From mwkimpel at gmail.com  Fri Jun 13 00:38:56 2008
From: mwkimpel at gmail.com (Mark Kimpel)
Date: Thu, 12 Jun 2008 18:38:56 -0400
Subject: [Rd] Rmpi segfault after install on Ubuntu Hardy Heron
In-Reply-To: <18511.50045.300225.144687@ron.nulle.part>
References: <6b93d1830806102146k1f91b723q2f7918d4a95043e6@mail.gmail.com>
	<18511.50045.300225.144687@ron.nulle.part>
Message-ID: <6b93d1830806121538t766daad8v367290677b799993@mail.gmail.com>

Dirk,

Configure concluded without errors. I am not running this on the HPC
cluster with icc, rather a separate local box used for testing and
learning. Its just an 64-bit Ubuntu 8.04 install on a 4-core machine.
LAM is not installed (I checked to make sure).

So, that leaves me with you last two options. Before I make my first
foray into using the R-debugger, I'd like to try you suggestion to
"Check ldd on Rmpi.so" but don't have a clue how to do so. Could you
instruct me?

Thanks to all for the helpful comments.
Mark

On Wed, Jun 11, 2008 at 8:22 AM, Dirk Eddelbuettel <edd at debian.org> wrote:
>
> On 11 June 2008 at 00:46, Mark Kimpel wrote:
> | 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"
>
> And it concluded without warnings or errors? Configure found all the right files?
>
> As Paul suggested, make sure you're not getting it mixed with
> exisiting LAM headers or MPICH2 headers or, say, that you're getting your gcc
> and icc experiemenst mixed up or ...  ?
>
> I control this by locally re-building the Debian packages for Open MPI. That
> way I only keep one -dev package for MPI and can ensure that I do not get
> mixups with other MPI installation. But then I do buy into the Package
> Management mantra, but not everybody does...
>
> | 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.
>
> Check ldd on Rmpi.so to ensure that you linked against what you thought you
> should link against.
>
> And if everything else fails, debug the compiled code and run R under the
> debuggger.  See the 'R Extensions' manual.
>
> | 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?
>
> I'd join.
>
> Dirk
>
> --
> Three out of two people have difficulties with fractions.
>
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>



-- 
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