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
> >
> >
> > _______________________________________________
> > users mailing list
> > 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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