\| output directory
	\|}		\|}


	'''Reference/Resource Files'''		'''Reference/Resource Files'''

Mktrost at 21:59, 23 October 2014

2014-10-23T21:59:04Z

← Older revision		Revision as of 17:59, 23 October 2014
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	** command-line options take priority over configuration file settings		** command-line options take priority over configuration file settings


			'''Output Directory'''
			* The output directory is required for running GotCloud, so GotCloud knows where to write its output
			{\| class="wikitable" style="margin: 1em 1em 1em 0; background-color: #f9f9f9; border: 1px #aaa solid; border-collapse: collapse;" border="1"
			! Configuration Key !! Command-line Flag !! colspan="3"\|Value Description
			\|-
			\|OUT_DIR\|\|--outdir \|\| output directory
			\|}

	'''Reference/Resource Files'''		'''Reference/Resource Files'''

Mktrost: Created page with "The GotCloud configuration file contains the run-time options, including software binaries and command line arguments. A default configuration file is automatically loaded. ..."

2014-10-23T21:48:11Z

Created page with "The GotCloud configuration file contains the run-time options, including software binaries and command line arguments. A default configuration file is automatically loaded. ..."

New page

The GotCloud configuration file contains the run-time options, including software binaries and command line arguments. A default configuration file is automatically loaded. Users may specify their own configuration file specifying just the values different than the defaults. The configuration file is not required if there are no values to override.

* Default GotCloud configuration file is <code>gotcloud/bin/gotcloudDefaults.conf</code>
* Comments begin with a <code>#</code>
* Format: <code>KEY = value </code>
** where <code>KEY</code> is the item being set and <code>value</code> is its new value
* Some settings can be defined both in the configuration file and on the GotCloud command-line
** command-line options take priority over configuration file settings

'''Reference/Resource Files'''
* See [[GotCloud: Genetic Reference and Resource Files]] for reference/resource file configuration settings

'''Cluster Configuration'''
Regardless of the type of cluster system used, GotCloud will wait for each job to complete after launching it. GotCloud will launch the maximum number of jobs in parallel, and wait until one finishes before sending another job to the cluster system.

{| class="wikitable" style="margin: 1em 1em 1em 0; background-color: #f9f9f9; border: 1px #aaa solid; border-collapse: collapse;" border="1"
! Configuration Key !! Command-line Flag !! colspan="3"|Value Description
|-
| rowspan="9"|BATCH_TYPE || rowspan="9"|--batchtype || colspan="3"|type of cluster system
|-
! Valid Values !! Command to Launch !! Command to Check for Completion
|-
| <code>mosix</code> || <code>mosbatch -E/tmp</code> || ''N/A - interactive type''
|-
| <code>sge</code> || <code>qsub</code>||<code>qstat -u $USER</code>
|-
| <code>sgei</code> || <code>qrsh -now n</code> || ''N/A - interactive type''
|-
| <code>pbs</code> || <code>qsub</code>||<code>qstat -u $USER</code>
|-
| <code>slurm</code> || <code>sbatch</code>||<code>squeue -u $USER</code>
|-
| <code>slurmi</code> || <code></code> || ''N/A - interactive type''
|-
| <code>local</code> || ''N/A - local command'' || ''N/A - interactive type''
|-
| BATCH_OPTS || --batchopts || colspan="3"| options to pass to your cluster type, example:
<pre>-j36,37,38,39,40,41,45,46,47,48,49</pre>
|}