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RudoRoemer / PDB2MovieWeb

Web-based front- and backend for PDB2Movie scripts
GNU General Public License v3.0
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corrected SLURM parameters #51

Closed RudoRoemer closed 5 years ago

RudoRoemer commented 5 years ago

https://bugzilla.csc.warwick.ac.uk/bugzilla/show_bug.cgi?id=13092

--- Comment #1 from Matthew Ismail ccsyab@warwick.ac.uk --- Hi Rudo,

There were a couple of things going on here. We had lost a default memory setting which means anything submitted without a memory request (which is a mistake in the first place) was grabbing too much RAM.

For your jobs, you have:

SBATCH --ntask=1

but "ntask" isn't a valid resource request: it should be "ntasks"; sbatch warns you about this (but accepts the job) which I guess you might not have noticed if the job submission was automated. You're also wanting 16 CPUs per task, which needs all the cores within a node (i.e. simply counting cores isn't enough when trying to work out if your job should be running).

You're also requesting multiple cores but without a per-core memory request:

SBATCH --mem=2000

If you wanted 2 GB per core, then:

SBATCH --mem-per-cpu=2000

is what you need.

Anyway, the system default memory setting is fixed for new job submissions so I'll resolve this now. If you think you need to re-open it, please make sure you've first corrected your own batch scripts and that any issues affect new job submissions once currently running jobs have come off (i.e. wait a day or so).

Thanks, Matt

RudoRoemer commented 5 years ago

This patch has been tested on pdb2movie-test.warwick.ac.uk.