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> 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>
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