[slurm-users] Strange behaviour with dynamically linked binary in batch job
steve.cousins at maine.edu
Thu Mar 31 13:30:31 UTC 2022
Is using "#!/bin/bash -l" enough to make it work?
On Thu, Mar 31, 2022 at 6:46 AM Sebastian Potthoff <
s.potthoff at uni-muenster.de> wrote:
> Just a quick follow up, that I could resolve the issue. Maybe this helps
> someone in the future.
> $BASH_ENV was pointing to a deprecated script, resetting the module
> environment. This only is an issue for non-interactive, non-login shells
> (i.e. sbatch) and the issue was therefore not seen when running in an
> interactive slurm session.
> I addition „ldd“ seems to create a subprocess/shell? Using
> /usr/lib64/ld-linux-x86-64.so.2 --list /path/to/binary
> did not have the described issue.
> Concerning other self-compile binaries, which seemed to work fine: those
> had a set an RPATH and were therefore always finding the correct MPI libs.
> Kind regards
> Am 30.03.2022 um 18:08 schrieb Sebastian Potthoff <
> s.potthoff at uni-muenster.de>:
> Hi Noam,
> Thanks for your suggestion - I already did this and confirmed the modules
> and LD_LIBARARY_PATH are set correctly. Also if there was something wrong
> here, all of this would not work with self-compiled binaries, which it
> does… which baffles me :-/
> Am 30.03.2022 um 17:51 schrieb Bernstein, Noam CIV USN NRL (6393)
> Washington DC (USA) <noam.bernstein at nrl.navy.mil>:
> One possibility is that something about the environment in the running
> batch job is making the "module load" commands fail, which they can do
> without any error (for old fashioned tcl-based env modules). Do "module
> list" after, and echo $LD_LIBRARY_PATH, to confirm that it really is being
> set correctly in the batch job.
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