From edd at debian.org  Wed Jun 11 14:22:21 2008
From: edd at debian.org (Dirk Eddelbuettel)
Date: Wed, 11 Jun 2008 07:22:21 -0500
Subject: [Rd] Rmpi segfault after install on Ubuntu Hardy Heron
In-Reply-To: <6b93d1830806102146k1f91b723q2f7918d4a95043e6@mail.gmail.com>
References: <6b93d1830806102146k1f91b723q2f7918d4a95043e6@mail.gmail.com>
Message-ID: <18511.50045.300225.144687@ron.nulle.part>


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.



[Rd] Rmpi segfault after install on Ubuntu Hardy Heron
Dirk Eddelbuettel