How did you compile SLURM? Did you add the contribs/pmi and/or contribs/pmi2 plugins to the install? Or did you use PMIx?
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 21:11, Andrés Marín Díaz <ama...@cesvima.upm.es<mailto:ama...@cesvima.upm.es>> wrote: 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<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>
