fsl_sub Environment variables
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:
export ENVVAR=VALUE
| Envrionment variable | Who sets | Purpose | Example 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}
Python:
import os
value = os.environ[os.environ['FSLSUB_VARIABLE']]
NSLOT_VAR = getenv('FSLSUB_VARIABLE')
N = getenv(NSLOT_VAR)