From osklyar at maninvestments.com  Wed Jun 11 11:38:59 2008
From: osklyar at maninvestments.com (Sklyar, Oleg (MI London))
Date: Wed, 11 Jun 2008 10:38:59 +0100
Subject: [Rd] Rmpi segfault after install on Ubuntu Hardy Heron
In-Reply-To: <6b93d1830806102146k1f91b723q2f7918d4a95043e6@mail.gmail.com>
References: <6b93d1830806102146k1f91b723q2f7918d4a95043e6@mail.gmail.com>
Message-ID: <1A68FCB28DE72F4BA3B967E6506CCE4302294977@mildnpexmb01.maninvestments.ad.man.com>

Does Rmpi work with OpenMPI at all? It calls lamboot on load from LAM
MPI. I would think that mpi_initialize calls a shared library function
from LAM MPI which simply does not exist in OpenMPI or which does
something different from what it expects. If you ever make Rmpi working
with OpenMPI I would be thankful for the solution. It does compile
against OpenMPI though because the header seems to be matching.

Dr Oleg Sklyar
Technology Group
Man Investments Ltd
+44 (0)20 7144 3803
osklyar at maninvestments.com 

> -----Original Message-----
> From: r-devel-bounces at r-project.org 
> [mailto:r-devel-bounces at r-project.org] On Behalf Of Mark Kimpel
> Sent: 11 June 2008 05:47
> To: r-devel at stat.math.ethz.ch; Dirk Eddelbuettel
> Subject: [Rd] Rmpi segfault after install on Ubuntu Hardy Heron
> 
> 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
> 
> 
> R version 2.7.0 Patched (2008-05-18 r45728) Copyright (C) 
> 2008 The R Foundation for Statistical Computing ISBN 3-900051-07-0
> 
> R is free software and comes with ABSOLUTELY NO WARRANTY.
> You are welcome to redistribute it under certain conditions.
> Type 'license()' or 'licence()' for distribution details.
> 
>   Natural language support but running in an English locale
> 
> R is a collaborative project with many contributors.
> Type 'contributors()' for more information and 'citation()' 
> on how to cite R or R packages in publications.
> 
> Type 'demo()' for some demos, 'help()' for on-line help, or 
> 'help.start()' for an HTML browser interface to help.
> Type 'q()' to quit R.
> 
> 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
> 
> 15032 Hunter Court, Westfield, IN 46074
> 
> (317) 490-5129 Work, & Mobile & VoiceMail
> (317) 663-0513 Home (no voice mail please)
> 
> ______________________________________________
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> 


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[Rd] Rmpi segfault after install on Ubuntu Hardy Heron
Sklyar, Oleg (MI London