Could be all that is needed is to add this:
mycluster ='sbatch --mail-type=FAIL --mail-user=<typeyouremailhere> -N 1
--ntasks-per-node=10 --partition=work --export=ALL -o
<pathtohomes>/%(username)s/logs/job.%J.out- e
<pathtohomes>/%(username)/logs/job.%J.err "%(command)s"'
and comment the lines
# if queue is not None ...
# pbcmd = ...
with a hashtag.
you can also simplify the slurm command (remove the --mail flags and the
-o logfile location flags) your cluster partition may not be called
"work" either.
Best, Martin
Am 22.02.2018 um 16:43 schrieb Martin Reuter:
Hi Lea,
I wrote that script to simplify processing on our cluster which uses
qsub PBS for submission. I have never used SLURM so far.
There is two functions that you (or someone who knows this stuff)
would need to modify:
def submit
and
def wait_jobs
The submit procedure basically issues a submit command (stored in
pbcmd). The examples there should help anyone who programs python to
modify it for a slurm submission.
The wait_jobs scripts runs a different command (here qstat and grep
user) to see how many jobs you are already running and waits until
this number sinks below maxjobs, then it continues submitting new
jobs. If you don't care about the number of submitted jobs (because
your cluster does the scheduling anyway), you can just write
" return" as the first line (before the " users = os....." line).
Still the submit block would have to be rewritten for slurm.
Best, Martin
Am 17.02.2018 um 12:13 schrieb Backhausen, Lea:
Dear FS experts,
I am trying to do a longitudinal analysis of around 250 adolescents
with up to 4 data points each. Given the complexity I would like to
use the long_submit_jobs script which is described here:
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Scripts
<https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Scripts>
Unfourtunately it does only run on launchpad and I would do the
analyses with SLURM using bash system.
Has anybody adopted the script so i will run with SLURM or does
anybody know where I should look to get information on this?
I have little scripting experience so any help would be greatly
appreciated!
Best,
Lea Backhausen, B.Sc.
Research assistant
Klinik und Poliklinik für Kinder- und Jugendpsychiatrie und
–psychotherapie
Tel. +49 (0)351 458-7166
Fax +49 (0)351 458-5754
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