Hi,

I am trying to test 'Rmpi' on Blacklight,
http://www.psc.edu/machines/sgi/uv/blacklight.php, in PSC.

The R code I am trying to run is very simple:

mpi.remote.exec(paste("I am",mpi.comm.rank(),"of",mpi.comm.size()))
mpi.remote.exec(paste("I am",Sys.info()1,"of",mpi.comm.size()))

The batch file:

#!/bin/csh
#PBS -l walltime=5:00
#PBS -l ncpus=16
#PBS -o test.out
#PBS -j oe
#PBS -q debug

# define module command
source /usr/share/modules/init/csh

set echo
date

# load R module
module load R/2.11.1
module load Rmpi
module swap mpt/2.04 mpt/2.01

# move to scratch space to run job
cd $SCRATCH

# copy input file to scratch space
cp $HOME/test.R .
cp $HOME/.Rprofile .

mpirun -np 16 R --no-save -q < test.R > test.Rout

However, here are some error messages I got:

 *** caught segfault ***
address (nil), cause 'memory not mapped'

Traceback:
 1: dyn.load(file, DLLpath = DLLpath, ...)
 2: library.dynam("Rmpi", pkg, lib)
 3: f(libname, pkgname)
 4: firstlib(which.lib.loc, package)
 5: doTryCatch(return(expr), name, parentenv, handler)
 6: tryCatchOne(expr, names, parentenv, handlers[[1L]])
 7: tryCatchList(expr, classes, parentenv, handlers)
 8: tryCatch(expr, error = function(e) {    call <- conditionCall(e)    if
(!is.null(call)) {        if (identical(call[[1L]],
quote(doTryCatch)))             call <- sys.call(-4L)        dcall <-
deparse(call)[1L]        prefix <- paste("Error in", dcall, ": ")
LONG <- 75L        msg <- conditionMessage(e)        sm <- strsplit(msg,
"\n")[[1L]]        w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type
= "w")        if (is.na(w))             w <- 14L + nchar(dcall, type = "b")
+ nchar(sm[1L],                 type = "b")        if (w >
LONG)             prefix <- paste(prefix, "\n  ", sep = "")    }    else
prefix <- "Error : "    msg <- paste(prefix, conditionMessage(e), "\n", sep
= "")    .Internal(seterrmessage(msg[1L]))    if (!silent &&
identical(getOption("show.error.messages"),         TRUE)) {
cat(msg, file = stderr())        .Internal(printDeferredWarnings())    }
invisible(structure(msg, class = "try-error"))})
 9: try(firstlib(which.lib.loc, package))
10: library(Rmpi, logical.return = TRUE)
aborting ...

Any idea how to fix this?

Many thanks,
Libo

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