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
[EMAIL PROTECTED]:~/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
(317) 490-5129 Work, & Mobile & VoiceMail
(317) 663-0513 Home (no voice mail please)
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