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

[Jim Maas]

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

[Gilles Gouaillardet]

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

Post by Jim Maas
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
/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
https://lists.open-mpi.org/mailman/listinfo/users

[Jim Maas]

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 <

Post by Gilles Gouaillardet
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

Post by Jim Maas
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,

Post by Jim Maas
asking for 6 slots (there are 12 on this machine) I get this error.

Where

Post by Jim Maas
can I start to debug it?
Thanks
J
------------------------------------------------------------

--------------

Post by Jim Maas
There are not enough slots available in the system to satisfy the 6 slots
/usr/lib/R/bin/Rscript
Either request fewer slots for your application, or make more slots
available
for use.
------------------------------------------------------------

--------------

Post by Jim Maas
Error in mpi.comm.spawn(slave = rscript, slavearg = args, nslaves =

count,

Post by Jim Maas
MPI_ERR_SPAWN: could not spawn processes
--
Jim Maas
jimmaasuk at gmail.com
_______________________________________________
users mailing list
https://lists.open-mpi.org/mailman/listinfo/users

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