> On Dec 7, 2017, at 3:26 PM, Artem Polyakov <artpo...@gmail.com> wrote:
>
> 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 <gwol...@njit.edu
> <mailto:gwol...@njit.edu>>:
>> On Dec 7, 2017, at 1:18 PM, Artem Polyakov <artpo...@gmail.com
>> <mailto:artpo...@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
export OMPI_MCA_btl=tcp,self
export OMPI_MCA_pml=ob1
srun --nodes=8 --ntasks-per-node=8 --ntasks=64 --mpi=pmi2 ./ep.C.64
This works —
AS Parallel Benchmarks 3.3 -- EP Benchmark
Number of random numbers generated: 8589934592
Number of active processes: 64
EP Benchmark Results:
CPU Time = 5.9208
N = 2^ 32
No. Gaussian Pairs = 3373275903.
Sums = 4.764367927992081D+04 -8.084072988045549D+04
Counts:
0 1572172634.
1 1501108549.
2 281805648.
3 17761221.
4 424017.
5 3821.
6 13.
7 0.
8 0.
9 0.
EP Benchmark Completed.
Class = C
Size = 8589934592
Iterations = 0
Time in seconds = 5.92
Total processes = 64
Compiled procs = 64
Mop/s total = 1450.82
Mop/s/process = 22.67
Operation type = Random numbers generated
Verification = SUCCESSFUL
Version = 3.3.1
Compile date = 07 Dec 2017
Compile options:
MPIF77 = mpif77
FLINK = $(MPIF77)
FMPI_LIB = -L/opt/local/easybuild/software/Compiler/GC...
FMPI_INC = -I/opt/local/easybuild/software/Compiler/GC...
FFLAGS = -O
FLINKFLAGS = -O
RAND = randi8
Please send feedbacks and/or the results of this run to:
NPB Development Team
Internet: n...@nas.nasa.gov
Hmm...
> 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
> gwol...@snode2.p-stheno.tartan.njit.edu
> <mailto:gwol...@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
> gwol...@snode2.p-stheno.tartan.njit.edu
> <mailto:gwol...@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
> gwol...@snode2.p-stheno.tartan.njit.edu
> <mailto:gwol...@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
> gwol...@snode2.p-stheno.tartan.njit.edu
> <mailto:gwol...@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
> gwol...@snode2.p-stheno.tartan.njit.edu
> <mailto:gwol...@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
> gwol...@snode2.p-stheno.tartan.njit.edu
> <mailto:gwol...@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
> gwol...@snode2.p-stheno.tartan.njit.edu
> <mailto:gwol...@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
> gwol...@snode2.p-stheno.tartan.njit.edu
> <mailto:gwol...@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
> gwol...@snode2.p-stheno.tartan.njit.edu
> <mailto:gwol...@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
> gwol...@snode2.p-stheno.tartan.njit.edu
> <mailto:gwol...@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
> gwol...@snode2.p-stheno.tartan.njit.edu
> <mailto:gwol...@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
> gwol...@snode2.p-stheno.tartan.njit.edu
> <mailto:gwol...@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
> gwol...@snode2.p-stheno.tartan.njit.edu
> <mailto:gwol...@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
> gwol...@snode2.p-stheno.tartan.njit.edu
> <mailto:gwol...@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
> gwol...@snode2.p-stheno.tartan.njit.edu
> <mailto:gwol...@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
> gwol...@snode2.p-stheno.tartan.njit.edu
> <mailto:gwol...@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
> gwol...@snode2.p-stheno.tartan.njit.edu
> <mailto:gwol...@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
> gwol...@snode2.p-stheno.tartan.njit.edu
> <mailto:gwol...@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
> gwol...@snode2.p-stheno.tartan.njit.edu
> <mailto:gwol...@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
> gwol...@snode2.p-stheno.tartan.njit.edu
> <mailto:gwol...@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
> gwol...@snode2.p-stheno.tartan.njit.edu
> <mailto:gwol...@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
> gwol...@snode2.p-stheno.tartan.njit.edu
> <mailto:gwol...@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
> gwol...@snode2.p-stheno.tartan.njit.edu
> <mailto:gwol...@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
> gwol...@snode2.p-stheno.tartan.njit.edu
> <mailto:gwol...@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
> gwol...@snode2.p-stheno.tartan.njit.edu
> <mailto:gwol...@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
> gwol...@snode2.p-stheno.tartan.njit.edu
> <mailto:gwol...@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
> gwol...@snode2.p-stheno.tartan.njit.edu
> <mailto:gwol...@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
> gwol...@snode2.p-stheno.tartan.njit.edu
> <mailto:gwol...@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
> gwol...@snode2.p-stheno.tartan.njit.edu
> <mailto:gwol...@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
> gwol...@snode2.p-stheno.tartan.njit.edu
> <mailto:gwol...@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
> gwol...@snode2.p-stheno.tartan.njit.edu
> <mailto:gwol...@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
> gwol...@snode2.p-stheno.tartan.njit.edu
> <mailto:gwol...@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 <gwol...@njit.edu
>> <mailto:gwol...@njit.edu>>:
>>
>>
>>> On Dec 7, 2017, at 12:51 PM, Artem Polyakov <artpo...@gmail.com
>>> <mailto:artpo...@gmail.com>> wrote:
>>>
>>> also please post the output of
>>> $ srun --mpi=list
>>
>> [gwolosh@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 <artpo...@gmail.com
>>> <mailto:artpo...@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 <gwol...@njit.edu
>>> <mailto:gwol...@njit.edu>>:
>>> Hello
>>>
>>> This is using Slurm version - 17.02.6 running on Scientific Linux release
>>> 7.4 (Nitrogen)
>>>
>>> [gwolosh@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>
>>> gwol...@njit.edu <mailto:gwol...@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)
