From mwkimpel at gmail.com  Fri Jun 13 04:00:11 2008
From: mwkimpel at gmail.com (Mark Kimpel)
Date: Thu, 12 Jun 2008 22:00:11 -0400
Subject: [Rd] Rmpi segfault after install on Ubuntu Hardy Heron
In-Reply-To: <18513.51861.102932.518310@ron.nulle.part>
References: <6b93d1830806102146k1f91b723q2f7918d4a95043e6@mail.gmail.com>
	<18511.50045.300225.144687@ron.nulle.part>
	<6b93d1830806121538t766daad8v367290677b799993@mail.gmail.com>
	<18513.51861.102932.518310@ron.nulle.part>
Message-ID: <6b93d1830806121900y1d77821aq818113f7aed89cb0@mail.gmail.com>

Dirk,

Did R CMD ldd $R_HOME/library/Rmpi/libs/Rmpi.so as suggested and
things looked okay. Not really wanting to mess with the debugger I
decided to use your prepackaged version. I completely uninstalled all
openmpi packages on my system using Synaptic and deleted my compiled
from source Rmpi from my site-library. Then I executed "sudo apt-get
install r-cran-rmpi" and things seemed to go smoothly. I put a soft
link from the library aptitude installed Rmpi into to my
~/R_HOME/site-library. I get exactly the same error as before. Does
the minimal debugging info below "options(error = recover) provide any
insight?  Mark

> require(Rmpi)
Loading required package: Rmpi

 *** caught segfault ***
address 0x2224008, 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(package, lib.loc = lib.loc, character.only = TRUE,
logical.return = TRUE,     warn.conflicts = warn.conflicts,
keep.source = keep.source,     version = version)
10: require(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: 2
Save workspace image? [y/n/c]: n
mkimpel at mkimpel-xps600:~/R_HOME/site-library-2.7.0/Rmpi$ R

R version 2.7.0 Patched (2008-05-18 r45728)
________________________________
#stuff deleted for brevity
______________________________________

> sessionInfo()
R version 2.7.0 Patched (2008-05-18 r45728)
x86_64-unknown-linux-gnu

locale:
LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] graph_1.18.1

loaded via a namespace (and not attached):
[1] cluster_1.11.10 tools_2.7.0



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

15032 Hunter Court, Westfield, IN 46074

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