[slurm-users] NAS benchmarks - problem with openmpi, slurm and pmi

Thu Dec 7 13:00:10 MST 2017


> On Dec 7, 2017, at 1:18 PM, Artem Polyakov <artpol84 at gmail.com> wrote:
> 
> Couple of things to try to locate the issue:
> 
> 1. To make sure that PMI is not working: have you tried to run something simple (like hello_world (https://github.com/open-mpi/ompi/blob/master/examples/hello_c.c <https://github.com/open-mpi/ompi/blob/master/examples/hello_c.c>) and ring (https://github.com/open-mpi/ompi/blob/master/examples/ring_c.c <https://github.com/open-mpi/ompi/blob/master/examples/ring_c.c>). Please try to run those two and post the results.
> 2. If hello is working and ring is not can you try to change the fabric to TCP: 
> $ export OMPI_MCA_btl=tcp,self
> $ export OMPI_MCA_pml=ob1
> $ srun ...
> 
> Please provide the outputs

srun --mpi=pmi2 --ntasks-per-node=8 --ntasks=16 ./hello_c > hello_c.out

Hello, world, I am 24 of 32, (Open MPI v1.10.3, package: Open MPI gwolosh at snode2.p-stheno.tartan.njit.edu Distribution, ident: 1.10.3, repo rev: v1.10.2-251-g9acf492, Jun 14, 2016, 150)
Hello, world, I am 0 of 32, (Open MPI v1.10.3, package: Open MPI gwolosh at snode2.p-stheno.tartan.njit.edu Distribution, ident: 1.10.3, repo rev: v1.10.2-251-g9acf492, Jun 14, 2016, 150)
Hello, world, I am 25 of 32, (Open MPI v1.10.3, package: Open MPI gwolosh at snode2.p-stheno.tartan.njit.edu Distribution, ident: 1.10.3, repo rev: v1.10.2-251-g9acf492, Jun 14, 2016, 150)
Hello, world, I am 1 of 32, (Open MPI v1.10.3, package: Open MPI gwolosh at snode2.p-stheno.tartan.njit.edu Distribution, ident: 1.10.3, repo rev: v1.10.2-251-g9acf492, Jun 14, 2016, 150)
Hello, world, I am 27 of 32, (Open MPI v1.10.3, package: Open MPI gwolosh at snode2.p-stheno.tartan.njit.edu Distribution, ident: 1.10.3, repo rev: v1.10.2-251-g9acf492, Jun 14, 2016, 150)
Hello, world, I am 2 of 32, (Open MPI v1.10.3, package: Open MPI gwolosh at snode2.p-stheno.tartan.njit.edu Distribution, ident: 1.10.3, repo rev: v1.10.2-251-g9acf492, Jun 14, 2016, 150)
Hello, world, I am 29 of 32, (Open MPI v1.10.3, package: Open MPI gwolosh at snode2.p-stheno.tartan.njit.edu Distribution, ident: 1.10.3, repo rev: v1.10.2-251-g9acf492, Jun 14, 2016, 150)
Hello, world, I am 31 of 32, (Open MPI v1.10.3, package: Open MPI gwolosh at snode2.p-stheno.tartan.njit.edu Distribution, ident: 1.10.3, repo rev: v1.10.2-251-g9acf492, Jun 14, 2016, 150)
Hello, world, I am 30 of 32, (Open MPI v1.10.3, package: Open MPI gwolosh at snode2.p-stheno.tartan.njit.edu Distribution, ident: 1.10.3, repo rev: v1.10.2-251-g9acf492, Jun 14, 2016, 150)
Hello, world, I am 4 of 32, (Open MPI v1.10.3, package: Open MPI gwolosh at snode2.p-stheno.tartan.njit.edu Distribution, ident: 1.10.3, repo rev: v1.10.2-251-g9acf492, Jun 14, 2016, 150)
