hoffmangroup / segway

Application for semi-automated genomic annotation.
http://segway.hoffmanlab.org/
GNU General Public License v2.0
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Setting hard memory limit constraints fails on certain systems #123

Open EricR86 opened 6 years ago

EricR86 commented 6 years ago

Original report (BitBucket issue) by Eric Roberts (Bitbucket: ericr86, GitHub: ericr86).


On job resubmission, segway-wrapper.sh attempts to raise both the hard and soft limits of virtual and resident set size memory.

If the hard limit of memory is not unlimited, only root users may increase the hard memory limit requested even after it has been lowered.

Perhaps a proprosal to fallback to attempting to change only the soft limit after failing to set both hard and soft limit.

e.g:

#!bash

ulimit -c 0 -v "$mem_limit_kb" -m "$mem_limit_kb" || (
ulimit -S -c 0 -v "$mem_limit_kb" -m "$mem_limit_kb" || exit 201)