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

Thu Dec 7 13:26:00 MST 2017

Given that ring is working I don't think that it's a PMI problem.

Can you try running NPB with the tcp btl parameters that I've provided? (I
assume you have TCP interconnect, let me know if it's not a case).

чт, 7 дек. 2017 г. в 12:03, Glenn (Gedaliah) Wolosh <gwolosh at njit.edu>:

> 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) and ring
> (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>:
>
>>
>>
>> On Dec 7, 2017, at 12:51 PM, Artem Polyakov <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>:
>>
>>> 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>:
>>>
>>>> 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 <(973)%20596-5437>
>>>> 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
>
> --
----- Best regards, Artem Polyakov (Mobile mail)
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