[mpich-discuss] MPI_Comm_spawn crosses node boundaries
Mccall, Kurt E. (MSFC-EV41)
kurt.e.mccall at nasa.gov
Mon Feb 7 12:41:26 CST 2022
Ken,
To review, I configured as follows:
$ configure CFLAGS=-DUSE_PMI2_API LIBS=-lpmi2 --with-pm=none --with-pmi=slurm --with-slurm=/opt/slurm < ...>
and ran srun with the argument --mpi=pmi2.
The job is stil segfaulting in MPI_Comm_spawn in one process and returning an error from MPI_Barrier in the other. Error messages below:
The MPI_Comm_spawn error:
backtrace for error: backtrace after receiving signal SIGSEGV:
/home/kmccall/Needles2/./NeedlesMpiMM() [0x45ab36]
/lib64/libpthread.so.0(+0x12c20) [0x7f4833387c20]
/lib64/libc.so.6(+0x15d6b7) [0x7f483310d6b7]
/lib64/libc.so.6(__strdup+0x12) [0x7f4833039802]
/lib64/libpmi2.so.0(+0x171c) [0x7f483294371c]
/lib64/libpmi2.so.0(+0x185e) [0x7f483294385e]
/lib64/libpmi2.so.0(PMI2_Job_Spawn+0x1a7) [0x7f48329453d8]
/home/kmccall/mpich-slurm-install-4.0_2/lib/libmpi.so.12(+0x23a7db) [0x7f4834e0a7db]
/home/kmccall/mpich-slurm-install-4.0_2/lib/libmpi.so.12(+0x1fc805) [0x7f4834dcc805]
/home/kmccall/mpich-slurm-install-4.0_2/lib/libmpi.so.12(MPI_Comm_spawn+0x507) [0x7f4834cea9f7]
The MPI_Barrier error:
MPI_Barrier returned the error MPI runtime error: Unknown error class, error stack:
internal_Barrier(84).......................: MPI_Barrier(MPI_COMM_WORLD) failed
MPIR_Barrier_impl(91)......................:
MPIR_Barrier_allcomm_auto(45)..............:
MPIR_Barrier_intra_dissemination(39).......:
MPIDI_CH3U_Complete_posted_with_error(1090): Process failed
Thanks,
Kurt
-----Original Message-----
From: Raffenetti, Ken <raffenet at anl.gov>
Sent: Friday, February 4, 2022 4:08 PM
To: Mccall, Kurt E. (MSFC-EV41) <kurt.e.mccall at nasa.gov>; discuss at mpich.org
Subject: [EXTERNAL] Re: [mpich-discuss] MPI_Comm_spawn crosses node boundaries
:(. We need to link -lpmi2 instead of -lpmi. This really needs a patch in our configure script, but adding this to your configure is worth a shot:
LIBS=-lpmi2
Ken
On 2/4/22, 1:56 PM, "Mccall, Kurt E. (MSFC-EV41)" <kurt.e.mccall at nasa.gov> wrote:
I added the CFLAGS argument and the configuration completed, but make ended with a link error.
lib/.libs/libmpi.so: undefined reference to `PMI2_Abort'
lib/.libs/libmpi.so: undefined reference to `PMI2_Info_GetJobAttr'
lib/.libs/libmpi.so: undefined reference to `PMI2_Job_Spawn'
lib/.libs/libmpi.so: undefined reference to `PMI2_Nameserv_publish'
lib/.libs/libmpi.so: undefined reference to `PMI2_Finalize'
lib/.libs/libmpi.so: undefined reference to `PMI2_KVS_Put'
lib/.libs/libmpi.so: undefined reference to `PMI2_Info_GetNodeAttr'
lib/.libs/libmpi.so: undefined reference to `PMI2_KVS_Get'
lib/.libs/libmpi.so: undefined reference to `PMI2_KVS_Fence'
lib/.libs/libmpi.so: undefined reference to `PMI2_Nameserv_unpublish'
lib/.libs/libmpi.so: undefined reference to `PMI2_Info_PutNodeAttr'
lib/.libs/libmpi.so: undefined reference to `PMI2_Job_GetId'
lib/.libs/libmpi.so: undefined reference to `PMI2_Init'
lib/.libs/libmpi.so: undefined reference to `PMI2_Nameserv_lookup'
collect2: error: ld returned 1 exit status
-----Original Message-----
From: Raffenetti, Ken <raffenet at anl.gov>
Sent: Friday, February 4, 2022 1:23 PM
To: Mccall, Kurt E. (MSFC-EV41) <kurt.e.mccall at nasa.gov>; discuss at mpich.org
Subject: [EXTERNAL] Re: [mpich-discuss] MPI_Comm_spawn crosses node boundaries
I think I see a new issue. The Slurm website documentation says that their PMI library doesn't support PMI_Spawn_multiple from the PMI 1 API. We can try to force PMI 2 and see what happens. Try adding this to your configure line.
