Thanks for your good advice.

I changed to R 2.14.1 and Rmpi works fine. :)

However, there is another problem when I try to use snow package.

This is error message I got:

MPI: bl1.psc.teragrid.org: 0x54e500004f90ba1f: /bin/sh: line 0: exec:
RMPISNOW: not found

I am sure RMPISNOW is in the working directory.

Thanks,
Libo

On Mon, Apr 30, 2012 at 7:10 AM, Stephen Weston
<stephen.b.weston@gmail.com>wrote:

> Hi Libo,
>
> The traceback that you include shows that you're not able to
> load the Rmpi package.  But it's not because Rmpi isn't
> installed, because it's getting a segmentation violation when
> trying to load the Rmpi shared library, which sounds like a bad
> installation of Rmpi.  But it's also possible that you're
> loading inconsistent module files in your batch script, or
> you're doing something in your .Rprofile that is breaking it.
>
> Since it looks like you're using system provided modules files,
> I suggest that you verify that you're using the correct
> procedure for loading R and Rmpi for the Blacklight cluster.  If
> you're following the correct procedures for the cluster, then
> you should report to the system administrators that the Rmpi
> installation is broken.
>
> - Steve
>
>
> On Mon, Apr 30, 2012 at 12:07 AM, Libo Sun <libosun@rams.colostate.edu>
> wrote:
> > 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
> >
> >        [[alternative HTML version deleted]]
> >
> > _______________________________________________
> > R-sig-hpc mailing list
> > R-sig-hpc@r-project.org
> > https://stat.ethz.ch/mailman/listinfo/r-sig-hpc
>

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