Hello, world, I am 5 of 32, (Open MPI v1.10.3, package: Open MPI gwolosh at snode2.p-stheno.tartan.njit.edu Distribution, ident: 1.10.3, repo rev: v1.10.2-251-g9acf492, Jun 14, 2016, 150)
Hello, world, I am 17 of 32, (Open MPI v1.10.3, package: Open MPI gwolosh at snode2.p-stheno.tartan.njit.edu Distribution, ident: 1.10.3, repo rev: v1.10.2-251-g9acf492, Jun 14, 2016, 150)
Hello, world, I am 3 of 32, (Open MPI v1.10.3, package: Open MPI gwolosh at snode2.p-stheno.tartan.njit.edu Distribution, ident: 1.10.3, repo rev: v1.10.2-251-g9acf492, Jun 14, 2016, 150)
Hello, world, I am 7 of 32, (Open MPI v1.10.3, package: Open MPI gwolosh at snode2.p-stheno.tartan.njit.edu Distribution, ident: 1.10.3, repo rev: v1.10.2-251-g9acf492, Jun 14, 2016, 150)
Hello, world, I am 6 of 32, (Open MPI v1.10.3, package: Open MPI gwolosh at snode2.p-stheno.tartan.njit.edu Distribution, ident: 1.10.3, repo rev: v1.10.2-251-g9acf492, Jun 14, 2016, 150)
Hello, world, I am 18 of 32, (Open MPI v1.10.3, package: Open MPI gwolosh at snode2.p-stheno.tartan.njit.edu Distribution, ident: 1.10.3, repo rev: v1.10.2-251-g9acf492, Jun 14, 2016, 150)
Hello, world, I am 22 of 32, (Open MPI v1.10.3, package: Open MPI gwolosh at snode2.p-stheno.tartan.njit.edu Distribution, ident: 1.10.3, repo rev: v1.10.2-251-g9acf492, Jun 14, 2016, 150)
Hello, world, I am 23 of 32, (Open MPI v1.10.3, package: Open MPI gwolosh at snode2.p-stheno.tartan.njit.edu Distribution, ident: 1.10.3, repo rev: v1.10.2-251-g9acf492, Jun 14, 2016, 150)
Hello, world, I am 19 of 32, (Open MPI v1.10.3, package: Open MPI gwolosh at snode2.p-stheno.tartan.njit.edu Distribution, ident: 1.10.3, repo rev: v1.10.2-251-g9acf492, Jun 14, 2016, 150)
Hello, world, I am 9 of 32, (Open MPI v1.10.3, package: Open MPI gwolosh at snode2.p-stheno.tartan.njit.edu Distribution, ident: 1.10.3, repo rev: v1.10.2-251-g9acf492, Jun 14, 2016, 150)
Hello, world, I am 20 of 32, (Open MPI v1.10.3, package: Open MPI gwolosh at snode2.p-stheno.tartan.njit.edu Distribution, ident: 1.10.3, repo rev: v1.10.2-251-g9acf492, Jun 14, 2016, 150)
Hello, world, I am 8 of 32, (Open MPI v1.10.3, package: Open MPI gwolosh at snode2.p-stheno.tartan.njit.edu Distribution, ident: 1.10.3, repo rev: v1.10.2-251-g9acf492, Jun 14, 2016, 150)
Hello, world, I am 10 of 32, (Open MPI v1.10.3, package: Open MPI gwolosh at snode2.p-stheno.tartan.njit.edu Distribution, ident: 1.10.3, repo rev: v1.10.2-251-g9acf492, Jun 14, 2016, 150)
Hello, world, I am 13 of 32, (Open MPI v1.10.3, package: Open MPI gwolosh at snode2.p-stheno.tartan.njit.edu Distribution, ident: 1.10.3, repo rev: v1.10.2-251-g9acf492, Jun 14, 2016, 150)
Hello, world, I am 11 of 32, (Open MPI v1.10.3, package: Open MPI gwolosh at snode2.p-stheno.tartan.njit.edu Distribution, ident: 1.10.3, repo rev: v1.10.2-251-g9acf492, Jun 14, 2016, 150)
