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Revision as of 17:48, 23 October 2014
, 17:48, 23 October 2014Created 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. ..."
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>
|}
* 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>
|}