CFLAGS=-DUSE_PMI2_API
Ken
On 2/4/22, 11:58 AM, "Mccall, Kurt E. (MSFC-EV41)" <kurt.e.mccall at nasa.gov> wrote:
Did that, and launched the job with "srun --mpi=none" and one of the processes failed when MPI_Comm_spawn was called. Note the :
internal_Comm_spawn(101)......: MPI_Comm_spawn(command=NeedlesMpiMM, argv=0x226b030, maxprocs=1, info=0x9c000000, 0, MPI_COMM_SELF, intercomm=0x7ffffda9448c, array_of_errcodes=0x7ffffda94378) failed
MPIDI_Comm_spawn_multiple(225): PMI_Spawn_multiple returned -1
The other process failed when MPI_Barrier was called:
internal_Barrier(84).......................: MPI_Barrier(MPI_COMM_WORLD) failed
MPIR_Barrier_impl(91)......................:
MPIR_Barrier_allcomm_auto(45)..............:
MPIR_Barrier_intra_dissemination(39).......:
MPIDI_CH3U_Complete_posted_with_error(1090): Process failed
MPI runtime error: Unknown error class, error stack:
internal_Barrier(84).......................: MPI_Barrier(MPI_COMM_WORLD) failed
MPIR_Barrier_impl(91)......................:
MPIR_Barrier_allcomm_auto(45)..............:
MPIR_Barrier_intra_dissemination(39).......:
MPIDI_CH3U_Complete_posted_with_error(1090): Process failed
MPI runtime error: Unknown error class, error stack:
internal_Barrier(84).......................: MPI_Barrier(MPI_COMM_WORLD) failed
MPIR_Barrier_impl(91)......................:
MPIR_Barrier_allcomm_auto(45)..............:
MPIR_Barrier_intra_dissemination(39).......:
MPIDI_CH3U_Complete_posted_with_error(1090): Process failed
MPI manager 1 threw exception: MPI runtime error: Unknown error class, error stack:
internal_Barrier(84).......................: MPI_Barrier(MPI_COMM_WORLD) failed
MPIR_Barrier_impl(91)......................:
MPIR_Barrier_allcomm_auto(45)..............:
MPIR_Barrier_intra_dissemination(39).......:
MPIDI_CH3U_Complete_posted_with_error(1090): Process failed
-----Original Message-----
From: Raffenetti, Ken <raffenet at anl.gov>
Sent: Friday, February 4, 2022 11:42 AM
To: Mccall, Kurt E. (MSFC-EV41) <kurt.e.mccall at nasa.gov>; discuss at mpich.org
Subject: [EXTERNAL] Re: [mpich-discuss] MPI_Comm_spawn crosses node boundaries
Yes, you should also use --with-pm=none. If using mpicc to build your application, you should not have to add -lpmi. The script will handle it for you.
If using another method, you might have to add it. These days with shared libraries, linkers are often able to manage "inter-library" dependencies just fine. Static builds are a different story.
Ken
On 2/4/22, 11:35 AM, "Mccall, Kurt E. (MSFC-EV41)" <kurt.e.mccall at nasa.gov> wrote:
Ken,
>> configure --with-slurm=/opt/slurm --with-pmi=slurm
That is similar to your first suggestion below. With the above, do I have to include --with-pm=none? I guess I also have to link my application with -lpmi, right?
