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Environment variables that can be set to control fsl_sub submitted tasks

Available Environment Variables

fsl_sub sets or can be controlled with the following shell variables. These can be set either for the duration of the fsl_sub run by prepending the call with the setting of the value:

ENVVAR=VALUE fsl_sub ...

or by exporting the value to your shell so that all subsequent calls will also have this variable set this way:


Envrionment variable​​Who sets​PurposeExample values
​FSLSUB_JOBID_VAR ​fsl_sub ​Variable name of Grid job id JOB_ID
​FSLSUB_ARRAYTASKID_VAR ​fsl_sub Variable name of Grid task id SGE_TASK_ID
​​FSLSUB_ARRAYSTARTID_VAR ​fsl_sub Variable name of Grid first task id SGE_TASK_FIRST
​FSLSUB_ARRAYENDID_VAR ​fsl_sub Variable name of Grid last task id SGE_TASK_LAST
​FSLSUB_ARRAYSTEPSIZE_VAR ​fsl_sub ​​Variable name of Grid step between task ids SGE_TASK_STEPSIZE
​FSLSUB_ARRAYCOUNT_VAR ​fsl_sub ​Variable name of Grid number of tasks in array ​Not supported in Grid Engine
​FSLSUB_MEMORY_REQUIRED ​You ​Advise fsl_sub of expected memory required ​32G
​FSLSUB_PROJECT ​You ​Name of Grid project to run jobs under ​MyProject
​FSLSUB_PARALLEL ​You/fsl_sub ​Control array task parallelism when running without a cluster engine (e.g. when a queued task itself submits an array task) ​4 (for four threads), 0 to let fsl_sub's shell plugin use all available cores
​FSLSUB_CONF You ​Provides the path to the configuration file /usr/local/etc/fslsub_conf.yml​
​FSLSUB_NSLOTS ​fsl_sub ​Variable name of Grid allocated slots ​NSLOTS
​FSLSUB_DEBUG ​You/fsl_sub ​Enable debugging in child fsl_sub ​1
​FSLSUB_PLUGINPATH ​You ​​Where to find installed plugins (do not change this variable) ​/path/to/folder
​FSLSUB_NOTIMELIMIT ​You ​Disable notification of job time to the cluster ​1​

​Where a FSLSUB_* variable is a reference to another variable you need to read the content of the referred to variable. This can be achieved as follows:

BASH: the number of slots is equal to ${!FSLSUB_VARIABLE}


import os
value = os.environ[os.environ['FSLSUB_VARIABLE']]


N = getenv(NSLOT_VAR)