GotCloud: Configuration: Difference between revisions
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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==== | |||
* 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==== | |||
* 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==== | |||
Regardless of the type of cluster system used, GotCloud will wait for each job to complete after launching it. | |||
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> | |||
{| class="wikitable" style="margin: 1em 1em 1em 0; background-color: #f9f9f9; border: 1px #aaa solid; border-collapse: collapse;" border="1" | {| class="wikitable" style="margin: 1em 1em 1em 0; background-color: #f9f9f9; border: 1px #aaa solid; border-collapse: collapse;" border="1" | ||
Latest revision as of 18:53, 23 October 2014
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
gotcloud/bin/gotcloudDefaults.conf - Comments begin with a
# - Format:
KEY = value- where
KEYis the item being set andvalueis its new value
- where
- 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
- A KEY can be used in another KEY's value by specifying $(KEY)
- Example:
KEY1 = value1KEY2 = $(KEY1)/value2
- When
KEY2is used, it will be equal to:value1/value2
- Example:
Output Directory
- The output directory is required for running GotCloud, so GotCloud knows where to write its output
| Configuration Key | Command-line Flag | Value Description | ||
|---|---|---|---|---|
| OUT_DIR | --outdir | output directory | ||
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.
- 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
fluxorpbs
| Configuration Key | Command-line Flag | Value Description | ||
|---|---|---|---|---|
| BATCH_TYPE | --batchtype | type of cluster system | ||
| Valid Values | Command to Launch | Command to Check for Completion | ||
mosix |
mosbatch -E/tmp |
N/A - interactive type | ||
sge |
qsub |
qstat -u $USER
| ||
sgei |
qrsh -now n |
N/A - interactive type | ||
pbs |
qsub |
qstat -u $USER
| ||
slurm |
sbatch |
squeue -u $USER
| ||
slurmi |
|
N/A - interactive type | ||
local |
N/A - local command | N/A - interactive type | ||
| BATCH_OPTS | --batchopts | options to pass to your cluster type, example:
-j36,37,38,39,40,41,45,46,47,48,49 | ||