Thanks,
Kurt
-----Original Message-----
From: Raffenetti, Ken <raffenet at anl.gov>
Sent: Friday, February 4, 2022 11:02 AM
To: Mccall, Kurt E. (MSFC-EV41) <kurt.e.mccall at nasa.gov>; discuss at mpich.org
Subject: [EXTERNAL] Re: [mpich-discuss] MPI_Comm_spawn crosses node boundaries
When running with srun you need to use the Slurm PMI library, not the embedded Simple PMI2 library. Simple PMI2 is API compatible, but uses a different wire protocol that the Slurm implementation. Try this instead:
configure --with-slurm=/opt/slurm --with-pmi=slurm
This will link the Slurm PMI library to MPICH. I do acknowledge how confusing this must be to users :). Probably a good FAQ topic for our Github discussions page.
Ken
On 2/3/22, 7:00 PM, "Mccall, Kurt E. (MSFC-EV41)" <kurt.e.mccall at nasa.gov> wrote:
Ken,
I'm trying to build MPICH 4.0 in several ways, one of which will be what you suggested below. For this particular attempt suggested by the Slurm MPI guide, I built it with
configure --with-slurm=/opt/slurm --with-pmi=pmi2/simple <etc>
and invoked it with
srun --mpi=pmi2 <etc>
The job is crashing with this message. Any idea what is wrong?
slurmstepd: error: mpi/pmi2: no value for key in req
slurmstepd: error: mpi/pmi2: no value for key in req
slurmstepd: error: mpi/pmi2: no value for key <99>èþ^? in req
slurmstepd: error: mpi/pmi2: no value for key in req
slurmstepd: error: mpi/pmi2: no value for key in req
slurmstepd: error: mpi/pmi2: no value for key ´2¾ÿ^? in req
slurmstepd: error: mpi/pmi2: no value for key ; in req
slurmstepd: error: mpi/pmi2: no value for key in req
slurmstepd: error: *** STEP 52227.0 ON n001 CANCELLED AT 2022-02-03T18:48:02 ***
-----Original Message-----
From: Raffenetti, Ken <raffenet at anl.gov>
Sent: Friday, January 28, 2022 3:15 PM
To: Mccall, Kurt E. (MSFC-EV41) <kurt.e.mccall at nasa.gov>; discuss at mpich.org
Subject: [EXTERNAL] Re: [mpich-discuss] MPI_Comm_spawn crosses node boundaries
On 1/28/22, 2:22 PM, "Mccall, Kurt E. (MSFC-EV41)" <kurt.e.mccall at nasa.gov> wrote:
Ken,
I confirmed that MPI_Comm_spawn fails completely if I build MPICH without the PMI2 option.
Dang, I thought that would work :(.
Looking at the Slurm documentation https://gcc02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fslurm.schedmd.com%2Fmpi_guide.html%23intel_mpiexec_hydra&data=04%7C01%7Ckurt.e.mccall%40nasa.gov%7C9249f74763f1428b909908d9e82adeef%7C7005d45845be48ae8140d43da96dd17b%7C0%7C0%7C637796093091225985%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=dcpAlSu4FLsL2o39rDH0t1jyzq4AYSOQlZXMReZmmJU%3D&reserved=0
it states "All MPI_comm_spawn work fine now going through hydra's PMI 1.1 interface." The full quote is below for reference.
1) how do I build MPICH to support hydra's PMI 1.1 interface?
That is the default, so no extra configuration should be needed. One thing I notice in your log output is that the Slurm envvars seems to have changed name from what we have in our source. E.g. SLURM_JOB_NODELIST vs. SLURM_NODELIST. Do your initial processes launch on the right nodes?
2) Can you offer any guesses on how to build Slurm to do the same? (I realize this isn't a Slurm forum 😊)
Hopefully you don't need to rebuild Slurm to do it. What you could try is configuring the Slurm PMI library when building MPICH. Add "--with-pm=none --with-pmi=slurm --with-slurm=<path/to/install>". Then use srun instead of mpiexec and see how it goes.
Ken
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