[mpich-discuss] MPI_Comm_spawn crosses node boundaries
Mccall, Kurt E. (MSFC-EV41)
kurt.e.mccall at nasa.gov
Fri Feb 4 13:55:59 CST 2022
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%7Ca5480a51646c422f6a0a08d9e813cfbe%7C7005d45845be48ae8140d43da96dd17b%7C0%7C0%7C637795994051660362%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=uYqw5Lre27S4mV9cnnfFW9qynHL7vSdJiqRfLI1QOAg%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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