[gridengine users] Fwd: error in parallel run openmpi for gridengine

Yong Wu wuy069 at gmail.com
Sun Apr 9 13:47:18 UTC 2017


Reuti,
Thanks for your reply again!

>I can assure you, that for me and others it's working.
But it's not working for me.

>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.
>Nevertheless:
>Can you try with the original Open MPI 2.0.2 and call ORCA with:
>https://orcaforum.cec.mpg.de/viewtopic.php?f=9&t=2656
I add an entry plm_rsh_agent=foo to the path of openmpi-mca-params.conf
(/share/apps/mpi/openmpi2.0.2-ifort/etc/openmpi-mca-params.conf), and
resubmit the job, but get the error: "[file orca_main/mainchk.cpp, line
130]: Error (ORCA_MAIN): ... aborting the run."

I enter the line "time /share/apps/orca4.0.0/orca test.inp "-mca
plm_rsh_agent foo --bind-to none" > ${SGE_O_WORKDIR}/test.log"  instead of
"time /share/apps/orca4.0.0/orca test.inp > ${SGE_O_WORKDIR}/test.log", and
get the same error: "[file orca_main/mainchk.cpp, line 130]: Error
(ORCA_MAIN): ... aborting the run."

>I'm not sure whether Open MPI will resolve the hostnames to their TCP/IP
address, or does just a literal comparison - which fails.
When used the mpich PE, I modify the startmpi.sh of all compute nodes,
I change the line in your PeHostfile2MachineFile() subroutine: "host=`echo
$line|cut -f1 -d" "|cut -f1 -d"."`" to "host=`echo $line|cut -f1 -d" "`"
 and  resubmit the job, but get the error: "[file orca_main/mainchk.cpp,
line 130]: Error (ORCA_MAIN): ... aborting the run."

Best regards,
Yong Wu

2017-04-09 18:27 GMT+08:00 Reuti <reuti at staff.uni-marburg.de>:

> -----BEGIN PGP SIGNED MESSAGE-----
> Hash: SHA1
>
> Hi,
>
> 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://www.mail-archive.com/
> users at lists.open-mpi.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.
>
> Nevertheless:
>
> Can you try with the original Open MPI 2.0.2 and call ORCA with:
>
> https://orcaforum.cec.mpg.de/viewtopic.php?f=9&t=2656
>
>
> > >Please change the line in your PeHostfile2MachineFile() subroutine:
> > >host=`echo $line|cut -f1 -d" "|cut -f1 -d"."`
> > >to:
> > >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
> -----BEGIN PGP SIGNATURE-----
> Comment: GPGTools - https://gpgtools.org
>
> iEYEARECAAYFAljqDHoACgkQo/GbGkBRnRo77QCgjcs9bKAKg0TPt2AUUOF3g/cb
> /sIAn23dn3HaYNGZ7+dqULfMtXyOOlD1
> =3uu2
> -----END PGP SIGNATURE-----
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://gridengine.org/pipermail/users/attachments/20170409/9c79282a/attachment.html>


More information about the users mailing list