hello all
i am busy testing some code that will be used for parallel computations
on a Moab cluster. I have written a C++ program and am linking it with R
using the .C command - this works correctly.
Extracts of the r code (as well as the *.sh file) is included below. I
am able to run the code successfully if I remove all of the doMPI
commands. i.e. outs=.C("prog1", all of the args )
executes correctly if one uses a loop. When I try and use doMPI i get
the following errors:
Error in { : task 1 failed - "C symbol name "prog1" not in load
table"
Calls: %dopar% -> <Anonymous>
eg.r code
----------------------------------------------------------------------------------------------------
library(doMPI)
cl <- startMPIcluster(count=2) #this will be changed later
registerDoMPI(cl)
#the input parameters!
...
#some vecs and matrices for the C program
...
#load the C code
dyn.load("/export/home/example/Runs/eg.so")
Est_Results<-foreach(data_iter = 1:nsamp, .combine="cbind",
.inorder=TRUE ) %dopar%
{
outs=.C("prog1", all of the args )
do more things
return( some things)
}
dyn.unload("/export/home/example/Runs/eg.so")
closeCluster(cl)
save.image("/export/home/example/Runs/eg.RData")
mpi.quit(save = "no")
----------------------------------------------------------------------------------------------------
eg.sh code
----------------------------------------------------------------------------------------------------
#MSUB -l nodes=1:ppn=1
#MSUB -l walltime=100:00:00
#MSUB -m be
#MSUB -V
#MSUB -o /export/home/example/Runs/eg.out
#MSUB -e /export/home/example/Runs/eg.err
#MSUB -d /export/home/example/Runs
mpirun --mca mpi_warn_on_fork 0 -np 1 /export/home/R-2.12.1/bin/R
--slave -f /export/home/example/Runs/eg.r
echo "DONE multiple run!"
----------------------------------------------------------------------------------------------------
###
UNIVERSITY OF CAPE TOWN
This e-mail is subject to the UCT ICT policies and e-mai...{{dropped:16}}
