Lost a line… Also helpful to check
$ srun -N3 which ompi_info From: users [mailto:users-boun...@lists.open-mpi.org] On Behalf Of Riebs, Andy via users Sent: Monday, April 27, 2020 10:59 AM To: Open MPI Users <users@lists.open-mpi.org> Cc: Riebs, Andy <andy.ri...@hpe.com> Subject: Re: [OMPI users] Can't start jobs with srun. Y’know, a quick check on versions and PATHs might be a good idea here. I suggest something like $ srun -N3 ompi_info |& grep "MPI repo" to confirm that all nodes are running the same version of OMPI. From: users [mailto:users-boun...@lists.open-mpi.org] On Behalf Of Prentice Bisbal via users Sent: Monday, April 27, 2020 10:25 AM To: users@lists.open-mpi.org<mailto:users@lists.open-mpi.org> Cc: Prentice Bisbal <pbis...@pppl.gov<mailto:pbis...@pppl.gov>> Subject: Re: [OMPI users] [External] Re: Can't start jobs with srun. Ralph, PMI2 support works just fine. It's just PMIx that seems to be the problem. We rebuilt Slurm with PMIx 3.1.5, but the problem persists. I've opened a ticket with Slurm support to see if it's a problem on Slurm's end. Prentice On 4/26/20 2:12 PM, Ralph Castain via users wrote: It is entirely possible that the PMI2 support in OMPI v4 is broken - I doubt it is used or tested very much as pretty much everyone has moved to PMIx. In fact, we completely dropped PMI-1 and PMI-2 from OMPI v5 for that reason. I would suggest building Slurm with PMIx v3.1.5 (https://github.com/openpmix/openpmix/releases/tag/v3.1.5) as that is what OMPI v4 is using, and launching with "srun --mpi=pmix_v3" On Apr 26, 2020, at 10:07 AM, Patrick Bégou via users <users@lists.open-mpi.org<mailto:users@lists.open-mpi.org>> wrote: I have also this problem on servers I'm benching at DELL's lab with OpenMPI-4.0.3. I've tried a new build of OpenMPI with "--with-pmi2". No change. Finally my work around in the slurm script was to launch my code with mpirun. As mpirun was only finding one slot per nodes I have used "--oversubscribe --bind-to core" and checked that every process was binded on a separate core. It worked but do not ask me why :-) Patrick Le 24/04/2020 à 20:28, Riebs, Andy via users a écrit : Prentice, have you tried something trivial, like "srun -N3 hostname", to rule out non-OMPI problems? Andy -----Original Message----- From: users [mailto:users-boun...@lists.open-mpi.org] On Behalf Of Prentice Bisbal via users Sent: Friday, April 24, 2020 2:19 PM To: Ralph Castain <r...@open-mpi.org<mailto:r...@open-mpi.org>>; Open MPI Users <users@lists.open-mpi.org<mailto:users@lists.open-mpi.org>> Cc: Prentice Bisbal <pbis...@pppl.gov<mailto:pbis...@pppl.gov>> Subject: Re: [OMPI users] [External] Re: Can't start jobs with srun. Okay. I've got Slurm built with pmix support: $ srun --mpi=list srun: MPI types are... srun: none srun: pmix_v3 srun: pmi2 srun: openmpi srun: pmix But now when I try to launch a job with srun, the job appears to be running, but doesn't do anything - it just hangs in the running state but doesn't do anything. Any ideas what could be wrong, or how to debug this? I'm also asking around on the Slurm mailing list, too Prentice On 4/23/20 3:03 PM, Ralph Castain wrote: You can trust the --mpi=list. The problem is likely that OMPI wasn't configured --with-pmi2 On Apr 23, 2020, at 11:59 AM, Prentice Bisbal via users <users@lists.open-mpi.org<mailto:users@lists.open-mpi.org>> wrote: --mpi=list shows pmi2 and openmpi as valid values, but if I set --mpi= to either of them, my job still fails. Why is that? Can I not trust the output of --mpi=list? Prentice On 4/23/20 10:43 AM, Ralph Castain via users wrote: No, but you do have to explicitly build OMPI with non-PMIx support if that is what you are going to use. In this case, you need to configure OMPI --with-pmi2=<path-to-the-pmi2-installation> You can leave off the path if Slurm (i.e., just "--with-pmi2") was installed in a standard location as we should find it there. On Apr 23, 2020, at 7:39 AM, Prentice Bisbal via users <users@lists.open-mpi.org<mailto:users@lists.open-mpi.org>> wrote: It looks like it was built with PMI2, but not PMIx: $ srun --mpi=list srun: MPI types are... srun: none srun: pmi2 srun: openmpi I did launch the job with srun --mpi=pmi2 .... Does OpenMPI 4 need PMIx specifically? On 4/23/20 10:23 AM, Ralph Castain via users wrote: Is Slurm built with PMIx support? Did you tell srun to use it? On Apr 23, 2020, at 7:00 AM, Prentice Bisbal via users <users@lists.open-mpi.org<mailto:users@lists.open-mpi.org>> wrote: I'm using OpenMPI 4.0.3 with Slurm 19.05.5 I'm testing the software with a very simple hello, world MPI program that I've used reliably for years. When I submit the job through slurm and use srun to launch the job, I get these errors: *** An error occurred in MPI_Init *** on a NULL communicator *** MPI_ERRORS_ARE_FATAL (processes in this communicator will now abort, *** and potentially your MPI job) [dawson029.pppl.gov:26070<http://dawson029.pppl.gov:26070>] Local abort before MPI_INIT completed completed successfully, but am not able to aggregate error messages, and not able to guarantee that all other processes were killed! *** An error occurred in MPI_Init *** on a NULL communicator *** MPI_ERRORS_ARE_FATAL (processes in this communicator will now abort, *** and potentially your MPI job) [dawson029.pppl.gov:26076<http://dawson029.pppl.gov:26076>] Local abort before MPI_INIT completed completed successfully, but am not able to aggregate error messages, and not able to guarantee that all other processes were killed! If I run the same job, but use mpiexec or mpirun instead of srun, the jobs run just fine. I checked ompi_info to make sure OpenMPI was compiled with Slurm support: $ ompi_info | grep slurm Configure command line: '--prefix=/usr/pppl/intel/2019-pkgs/openmpi-4.0.3' '--disable-silent-rules' '--enable-shared' '--with-pmix=internal' '--with-slurm' '--with-psm' MCA ess: slurm (MCA v2.1.0, API v3.0.0, Component v4.0.3) MCA plm: slurm (MCA v2.1.0, API v2.0.0, Component v4.0.3) MCA ras: slurm (MCA v2.1.0, API v2.0.0, Component v4.0.3) MCA schizo: slurm (MCA v2.1.0, API v1.0.0, Component v4.0.3) Any ideas what could be wrong? Do you need any additional information? Prentice