Hello, world, I am 26 of 32, (Open MPI v1.10.3, package: Open MPI gwolosh at snode2.p-stheno.tartan.njit.edu Distribution, ident: 1.10.3, repo rev: v1.10.2-251-g9acf492, Jun 14, 2016, 150)
Hello, world, I am 16 of 32, (Open MPI v1.10.3, package: Open MPI gwolosh at snode2.p-stheno.tartan.njit.edu Distribution, ident: 1.10.3, repo rev: v1.10.2-251-g9acf492, Jun 14, 2016, 150)
Hello, world, I am 14 of 32, (Open MPI v1.10.3, package: Open MPI gwolosh at snode2.p-stheno.tartan.njit.edu Distribution, ident: 1.10.3, repo rev: v1.10.2-251-g9acf492, Jun 14, 2016, 150)
Hello, world, I am 28 of 32, (Open MPI v1.10.3, package: Open MPI gwolosh at snode2.p-stheno.tartan.njit.edu Distribution, ident: 1.10.3, repo rev: v1.10.2-251-g9acf492, Jun 14, 2016, 150)
Hello, world, I am 21 of 32, (Open MPI v1.10.3, package: Open MPI gwolosh at snode2.p-stheno.tartan.njit.edu Distribution, ident: 1.10.3, repo rev: v1.10.2-251-g9acf492, Jun 14, 2016, 150)
Hello, world, I am 15 of 32, (Open MPI v1.10.3, package: Open MPI gwolosh at snode2.p-stheno.tartan.njit.edu Distribution, ident: 1.10.3, repo rev: v1.10.2-251-g9acf492, Jun 14, 2016, 150)
Hello, world, I am 12 of 32, (Open MPI v1.10.3, package: Open MPI gwolosh at snode2.p-stheno.tartan.njit.edu Distribution, ident: 1.10.3, repo rev: v1.10.2-251-g9acf492, Jun 14, 2016, 150)

 srun --mpi=pmi2 --ntasks-per-node=8 --ntasks=16 --nodes=2 ./ring_c > ring_c.out

Process 1 exiting
Process 12 exiting
Process 14 exiting
Process 13 exiting
Process 3 exiting
Process 11 exiting
Process 5 exiting
Process 6 exiting
Process 2 exiting
Process 4 exiting
Process 9 exiting
Process 10 exiting
Process 7 exiting
Process 15 exiting
Process 0 sending 10 to 1, tag 201 (16 processes in ring)
Process 0 sent to 1
Process 0 decremented value: 9
Process 0 decremented value: 8
Process 0 decremented value: 7
Process 0 decremented value: 6
Process 0 decremented value: 5
Process 0 decremented value: 4
Process 0 decremented value: 3
Process 0 decremented value: 2
Process 0 decremented value: 1
Process 0 decremented value: 0
Process 0 exiting
Process 8 exiting

> 
> 2017-12-07 10:05 GMT-08:00 Glenn (Gedaliah) Wolosh <gwolosh at njit.edu <mailto:gwolosh at njit.edu>>:
> 
> 
>> On Dec 7, 2017, at 12:51 PM, Artem Polyakov <artpol84 at gmail.com <mailto:artpol84 at gmail.com>> wrote:
>> 
>> also please post the output of
>> $ srun --mpi=list
> 
> [gwolosh at p-slogin bin]$ srun --mpi=list
> srun: MPI types are...
> srun: mpi/mpich1_shmem
> srun: mpi/mpich1_p4
> srun: mpi/lam
> srun: mpi/openmpi
> srun: mpi/none
> srun: mpi/mvapich
> srun: mpi/mpichmx
> srun: mpi/pmi2
> srun: mpi/mpichgm
> 
> 
>> 
>> When job crashes - is there any error messages in the relevant slurmd.log's or output on the screen?
