Batch System API¶
The batch system interface is used by Toil to abstract over different ways of running
batches of jobs, for example Slurm, GridEngine, Mesos, Parasol and a single node. The
toil.batchSystems.abstractBatchSystem.AbstractBatchSystem API is implemented to
run jobs using a given job management system, e.g. Mesos.
Batch System Enivronmental Variables¶
Environmental variables allow passing of scheduler specific parameters.
For SLURM:
export TOIL_SLURM_ARGS="-t 1:00:00 -q fatq"
For TORQUE there are two environment variables - one for everything but the resource requirements, and another - for resources requirements (without the -l prefix):
export TOIL_TORQUE_ARGS="-q fatq"
export TOIL_TORQUE_REQS="walltime=1:00:00"
For GridEngine (SGE, UGE), there is an additional environmental variable to define the parallel environment for running multicore jobs:
export TOIL_GRIDENGINE_PE='smp'
export TOIL_GRIDENGINE_ARGS='-q batch.q'
For HTCondor, additional parameters can be included in the submit file passed to condor_submit:
export TOIL_HTCONDOR_PARAMS='requirements = TARGET.has_sse4_2 == true; accounting_group = test'
The environment variable is parsed as a semicolon-separated string of parameter = value pairs.
