[slurm-users] Failed to launch jobs with mpirun after upgrading to Slurm 19.05
Andrés Marín Díaz
amarin at cesvima.upm.es
Thu Jun 6 11:11:57 UTC 2019
Hello,
Yes, we have recompiled OpenMPI with integration with SLURM 19.05 but
the problem remains.
We have also tried to recompile OpenMPI without integration with SLURM.
In this case executions fail with srun, but with mpirun it continues to
work in SLURM 18.08 and fails in 19.05 in the same way.
Thank you very much once more.
El 06/06/2019 a las 12:46, Sean Crosby escribió:
> Hi Andrés,
>
> Did you recompile OpenMPI after updating to SLURM 19.05?
>
> Sean
>
> --
> Sean Crosby
> Senior DevOpsHPC Engineer and HPC Team Lead | Research Platform Services
> Research Computing | CoEPP | School of Physics
> University of Melbourne
>
>
> On Thu, 6 Jun 2019 at 20:11, Andrés Marín Díaz <amarin at cesvima.upm.es
> <mailto:amarin at cesvima.upm.es>> wrote:
>
> Thank you very much for the help, I update some information.
>
> - If we use Intel MPI (IMPI) mpirun it works correctly.
> - If we use mpirun without using the scheduler it works correctly.
> - If we use srun with software compiled with OpenMPI it works
> correctly.
> - If we use SLURM 18.08.6 it works correctly.
> - If we use SLURM 19.05.0 and mpirun inside the sbatch script then we
> get the error:
> --------------------------------------------------------------------------
> An ORTE daemon has unexpectedly failed after launch and before
> communicating back to mpirun. This could be caused by a number
> of factors, including an inability to create a connection back
> to mpirun due to lack of common network interfaces and / or no
> route found between them. Please check network connectivity
> (including firewalls and network routing requirements).
> --------------------------------------------------------------------------
>
> Trying to trace the problem:
> - Mpirun is a binary and can not be traced with batch -x.
> - I've done a "strace mpirun hostname" to see if it helps, but i
> am not
> able to see where the problem may be.
>
> Here is the exit from the strace:
> https://cloud.cesvima.upm.es/index.php/s/hWQMkwU5zW7J8RW
>
> And here the slurmd log with verbose level 5:
> Main node (slurmd log):
> 2019-06-06T09:51:54.255743+00:00 r1n1 slurmd[108517]:
> _run_prolog:
> run job script took usec=7
> 2019-06-06T09:51:54.256118+00:00 r1n1 slurmd[108517]:
> _run_prolog:
> prolog with lock for job 11057 ran for 0 seconds
> 2019-06-06T09:51:54.258887+00:00 r1n1 slurmd[108517]:
> task_p_slurmd_batch_request: 11057
> 2019-06-06T09:51:54.259317+00:00 r1n1 slurmd[108517]:
> task/affinity: job 11057 CPU input mask for node: 0x0000000001
> 2019-06-06T09:51:54.259680+00:00 r1n1 slurmd[108517]:
> task/affinity: job 11057 CPU final HW mask for node: 0x0000000001
> 2019-06-06T09:51:54.279614+00:00 r1n1 slurmstepd[108548]: task
> affinity plugin loaded with CPU mask
> 000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000ffffffffff
> 2019-06-06T09:51:54.280312+00:00 r1n1 slurmstepd[108548]: Munge
> credential signature plugin loaded
> 2019-06-06T09:51:54.302921+00:00 r1n1 slurmstepd[108548]:
> task/cgroup: /slurm/uid_2000/job_11057: alloc=1024MB mem.limit=1024MB
> memsw.limit=unlimited
> 2019-06-06T09:51:54.303592+00:00 r1n1 slurmstepd[108548]:
> task/cgroup: /slurm/uid_2000/job_11057/step_extern: alloc=1024MB
> mem.limit=1024MB memsw.limit=unlimited
> 2019-06-06T09:51:54.330322+00:00 r1n1 slurmd[108517]: Launching
> batch job 11057 for UID 2000
> 2019-06-06T09:51:54.353196+00:00 r1n1 slurmstepd[108556]: task
> affinity plugin loaded with CPU mask
> 000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000ffffffffff
> 2019-06-06T09:51:54.353899+00:00 r1n1 slurmstepd[108556]: Munge
> credential signature plugin loaded
> 2019-06-06T09:51:54.366478+00:00 r1n1 slurmstepd[108556]:
> task/cgroup: /slurm/uid_2000/job_11057: alloc=1024MB mem.limit=1024MB
> memsw.limit=unlimited
> 2019-06-06T09:51:54.366755+00:00 r1n1 slurmstepd[108556]:
> task/cgroup: /slurm/uid_2000/job_11057/step_batch: alloc=1024MB
> mem.limit=1024MB memsw.limit=unlimited
> 2019-06-06T09:51:54.393325+00:00 r1n1 slurmstepd[108556]: debug
> level = 2
> 2019-06-06T09:51:54.393754+00:00 r1n1 slurmstepd[108556]:
> starting
> 1 tasks
> 2019-06-06T09:51:54.401243+00:00 r1n1 slurmstepd[108556]: task 0
> (108561) started 2019-06-06T09:51:54
> 2019-06-06T09:51:54.416396+00:00 r1n1 slurmstepd[108561]:
> task_p_pre_launch: Using sched_affinity for tasks
> 2019-06-06T09:51:56.514908+00:00 r1n1 slurmstepd[108556]: task 0
> (108561) exited with exit code 1.
