Re: [OMPI users] OMPI users] upgraded mpi and R and now cannot find slots

Not sure exactly how but back up and running, with all cores. Thanks to all. Hopefully the new binary for Ubuntu with open-mpi 3.0.0 won't be too far away. Very Best, J On 3 October 2017 at 21:06, r...@open-mpi.org wrote: > You can add it to the default MCA param file, if

Re: [OMPI users] OMPI users] upgraded mpi and R and now cannot find slots

You can add it to the default MCA param file, if you want - /etc/openmpi-mca-params.conf > On Oct 3, 2017, at 12:44 PM, Jim Maas 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

Re: [OMPI users] OMPI users] upgraded mpi and R and now cannot find slots

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 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 >

Re: [OMPI users] OMPI users] upgraded mpi and R and now cannot find slots

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 wrote: > > Tried this and got this error, and

Re: [OMPI users] OMPI users] upgraded mpi and R and now cannot find slots

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

Re: [OMPI users] OMPI users] upgraded mpi and R and now cannot find slots

Previously it worked fine if I asked for 12, I'm sure you are correct, it is only 6 physical cores, but with hyperthreading or whatever, it looks like 12. The system monitor shows 12. Thanks J On 3 October 2017 at 15:07, Gilles Gouaillardet < gilles.gouaillar...@gmail.com> wrote: > Thanks, i

Re: [OMPI users] OMPI users] upgraded mpi and R and now cannot find slots

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

Re: [OMPI users] upgraded mpi and R and now cannot find slots

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

Re: [OMPI users] upgraded mpi and R and now cannot find slots

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

[OMPI users] upgraded mpi and R and now cannot find slots

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