[R-sig-hpc] multi-threaded R/MPI jobs using SGE
renaud at mancala.cbio.uct.ac.za
Wed Sep 22 13:08:52 CEST 2010
I want to run an MPI-multithread job on our local cluster (Rocks + SGE).
My R script uses the doMPI/doMC packages to compute, say 10 tasks.
I'd like to compute each task using as many CPUs available on a
worker-host (meaning all available and assigned slots by SGE).
Suppose I know each host as 4 slots.
1. SGE question: ideally I'd like to be able to ask for say 9 slots,
allocated on 3 hosts (4 + 4 + 1), using the isolated slot to run the
This way I can spawn one master, two 4-core workers to perform the tasks.
I read one can configure an SGE parallel environment to pass to qsub -pe
<pe_name> to ensure the allocation follows this rule.
Has anybody this kind of environment available on its cluster?
Would this one work?
start_proc_args /opt/gridengine/mpi/startmpi.sh -catch_rsh $pe_hostfile
2. Rmpi/doMPI question: suppose I cannot be sure the slots are allocated
in such a way, say I get (2+2+3+2). This means that other users are
using the other CPUs, which I do not want to over-use. Currently when I
registerDoMC() it registers all 4 CPUs which interferes with the other
Is it possible from within R to figure out which worker-host is running
the code and the number of CPU I am allowed to use on it?
3. If anybody has successfully done this kind of thing, please let me
Computational Biology - University of Cape Town
UNIVERSITY OF CAPE TOWN
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