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.


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_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.

Batch System API