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> 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> 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
>> >
>> >
>> > _______________________________________________
>> > users mailing list
>> > users@lists.open-mpi.org
>> > https://lists.open-mpi.org/mailman/listinfo/users
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>>
>
>
>
> --
>
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