> 
> on screen —
> 
> [snode4][[274,1],24][connect/btl_openib_connect_udcm.c:1448:udcm_wait_for_send_completion] send failed with verbs status 2
> [snode4:5175] *** An error occurred in MPI_Bcast
> [snode4:5175] *** reported by process [17956865,24]
> [snode4:5175] *** on communicator MPI_COMM_WORLD
> [snode4:5175] *** MPI_ERR_OTHER: known error not in list
> [snode4:5175] *** MPI_ERRORS_ARE_FATAL (processes in this communicator will now abort,
> [snode4:5175] ***    and potentially your MPI job)
> mlx4: local QP operation err (QPN 0005f3, WQE index 40000, vendor syndrome 6c, opcode = 5e)
> srun: Job step aborted: Waiting up to 32 seconds for job step to finish.
> [snode4][[274,1],31][connect/btl_openib_connect_udcm.c:1448:udcm_wait_for_send_completion] send failed with verbs status 2
> slurmstepd: error: *** STEP 274.0 ON snode1 CANCELLED AT 2017-12-07T12:55:46 ***
> [snode4:5182] *** An error occurred in MPI_Bcast
> [snode4:5182] *** reported by process [17956865,31]
> [snode4:5182] *** on communicator MPI_COMM_WORLD
> [snode4:5182] *** MPI_ERR_OTHER: known error not in list
> [snode4:5182] *** MPI_ERRORS_ARE_FATAL (processes in this communicator will now abort,
> [snode4:5182] ***    and potentially your MPI job)
> mlx4: local QP operation err (QPN 0005f7, WQE index 40000, vendor syndrome 6c, opcode = 5e)
> [snode4][[274,1],27][connect/btl_openib_connect_udcm.c:1448:udcm_wait_for_send_completion] send failed with verbs status 2
> [snode4:5178] *** An error occurred in MPI_Bcast
> [snode4:5178] *** reported by process [17956865,27]
> [snode4:5178] *** on communicator MPI_COMM_WORLD
> [snode4:5178] *** MPI_ERR_OTHER: known error not in list
> [snode4:5178] *** MPI_ERRORS_ARE_FATAL (processes in this communicator will now abort,
> [snode4:5178] ***    and potentially your MPI job)
> mlx4: local QP operation err (QPN 0005fa, WQE index 40000, vendor syndrome 6c, opcode = 5e)
> srun: error: snode4: tasks 24,31: Exited with exit code 16
> srun: error: snode4: tasks 25-30: Killed
> srun: error: snode5: tasks 32-39: Killed
> srun: error: snode3: tasks 16-23: Killed
> srun: error: snode8: tasks 56-63: Killed
> srun: error: snode7: tasks 48-55: Killed
> srun: error: snode1: tasks 0-7: Killed
> srun: error: snode2: tasks 8-15: Killed
> srun: error: snode6: tasks 40-47: Killed
> 
> Nothing striking in the slurmd log
> 
> 
>> 
>> 2017-12-07 9:49 GMT-08:00 Artem Polyakov <artpol84 at gmail.com <mailto:artpol84 at gmail.com>>:
>> Hello,
>> 
>> what is the value of MpiDefault option in your Slurm configuration file?
>> 
>> 2017-12-07 9:37 GMT-08:00 Glenn (Gedaliah) Wolosh <gwolosh at njit.edu <mailto:gwolosh at njit.edu>>:
>> Hello
>> 
>> This is using Slurm version - 17.02.6 running on Scientific Linux release 7.4 (Nitrogen)
>> 
>> [gwolosh at p-slogin bin]$ module li
>> 
>> Currently Loaded Modules:
>>   1) GCCcore/.5.4.0 (H)   2) binutils/.2.26 (H)   3) GCC/5.4.0-2.26   4) numactl/2.0.11   5) hwloc/1.11.3   6) OpenMPI/1.10.3
>> 
>> If I run
>> 
>> srun --nodes=8 --ntasks-per-node=8 --ntasks=64  ./ep.C.64
>> 
>> It runs successfuly but I get a message —
>> 
>> PMI2 initialized but returned bad values for size/rank/jobid.
