[slurm-users] HELP: error between compilation and execution on gpu cluster

[Saksham Pande 5-Year IDD Physics]

Hi everyone,

I am trying to run a simulation software on slurm using openmpi-4.1.1 and cuda/11.1.

On executing, I get the following error:

srun --mpi=pmi2 --nodes=1 --ntasks-per-node=5 --partition=gpu --gres=gpu:1 --time=02:00:00 --pty bash -i

./<execultable>

```._____________________________________________________________________________________
|
| Initial checks...
| All good.
|_____________________________________________________________________________________
[gpu008:162305] OPAL ERROR: Not initialized in file pmix3x_client.c at line 112
--------------------------------------------------------------------------
The application appears to have been direct launched using "srun",
but OMPI was not built with SLURM's PMI support and therefore cannot
execute. There are several options for building PMI support under
SLURM, depending upon the SLURM version you are using:

  version 16.05 or later: you can use SLURM's PMIx support. This
  requires that you configure and build SLURM --with-pmix.

  Versions earlier than 16.05: you must use either SLURM's PMI-1 or
  PMI-2 support. SLURM builds PMI-1 by default, or you can manually
  install PMI-2. You must then build Open MPI using --with-pmi pointing
  to the SLURM PMI library location.

Please configure as appropriate and try again.
--------------------------------------------------------------------------
*** An error occurred in MPI_Init
*** on a NULL communicator
*** MPI_ERRORS_ARE_FATAL (processes in this communicator will now abort,
***    and potentially your MPI job)
[gpu008:162305] Local abort before MPI_INIT completed completed successfully, but am not able to aggregate error messages, and not able to guarantee that all other processes were killed!```

using the following modules: gcc/10.2 openmpi/4.1.1 cuda/11.1

on using which mpic++ or mpirun or nvcc, I get the module paths only, which looks correct.

I also changed the $PATH and $LD_LIBRARY_PATH based on ldd <executable>, but still the same error.

[sakshamp.phy20.itbhu@login2 menura]$ srun --mpi=list
srun: MPI types are...
srun: cray_shasta
srun: none
srun: pmi2

What should I do from here, been stuck on this error for 6 days now? If there is any build difference, I will have to tell the sysadmin.

Since there is an openmpi pairing error with slurm, are there other error I could expect between cuda and openmpi?

Thanks

[Saksham Pande 5-Year IDD Physics]

[Juergen Salk]

Hi,

I am not sure if this related to GPUs. I rather think the issue has to do with
how your OpenMPI has been built.

What does ompi_info command show? Look for "Configure command line" in
the output. Does this include '--with-slurm' and '--with-pmi' flags?

To my very best knowledge, both flags need to be set for OpenMPI to
work with srun.

Also see:

https://www.open-mpi.org/faq/?category=slurm#slurm-direct-srun-mpi-apps

https://slurm.schedmd.com/mpi_guide.html#open_mpi

Best regards
Jürgen


* Saksham Pande 5-Year IDD Physics <saksham.p...@itbhu.ac.in> [230519 07:42]:

[Saksham Pande 5-Year IDD Physics]

Thank you for responding.

The output of ompi_info regarding configuration is

Configure command line: '--build=x86_64-redhat-linux-gnu'
                          '--host=x86_64-redhat-linux-gnu'
                          '--program-prefix=' '--disable-dependency-tracking'
                          '--prefix=/usr/mpi/gcc/openmpi-4.0.2a1'
                          '--exec-prefix=/usr/mpi/gcc/openmpi-4.0.2a1'
                          '--bindir=/usr/mpi/gcc/openmpi-4.0.2a1/bin'
                          '--sbindir=/usr/mpi/gcc/openmpi-4.0.2a1/sbin'
                          '--sysconfdir=/usr/mpi/gcc/openmpi-4.0.2a1/etc'
                          '--datadir=/usr/mpi/gcc/openmpi-4.0.2a1/share'
                          '--includedir=/usr/mpi/gcc/openmpi-4.0.2a1/include'
                          '--libdir=/usr/mpi/gcc/openmpi-4.0.2a1/lib64'
                          '--libexecdir=/usr/mpi/gcc/openmpi-4.0.2a1/libexec'
                          '--localstatedir=/var' '--sharedstatedir=/var/lib'
                          '--mandir=/usr/mpi/gcc/openmpi-4.0.2a1/share/man'
                          '--infodir=/usr/mpi/gcc/openmpi-4.0.2a1/share/info'
                          '--with-platform=contrib/platform/mellanox/optimized'

BUT
                MCA pmix: flux (MCA v2.1.0, API v2.0.0, Component v4.0.2)
                MCA pmix: isolated (MCA v2.1.0, API v2.0.0, Component v4.0.2)
                MCA pmix: pmix3x (MCA v2.1.0, API v2.0.0, Component v4.0.2)

                 MCA ess: pmi (MCA v2.1.0, API v3.0.0, Component v4.0.2)
                 MCA ess: singleton (MCA v2.1.0, API v3.0.0, Component v4.0.2)
                 MCA ess: slurm (MCA v2.1.0, API v3.0.0, Component v4.0.2)

are also present and contain references to pmi and slurm.

[Saksham Pande 5-Year IDD Physics]

Hello,

is writing the --with-pmi flag sufficient or do I have to write it in the form --with-pmi=<some directory>, where it points to a directory, and if so, where? Slightly confused by the syntax provided in the documentation.

[sakshamp.phy20.itbhu@login2]$ srun --mpi=list

srun: MPI types are...
srun: cray_shasta
srun: none
srun: pmi2

If any more info is needed for context, please let me know.

Regards