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> 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> 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.conf) ?
>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> 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
>>
>>
>
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>> users@lists.open-mpi.org
>> https://lists.open-mpi.org/mailman/listinfo/users
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>
>
>
>
>--
>
>Jim Maas
>74 Turner Road
>
>Norwich, Norfolk, UK.
>NR2 4HB
>
>jimmaasuk at gmail.com
>
>http://www.jamaas.com
>+ 44 (0)771 985 8698
>
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