We have found that virtually all Rmpi jobs need to be started with
$ mpirun -np 1 R CMD BATCH
This is, as I understand it, because the first R will initialize the
MPI environment and then when you create the cluster, it wants to be
able to start the rest of the processes. When you intialize
Note this is just a workaround, this simply disables the mxm mtl (e.g.
Mellanox optimized infiniband driver).
basically, there are two ways to run a single task mpi program (a.out)
- mpirun -np 1 ./a.out (this is the "standard" way)
- ./a.out (aka singleton mode)
the logs you posted do not s
On Jul 11, 2016, at 3:25 PM, Mahmood Naderan wrote:
> # ls -l libmpi*
> -rw-r--r-- 1 root root 1029580 Jul 11 23:51 libmpi_mpifh.a
> -rw-r--r-- 1 root root 17292 Jul 11 23:51 libmpi_usempi.a
These are the two for v1.10.x.
Sorry; one thing I wasn't clear on (I had forgotten): the libraries cha
Excuse me... that command only creates libmpi_f90.a for V1.6.5.
What about V1.10.3? I don't see such file even with --enable-static. Does
it have a different name?
# ls -l libmpi*
-rw-r--r-- 1 root root 5888466 Jul 11 23:51 libmpi.a
-rw-r--r-- 1 root root 962656 Jul 11 23:51 libmpi_cxx.a
-rwxr-x
Dear Gilles,
I tried export OMPI_MCA_pml=ob1, and it worked! Thank you very much for
your brilliant suggestion.
By the way, I don't really understand what do you mean by '*can you also
extract the command tha launch the test ?*'...
Cheers,
Pan
IBM will be helping to support the LSF functionality in Open MPI. We don't
have any detailed documentation just yet, other than the FAQ on the Open
MPI site. However, the LSF components in Open MPI should be functional in
the latest releases. I've tested recently with LSF 9.1.3 and 10.1.
I pushed
Looks like you are compiling with slurm support.
If so, you need to remove the "-pthread" from libslurm.la and libpmi.la
On 07/11/2016 02:54 PM, Michael Di Domenico wrote:
> I'm trying to get openmpi compiled using the PGI compiler.
>
> the configure goes through and the code starts to compile,
On Mon, Jul 11, 2016 at 9:11 AM, Gilles Gouaillardet
wrote:
> Can you try the latest 1.10.3 instead ?
i can but it'll take a few days to pull the software inside.
> btw, do you have a license for the pgCC C++ compiler ?
> fwiw, FreePGI on OSX has no C++ license and PGI C and gnu g++ does not wor
Can you try the latest 1.10.3 instead ?
btw, do you have a license for the pgCC C++ compiler ?
fwiw, FreePGI on OSX has no C++ license and PGI C and gnu g++ does not work
together out of the box, hopefully I will have a fix ready sometimes this
week
Cheers,
Gilles
On Monday, July 11, 2016, Mich
I'm trying to get openmpi compiled using the PGI compiler.
the configure goes through and the code starts to compile, but then
gets hung up with
entering: openmpi-1.10.2/opal/mca/common/pmi
CC common_pmi.lo
CCLD libmca_common_pmi.la
pgcc-Error-Unknown switch: - pthread
That could be specific to mtl/mxm
could you
export OMPI_MCA_pml=ob1
and try again ?
can you also extract the command tha launch the test ?
I am curious whether this is via mpirun or as a singleton
Cheers,
Gilles
On Monday, July 11, 2016, pan yang wrote:
> Dear OpenMPI community,
>
> I faced
Dear OpenMPI community,
I faced this problem when I am installing the Rmpi:
> install.packages('Rmpi',repos='http://cran.r-project.org
',configure.args=c(
+ '--with-Rmpi-include=/usr/mpi/gcc/openmpi-1.8.2/include/',
+ '--with-Rmpi-libpath=/usr/mpi/gcc/openmpi-1.8.2/lib64/',
+ '--with-Rmpi-type=OP
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