Gilles Gouaillardet
2017-10-03 14:07:25 UTC
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
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
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 runningÂ
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
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
users mailing list
https://lists.open-mpi.org/mailman/listinfo/users
--
Jim Maas
74 Turner Road
Norwich, Norfolk, UK.
NR2 4HB
jimmaasuk at gmail.com
http://www.jamaas.com
+ 44 (0)771 985 8698
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 runningÂ
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
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
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
_______________________________________________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
users mailing list
https://lists.open-mpi.org/mailman/listinfo/users
--
Jim Maas
74 Turner Road
Norwich, Norfolk, UK.
NR2 4HB
jimmaasuk at gmail.com
http://www.jamaas.com
+ 44 (0)771 985 8698