You can add it to the default MCA param file, if you want - <prefix>/etc/openmpi-mca-params.conf
> On Oct 3, 2017, at 12:44 PM, Jim Maas <jimmaa...@gmail.com> wrote: > > Thanks RHC .... where do I put that so it will be in the environment? > > J > > On 3 October 2017 at 16:01, r...@open-mpi.org <mailto:r...@open-mpi.org> > <r...@open-mpi.org <mailto:r...@open-mpi.org>> wrote: > As Gilles said, we default to slots = cores, not HTs. If you want to treat > HTs as independent cpus, then you need to add > OMPI_MCA_hwloc_base_use_hwthreads_as_cpus=1 in your environment. > >> On Oct 3, 2017, at 7:27 AM, Jim Maas <jimmaa...@gmail.com >> <mailto:jimmaa...@gmail.com>> wrote: >> >> Tried this and got this error, and slots are available, nothing else is >> running. >> >> > cl <- startMPIcluster(count=7) >> -------------------------------------------------------------------------- >> There are not enough slots available in the system to satisfy the 7 slots >> that were requested by the application: >> /usr/local/lib/R/bin/Rscript >> >> Either request fewer slots for your application, or make more slots available >> for use. >> -------------------------------------------------------------------------- >> Error in mpi.comm.spawn(slave = rscript, slavearg = args, nslaves = count, >> : >> MPI_ERR_SPAWN: could not spawn processes >> > >> >> On 3 October 2017 at 15:07, Gilles Gouaillardet >> <gilles.gouaillar...@gmail.com <mailto:gilles.gouaillar...@gmail.com>> wrote: >> Thanks, i will have a look at it. >> >> By default, a slot is a core, so there are 6 slots on your system. >> Could your app spawn 6 procs on top of the initial proc ? That would be 7 >> slots and there are only 6. >> What if you ask 5 slots only ? >> >> With some parameters i do not know off hand, you could either oversubscribe >> or use hyperthreads as slots. In both cases, 7 slots would be available. >> >> Cheers, >> >> Gilles >> >> Jim Maas <jimmaa...@gmail.com <mailto:jimmaa...@gmail.com>> wrote: >> Thanks Gilles, relative noob here at this level, apologies if nonsensical! >> >> I removed previous versions of open mpi which were compiled from source >> using sudo make uninstall ... >> downloaded new open-mpi 3.0.0 in tar.gz >> configure --disable-dlopen >> sudo make install >> >> >> then ran sudo ldconfig >> >> updated R, downloaded R-3.4.2.tar.gz >> ./configure >> sudo make install >> >> >> Then run R from sudo >> >> sudo R >> once running >> install.packages("Rmpi") >> install.packages("doMPI") >> >> both of these load and test fine during install >> >> Then from R run >> >> rm(list=ls(all=TRUE)) >> library(doMPI) >> >> ## load MPI cluster >> cl <- startMPIcluster(count=6) >> >> >> At this point it throws the error, doesn't find any of the slots. >> >> There is a precompiled version of Rmpi that installs an older version of >> open-mpi directly from Ubuntu, but I think the mpi version is an older one >> so I wanted to try using the new version. >> >> >> I use this 6 core (12) as test bed before uploading to a cluster. It is >> Ubuntu 16.04 Linux, lstopo pdf is attached. >> >> Thanks, >> >> J >> >> >> On 3 October 2017 at 14:06, Gilles Gouaillardet >> <gilles.gouaillar...@gmail.com <mailto:gilles.gouaillar...@gmail.com>> wrote: >> Hi Jim, >> >> can you please provide minimal instructions on how to reproduce the issue ? >> we know Open MPI, but i am afraid few or none of us know about Rmpi nor >> doMPI. >> once you explain how to download and build these, and how to run the >> failing test, >> we ll be able to investigate that. >> >> also, can you describe your environment ? >> i assume one ubuntu machine, can you please run >> lstopo >> on and post the output ? >> >> did you use to have some specific settings in the system-wide conf >> file (e.g. /.../etc/openmpi-mca-params.co <http://openmpi-mca-params.co/>nf) >> ? >> if yes, can you post these, the syntax might have changed in 3.0.0 >> >> Cheers, >> >> Gilles >> >> On Tue, Oct 3, 2017 at 7:34 PM, Jim Maas <jimmaa...@gmail.com >> <mailto:jimmaa...@gmail.com>> wrote: >> > I've used this for years, just updated open-mpi to 3.0.0 and reloaded R, >> > have reinstalled doMPI and thus Rmpi but when I try to use startMPICluster, >> > asking for 6 slots (there are 12 on this machine) I get this error. Where >> > can I start to debug it? >> > >> > Thanks >> > J >> > -------------------------------------------------------------------------- >> > There are not enough slots available in the system to satisfy the 6 slots >> > that were requested by the application: >> > /usr/lib/R/bin/Rscript >> > >> > Either request fewer slots for your application, or make more slots >> > available >> > for use. >> > -------------------------------------------------------------------------- >> > Error in mpi.comm.spawn(slave = rscript, slavearg = args, nslaves = count, >> > : >> > MPI_ERR_SPAWN: could not spawn processes >> > -- >> > Jim Maas >> > >> > jimmaasuk at gmail.com <http://gmail.com/> >> > >> > >> > _______________________________________________ >> > users mailing list >> > users@lists.open-mpi.org <mailto:users@lists.open-mpi.org> >> > https://lists.open-mpi.org/mailman/listinfo/users >> > <https://lists.open-mpi.org/mailman/listinfo/users> >> _______________________________________________ >> users mailing list >> users@lists.open-mpi.org <mailto:users@lists.open-mpi.org> >> https://lists.open-mpi.org/mailman/listinfo/users >> <https://lists.open-mpi.org/mailman/listinfo/users> >> >> >> >> -- >> >> _______________________________________________ >> users mailing list >> users@lists.open-mpi.org <mailto:users@lists.open-mpi.org> >> https://lists.open-mpi.org/mailman/listinfo/users >> <https://lists.open-mpi.org/mailman/listinfo/users> >> >> >> >> _______________________________________________ >> users mailing list >> users@lists.open-mpi.org <mailto:users@lists.open-mpi.org> >> https://lists.open-mpi.org/mailman/listinfo/users >> <https://lists.open-mpi.org/mailman/listinfo/users> > > _______________________________________________ > users mailing list > users@lists.open-mpi.org <mailto:users@lists.open-mpi.org> > https://lists.open-mpi.org/mailman/listinfo/users > <https://lists.open-mpi.org/mailman/listinfo/users> > > > > > _______________________________________________ > users mailing list > users@lists.open-mpi.org > https://lists.open-mpi.org/mailman/listinfo/users
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