pbs: honour walltime and account target options#428
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PBS backend silently dropped walltime and account from TARGET_DEFAULTS,
making long jobs hit cluster default walltimes and ignoring accounting
on sites that require -A.
- walltime: added to TARGET_DEFAULTS (default 01:00:00) and emitted as
#PBS -l walltime={walltime}.
- account: added to TARGET_DEFAULTS (default "") with conditional
emission - the #PBS -A line is omitted when empty so sites that don't
use accounting are unaffected.
Contributor
Author
|
@micknudsen I hope that's ok I added these! |
Collaborator
|
Thanks a lot for the contribution, @nicorap! |
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The PBS backend's
TARGET_DEFAULTScurrently lists onlyqueue,memory,and
cores. Any target that setswalltimeoraccounttriggers the"Option X not supported by backend. Ignored." warning and qsub falls back
to the cluster's default walltime / no accounting. On sites with short
defaults this silently kills long-running jobs; on sites that require an
account string for billing, jobs can't be submitted at all.
Both options are already standard on the SLURM backend, and PBS itself
universally supports
#PBS -l walltime=...and#PBS -A <account>(Torque, OpenPBS, PBS Pro).
Changes:
walltimeadded toTARGET_DEFAULTS(default01:00:00) and emittedas
#PBS -l walltime={walltime}.accountadded toTARGET_DEFAULTS(default"") with conditionalemission in
compile_script- the-Aline is omitted entirely whenno account is configured, so sites that don't use accounting are
unaffected.
Tested under OpenPBS/Moab at the Danish National Genome Center