Re: [OMPI users] Problem when installing Rmpi package in HPC cluster

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

Re: [OMPI users] Problem when installing Rmpi package in HPC cluster

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

Re: [OMPI users] Need libmpi_f90.a

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

Re: [OMPI users] Need libmpi_f90.a

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

Re: [OMPI users] Problem when installing Rmpi package in HPC cluster

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

Re: [OMPI users] Can OMPI 1.8.8 or later support LSF 9.1.3 or 10.1?

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

Re: [OMPI users] openmpi 1.10.2 and PGI 15.9

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,

Re: [OMPI users] openmpi 1.10.2 and PGI 15.9

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

Re: [OMPI users] openmpi 1.10.2 and PGI 15.9

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,

[OMPI users] openmpi 1.10.2 and PGI 15.9

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

Re: [OMPI users] Problem when installing Rmpi package in HPC cluster

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

[OMPI users] Problem when installing Rmpi package in HPC cluster

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/', +