[Slackbuilds-users] openmpi request

[Emmanuel]

Hi Karel, I've just updated the openmpi slackbuild.

The option --with-pmi=pmi2  was giving me the following errors:

checking if user requested PMI support... yes
checking for pmi.h in pmi2... not found
checking for pmi.h in pmi2/include... not found
checking for pmi.h in pmi2/include/slurm... not found
checking for libpmi in pmi2/lib... checking for libpmi in pmi2/lib64... not
found
checking for pmi2.h in pmi2... not found
checking for pmi2.h in pmi2/include... not found
checking for pmi2.h in pmi2/include/slurm... not found
checking for libpmi2 in pmi2/lib... checking for libpmi2 in pmi2/lib64...
not found
checking for pmix.h in pmi2... not found
checking for pmix.h in pmi2/include... not found
checking can PMI support be built... no
configure: WARNING: PMI support requested (via --with-pmi) but neither
pmi.h,
configure: WARNING: pmi2.h or pmix.h were found under locations:
configure: WARNING:     pmi2
configure: WARNING:     pmi2/slurm
configure: WARNING: Specified path: pmi2
configure: WARNING: OR neither libpmi, libpmi2, or libpmix were found under:
configure: WARNING:     /lib
configure: WARNING:     /lib64
configure: WARNING: Specified path:
configure: error: Aborting

What version of slurm are you using?
I've added --with-slurm --with-pmix as optional dependencies to openmpi and
also updated slurm to the latest version.

Let me know if you find any more problems :-)

Best regards.




On Thu, Jul 25, 2019 at 12:54 PM Karel Venken <k.venken at online.be> wrote:

> Emmanuel wrote:
> >
> >
> > On Thu, Jul 25, 2019 at 5:04 AM Robby Workman
> > <rworkman at slackbuilds.org <mailto:rworkman at slackbuilds.org>> wrote:
> >
> >     On Thu, 25 Jul 2019 09:58:03 +0200
> >     Karel Venken <kava0418 at online.be <mailto:kava0418 at online.be>> wrote:
> >
> >     > Hi,
> >     >
> >     > For installing our cluster we need to add to the
> >     openmpi.Slackbuilds
> >     > with --with-pmi=pmi2 configure option. So it becomes:
> >     >
> >     > ./configure \
> >     >    --prefix=/usr \
> >     >    --sysconfdir=/etc \
> >     >    --localstatedir=/var/lib \
> >     >    --mandir=/usr/man/ \
> >     >    --enable-mpi1-compability \
> >     >    --docdir=/usr/doc/$PRGNAM-$VERSION \
> >     >    --disable-static \
> >     >    --libdir=/usr/lib${LIBDIRSUFFIX} \
> >     >    --build=$ARCH-slackware-linux \
> >     >    --with-pmi=pmi2
> >     >
> >     >
> >     > The background is to use mpi with slurm and a NUMA kernel - we
> build
> >     > it ourself. Without this parameter openmpi crashes. Would this be
> an
> >     > option?
> >
> >
> >     CCing SBo maintainer of openmpi; if there's no response and/or an
> >     update with that fixed within a few weeks, follow up with us and
> >     we'll handle it directly.
> >
> >     -RW
> >
> >
> > Hi Karel,
> >
> > I'm the maintainer of openmpi and slurm, let me try this parameter in
> > my cluster because we haven't had issues with the current package and
> > slurm (and also with several versions of openmpi, 1.8.x, 1.10.x,
> > 2.1.1). Can you send me the exact error? Have you modified the slurm
> > build script to add --with-pmi?  are you running mpirun in the slurm
> > submit job script or srun?
> >
> > In any case, I will submit a new version of the script in the next few
> > days.
> >
>
> Hi Emmanuel,
>
> Thanks for answering so soon. I added optional dependencies numactl
> hwloc and rrdtool to slurm and of course for building I set the
> environment with HWLOC=yes RRDTOOL=yes
>
> (We also integrate slurm with ganglia, but that's besides the point
> here, just to mention we activated rrdtool there as well)
>
> The error was produced by one of our applications warning about numa and
> then crashing/hanging at the mpi request. Everything then worked fine
> when we changed this compilation. (I have had a discussion in the
> slackware newsgroup about NUMA)
>
> I am sorry that I didn't keep the log of the application.
>
> FWW, to allow this application to use memory shared over different nodes
> we also had to recompile the kernel with NUMA option enabled (the stock
> kernel has it turned off, but, if I am correct, the current version has
> it activated)
>
> If this goes beyond what you can/want to investigate, that's OK. I am
> already thankful you want to give it a look. Anf, of course, if it is a
> problem in version 14.2, we 'll pick it up again if needed when a new
> version arrives.
>
> kind regards,
>
> Karel.
>
>
>
>
>
>
>
>

-- 
*****************
   Emmanuel
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