>> This is symptomatic of either a failure to use the
>> "--mpi=pmi2" flag in SLURM, or a borked PMI2 installation.
>> If running under SLURM, try adding "-mpi=pmi2" to your
>> srun command line. If that doesn't work, or if you are
>> not running under SLURM, try removing or renaming the
>> pmi2.h header file so PMI2 support will not automatically
>> be built, reconfigure and build OMPI, and then try again
>> with only PMI1 support enabled.
>> 
>> If I run
>> 
>> srun --nodes=8 --ntasks-per-node=8 --ntasks=64  —mpi=pmi2 ./ep.C.64
>> 
>> The job crashes
>> 
>> If I run via sbatch —
>> 
>> #!/bin/bash
>> # Job name:
>> #SBATCH --job-name=nas_bench
>> #SBATCH --nodes=8
>> #SBATCH --ntasks=64
>> #SBATCH --ntasks-per-node=8
>> #SBATCH --time=48:00:00
>> #SBATCH --output=nas.out.1
>> #
>> ## Command(s) to run (example):
>> module use $HOME/easybuild/modules/all/Core
>> module load GCC/5.4.0-2.26 OpenMPI/1.10.3
>> mpirun -np 64  ./ep.C.64
>> 
>> the job crashes
>> 
>> Using easybuild, these are my config options for ompi —
>> 
>> configopts = '--with-threads=posix --enable-shared --enable-mpi-thread-multiple --with-verbs '
>> configopts += '--enable-mpirun-prefix-by-default '  # suppress failure modes in relation to mpirun path
>> configopts += '--with-hwloc=$EBROOTHWLOC '  # hwloc support
>> configopts += '--disable-dlopen '  # statically link component, don't do dynamic loading
>> configopts += '--with-slurm --with-pmi ‘
>> 
>> And finally —
>> 
>> $ ldd /opt/local/easybuild/software/Compiler/GCC/5.4.0-2.26/OpenMPI/1.10.3/bin/orterun | grep pmi
>>         libpmi.so.0 => /usr/lib64/libpmi.so.0 (0x00007f0129d6d000)
>>         libpmi2.so.0 => /usr/lib64/libpmi2.so.0 (0x00007f0129b51000)
>> 
>> $ ompi_info | grep pmi
>>                   MCA db: pmi (MCA v2.0.0, API v1.0.0, Component v1.10.3)
>>                  MCA ess: pmi (MCA v2.0.0, API v3.0.0, Component v1.10.3)
>>              MCA grpcomm: pmi (MCA v2.0.0, API v2.0.0, Component v1.10.3)
>>               MCA pubsub: pmi (MCA v2.0.0, API v2.0.0, Component v1.10.3)
>> 
>> 
>> Any suggestions?
>> _______________
>> Gedaliah Wolosh
>> IST Academic and Research Computing Systems (ARCS)
>> NJIT
>> GITC 2203
>> 973 596 5437 <tel:(973)%20596-5437>
>> gwolosh at njit.edu <mailto:gwolosh at njit.edu>
>> 
>> 
>> 
>> 
>> -- 
>> С Уважением, Поляков Артем Юрьевич
>> Best regards, Artem Y. Polyakov
>> 
>> 
>> 
>> -- 
>> С Уважением, Поляков Артем Юрьевич
>> Best regards, Artem Y. Polyakov
> 
> 
> 
> 
> -- 
> С Уважением, Поляков Артем Юрьевич
> Best regards, Artem Y. Polyakov

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