[gridengine users] Fwd: error in parallel run openmpi for gridengine
reuti at staff.uni-marburg.de
Sun Apr 9 10:27:06 UTC 2017
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Am 09.04.2017 um 11:14 schrieb Yong Wu:
> Dear Reuti,
> Thank you very much!
> The jobname.nodes file is not necessary for parallel ORCA. And my "mpivars.sh" is also not a problem.
> ORCA3.0.3 program is compiled with openmpi-1.6.5, which can run normally on multiple node in gridengine.
> While ORCA4.0.0 program is compiled with openmpi-2.0.2, and cannot run on multiple node in gridengine.
> Maybe it is a bug of openmpi-2.0.x for the orca running on multiple node in gridengine.
I can assure you, that for me and others it's working.
> I download the latest stable version of openmpi, but the error is also appeared in openmpi-2.1.0. The bug maybe not fixed in the latest stable version.
> >The Open MPI bug you checked already: https://firstname.lastname@example.org/msg30824.html
> Thanks for your information. I read it, but I am not solve this problem. I modify the code file of "orte/mca/plm/rsh/plm_rsh_component.c" following this address：https://github.com/open-mpi/ompi/commit/dee2d8646d2e2055e2c86db9c207403366a2453d#diff-f556f53efc98e71d3bd13ee9945949fe
> and recompiled the openmpi, but has no effect.
Aha, I only set the $OMP_ROOT/etc/openmpi-mca-params.conf to have an entry plm_rsh_agent=foo to have it set for all users automatically.
I didn't played with a source modification though.
Can you try with the original Open MPI 2.0.2 and call ORCA with:
> >Please change the line in your PeHostfile2MachineFile() subroutine:
> >host=`echo $line|cut -f1 -d" "|cut -f1 -d"."`
> >host=`echo $line|cut -f1 -d" "`
> >This should leave the ".local" domain,
> This is also not a problem. Because of my “/etc/hosts”
> 10.1.1.1 cluster.local cluster
> 10.1.255.254 compute-0-0.local compute-0-0
> 10.1.255.253 compute-0-1.local compute-0-1
> 10.1.255.244 compute-0-10.local compute-0-10
> 10.1.255.243 compute-0-11.local compute-0-11
I'm not sure whether Open MPI will resolve the hostnames to their TCP/IP address, or does just a literal comparison - which fails.
- -- Reuti
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