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 <ama...@cesvima.upm.es
<mailto:ama...@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)
ama...@cesvima.upm.es <mailto:ama...@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)
ama...@cesvima.upm.es | tel 910679676
www.cesvima.upm.es | www.twitter.com/cesvima | www.fb.com/cesvima
