From mwkimpel at gmail.com  Wed Jun 11 06:46:51 2008
From: mwkimpel at gmail.com (Mark Kimpel)
Date: Wed, 11 Jun 2008 00:46:51 -0400
Subject: [Rd] Rmpi segfault after install on Ubuntu Hardy Heron
Message-ID: <6b93d1830806102146k1f91b723q2f7918d4a95043e6@mail.gmail.com>

I just installed Rmpi on my 64-bit Ubuntu Hardy Heron OS and using the
following without errors:
"R CMD INSTALL Rmpi_0.5-5.tar.gz --configure-args=--with-mpi=/usr/lib64/openmpi"

Immediately at library(Rmpi) I get the segfault displayed in my
complete output below. My first thought is that perhaps I used the
wrong library for openmpi, but with my 64 bit install it seemed like a
logical choice and the install went without a hitch.

Two other general comments:
1. Am I addressing this to the correct list or should I use R-help? As
I read the posting guide, I'm not sure.
2. Has anyone considered an R-SIG-HPC list? Anyone besides me interested?

Mark


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Loading required package: datasets
Loading required package: utils
Loading required package: grDevices
Loading required package: graphics
Loading required package: stats
Loading required package: graph
[1] "packages do not need updated"
> options(STERM='iESS', editor='emacsclient')
> library("Rmpi")

 *** caught segfault ***
address 0x2104008, cause 'memory not mapped'

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

Possible actions:
1: abort (with core dump, if enabled)
2: normal R exit
3: exit R without saving workspace
4: exit R saving workspace
Selection:

-- 
Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry
Indiana University School of Medicine

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[Rd] Rmpi segfault after install on Ubuntu Hardy Heron
Mark Kimpel