PBS job scheduler support.
Neil Venables
Branch: nvenables/snakemake:master
Branch: snakemake/snakemake:master
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Closed by: Johannes Köster·2017-11-30
Improved PBS cluster support with job dependencies using a qsub.py wrapper and DRMAA with immediate submit.
The following params are supported by the qsub.py and PBS DRMAA executor:
mod - space separated list of linux software modules.
node - set the ppn resource request (defaults to the thread declaration).
mem - set the memory resource request.
walltime - set the walltime resource.
workdir - set the working directory for sterr and stdout.
A new variable {assignments} is now available in the jobscript. It will generate the parameters as assignment statements of the form key='value'.
The variables are prefixed with SM_, and sub-dictionaries are separated with an underscore.
This enables automatically generating things in the jobscript.sh, such as loading modules. An example jobscript might be:
{assignments} module load ${{SM_params_mod}} > /dev/null 2>&1 {exec_job}Included are two test cases for verifying the new functionality. I have created a vagrant VM with Torque and environment modules installed for testing: https://bitbucket.org/nvenables/vagrant-torque