Matthias,
do you run the MPI application with mpirun or srun?
The error log suggests you are using srun, and SLURM only provides only PMI
support.
If this is the case, then you have three options:
- use mpirun
- rebuild Open MPI with PMI support as Ralph previously explained
- use SLURM PMIx:
srun --mpi=list
will list the PMI flavors provided by SLURM
a) if PMIx is not supported, contact your sysadmin and ask for it
b) if PMIx is supported but is not the default, ask for it, for example
with
srun --mpi=pmix_v3 ...
Cheers,
Gilles
On Tue, Jan 25, 2022 at 12:30 AM Ralph Castain via users <
users@lists.open-mpi.org> wrote:
> You should probably ask them - I see in the top one that they used a
> platform file, which likely had the missing option in it. The bottom one
> does not use that platform file, so it was probably missed.
>
>
> > On Jan 24, 2022, at 7:17 AM, Matthias Leopold via users <
> users@lists.open-mpi.org> wrote:
> >
> > To be sure: both packages were provided by NVIDIA (I didn't compile them)
> >
> > Am 24.01.22 um 16:13 schrieb Matthias Leopold:
> >> Thx, but I don't see this option in any of the two versions:
> >> /usr/mpi/gcc/openmpi-4.1.2a1/bin/ompi_info (works with slurm):
> >> Configure command line: '--build=x86_64-linux-gnu' '--prefix=/usr'
> '--includedir=${prefix}/include' '--mandir=${prefix}/share/man'
> '--infodir=${prefix}/share/info' '--sysconfdir=/etc' '--localstatedir=/var'
> '--disable-silent-rules' '--libexecdir=${prefix}/lib/openmpi'
> '--disable-maintainer-mode' '--disable-dependency-tracking'
> '--prefix=/usr/mpi/gcc/openmpi-4.1.2a1'
> '--with-platform=contrib/platform/mellanox/optimized'
> >> lmod ompi (doesn't work with slurm)
> >> Configure command line:
> '--prefix=/proj/nv/libraries/Linux_x86_64/dev/openmpi4/205295-dev-clean-1'
> 'CC=nvc -nomp' 'CXX=nvc++ -nomp' 'FC=nvfortran -nomp' 'CFLAGS=-O1 -fPIC
> -c99 -tp p7-64' 'CXXFLAGS=-O1 -fPIC -tp p7-64' 'FCFLAGS=-O1 -fPIC -tp
> p7-64' 'LD=ld' '--enable-shared' '--enable-static' '--without-tm'
> '--enable-mpi-cxx' '--disable-wrapper-runpath'
> '--enable-mpirun-prefix-by-default' '--with-libevent=internal'
> '--with-slurm' '--without-libnl' '--enable-mpi1-compatibility'
> '--enable-mca-no-build=btl-uct' '--without-verbs'
> '--with-cuda=/proj/cuda/11.0/Linux_x86_64'
> '--with-ucx=/proj/nv/libraries/Linux_x86_64/dev/openmpi4/205295-dev-clean-1'
> Matthias
> >> Am 24.01.22 um 15:59 schrieb Ralph Castain via users:
> >>> If you look at your configure line, you forgot to include
> --with-pmi=<path-to-slurm-pmi-lib>. We don't build the Slurm PMI support by
> default due to the GPL licensing issues - you have to point at it.
> >>>
> >>>
> >>>> On Jan 24, 2022, at 6:41 AM, Matthias Leopold via users <
> users@lists.open-mpi.org> wrote:
> >>>>
> >>>> Hi,
> >>>>
> >>>> we have 2 DGX A100 machines and I'm trying to run nccl-tests (
> https://github.com/NVIDIA/nccl-tests) in various ways to understand how
> things work.
> >>>>
> >>>> I can successfully run nccl-tests on both nodes with Slurm (via srun)
> when built directly on a compute node against Open MPI 4.1.2 coming from a
> NVIDIA deb package.
> >>>>
> >>>> I can also build nccl-tests in a lmod environment with NVIDIA HPC SDK
> 21.09 with Open MPI 4.0.5. When I run this with Slurm (via srun) I get the
> following message:
> >>>>
> >>>> [foo:1140698] OPAL ERROR: Error in file
> ../../../../../opal/mca/pmix/pmix3x/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)
> >>>>
> >>>>
> >>>>
> >>>> When I look at PMI support in both Open MPI packages I don't see a
> lot of difference:
> >>>>
> >>>> “/usr/mpi/gcc/openmpi-4.1.2a1/bin/ompi_info --parsable | grep -i pmi”:
> >>>>
> >>>> mca:pmix:isolated:version:“mca:2.1.0”
> >>>> mca:pmix:isolated:version:“api:2.0.0”
> >>>> mca:pmix:isolated:version:“component:4.1.2”
> >>>> mca:pmix:flux:version:“mca:2.1.0”
> >>>> mca:pmix:flux:version:“api:2.0.0”
> >>>> mca:pmix:flux:version:“component:4.1.2”
> >>>> mca:pmix:pmix3x:version:“mca:2.1.0”
> >>>> mca:pmix:pmix3x:version:“api:2.0.0”
> >>>> mca:pmix:pmix3x:version:“component:4.1.2”
> >>>> mca:ess:pmi:version:“mca:2.1.0”
> >>>> mca:ess:pmi:version:“api:3.0.0”
> >>>> mca:ess:pmi:version:“component:4.1.2”
> >>>>
> >>>> “/msc/sw/hpc-sdk/Linux_x86_64/21.9/comm_libs/mpi/bin/ompi_info
> --parsable | grep -i pmi”:
> >>>>
> >>>> mca:pmix:isolated:version:“mca:2.1.0”
> >>>> mca:pmix:isolated:version:“api:2.0.0”
> >>>> mca:pmix:isolated:version:“component:4.0.5”
> >>>> mca:pmix:pmix3x:version:“mca:2.1.0”
> >>>> mca:pmix:pmix3x:version:“api:2.0.0”
> >>>> mca:pmix:pmix3x:version:“component:4.0.5”
> >>>> mca:ess:pmi:version:“mca:2.1.0”
> >>>> mca:ess:pmi:version:“api:3.0.0”
> >>>> mca:ess:pmi:version:“component:4.0.5”
> >>>>
> >>>> I don't know if that's the right place I'm looking at, but to me it
> seems it's an Open MPI topic, this is why I'm posting here. Please explain
> what's missing in my case.
> >>>>
> >>>> Slurm is 21.08.5. "MpiDefault" in slurm.conf is "pmix".
> >>>> Both Open MPI versions have Slurm support.
> >>>>
> >>>> thx
> >>>> Matthias
> >>>
> >>>
> >
> > --
> > Matthias Leopold
> > IT Systems & Communications
> > Medizinische Universität Wien
> > Spitalgasse 23 / BT 88 / Ebene 00
> > A-1090 Wien
> > Tel: +43 1 40160-21241
> > Fax: +43 1 40160-921200
>
>
