[R-sig-hpc] Recommended method for mutlithreaded, multinode in R?
mtmorg@n@b|oc @end|ng |rom gm@||@com
Mon Jun 10 22:16:14 CEST 2019
The pbdR project https://pbdr.org adopts a more traditional HPC approach, including in the pbdMPI package on CRAN.
~$ mpiexec -np 2 R --slave -e "cat('hi\n')"
On 6/10/19, 3:54 PM, "R-sig-hpc on behalf of Bennet Fauber" <r-sig-hpc-bounces using r-project.org on behalf of bennet using umich.edu> wrote:
Are there standard combinations of packages that people use when they
want to use R on multiple nodes and have the R processes on those
nodes call threaded C++ libraries?
For example, if this were straight MPI, one might use a scheduler to
get 8 cores per node assigned to a job, but then only start two MPI
processes per node so that OpenMP for each of those process would have
access to 4 cores.
Most of the ways I've seen to get R going seem to assume that Rmpi
will be used, and that the master R process will be started and it
will in turn spawn one R process for each core in the job.
Has someone written a way to do this where one might do something like
this with OpenMPI ( or the equivalent with a different MPI)
$ mpirun -pernode R hybrid.R
where the hybrid.R would be able to come up and know how to find its
tasks and do them?
Thanks in advance for any pointers anyone might have.
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