> 2019-06-06T09:51:56.554430+00:00 r1n1 slurmstepd[108556]: job
> 11057
> completed with slurm_rc = 0, job_rc = 256
> 2019-06-06T09:51:56.554847+00:00 r1n1 slurmstepd[108556]:
> sending
> REQUEST_COMPLETE_BATCH_SCRIPT, error:0 status:256
> 2019-06-06T09:51:56.559856+00:00 r1n1 slurmstepd[108556]:
> done with job
> 2019-06-06T09:51:56.596762+00:00 r1n1 slurmstepd[108548]: Sent
> signal 18 to 11057.4294967295
> 2019-06-06T09:51:56.598072+00:00 r1n1 slurmstepd[108548]: Sent
> signal 15 to 11057.4294967295
> 2019-06-06T09:51:56.599141+00:00 r1n1 slurmstepd[108548]:
> _oom_event_monitor: oom-kill event count: 1
> 2019-06-06T09:51:56.641170+00:00 r1n1 slurmstepd[108548]:
> done with job
>
> Secundary node (slurmd log):
> 2019-06-06T09:51:54.256047+00:00 r1n2 slurmd[84916]:
> _run_prolog:
> run job script took usec=7
> 2019-06-06T09:51:54.256432+00:00 r1n2 slurmd[84916]:
> _run_prolog:
> prolog with lock for job 11057 ran for 0 seconds
> 2019-06-06T09:51:54.279763+00:00 r1n2 slurmstepd[84954]: task
> affinity plugin loaded with CPU mask
> 000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000ffffffffff
> 2019-06-06T09:51:54.280448+00:00 r1n2 slurmstepd[84954]: Munge
> credential signature plugin loaded
> 2019-06-06T09:51:54.313852+00:00 r1n2 slurmstepd[84954]:
> task/cgroup: /slurm/uid_2000/job_11057: alloc=1024MB mem.limit=1024MB
> memsw.limit=unlimited
> 2019-06-06T09:51:54.314502+00:00 r1n2 slurmstepd[84954]:
> task/cgroup: /slurm/uid_2000/job_11057/step_extern: alloc=1024MB
> mem.limit=1024MB memsw.limit=unlimited
> 2019-06-06T09:51:56.564758+00:00 r1n2 slurmstepd[84954]: Sent
> signal 18 to 11057.4294967295
> 2019-06-06T09:51:56.608028+00:00 r1n2 slurmstepd[84954]: Sent
> signal 15 to 11057.4294967295
> 2019-06-06T09:51:56.609259+00:00 r1n2 slurmstepd[84954]:
> _oom_event_monitor: oom-kill event count: 1
> 2019-06-06T09:51:56.638334+00:00 r1n2 slurmstepd[84954]: done
> with job
>
> Thank you very much again.
>
> --
> Andrés Marín Díaz
>
> Servicio de Infraestructura e Innovación
> Universidad Politécnica de Madrid
>
> Centro de Supercomputación y Visualización de Madrid (CeSViMa)
> Campus de Montegancedo. 28223, Pozuelo de Alarcón, Madrid (ES)
> amarin at cesvima.upm.es <mailto:amarin at cesvima.upm.es> | tel 910679676
>
> www.cesvima.upm.es <http://www.cesvima.upm.es> |
> www.twitter.com/cesvima <http://www.twitter.com/cesvima> |
> www.fb.com/cesvima <http://www.fb.com/cesvima>
>
>
>
--
Andrés Marín Díaz
Servicio de Infraestructura e Innovación
Universidad Politécnica de Madrid
Centro de Supercomputación y Visualización de Madrid (CeSViMa)
Campus de Montegancedo. 28223, Pozuelo de Alarcón, Madrid (ES)
amarin at cesvima.upm.es | tel 910679676
www.cesvima.upm.es | www.twitter.com/cesvima | www.fb.com/cesvima
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