From edd at debian.org  Fri Jun 13 03:17:09 2008
From: edd at debian.org (Dirk Eddelbuettel)
Date: Thu, 12 Jun 2008 20:17:09 -0500
Subject: [Rd] Rmpi segfault after install on Ubuntu Hardy Heron
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Message-ID: <18513.51861.102932.518310@ron.nulle.part>


On 12 June 2008 at 18:38, Mark Kimpel wrote:
| 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?

ldd is a command so try 'man ldd'; or just use what Oleg and Martin showed
you.

You still told us where you got R, Rmpi, and Open MPI from.  You could just
do

	$ sudo apt-get install r-cran-rmpi

and get Rmpi installed along with its dependencies (eg R and Open MPI).  That
just works on Debian.  It also worked, as I recall, on Ubuntu 'Gutsy' aka 7.10.

However, on Ubuntu 'Hardy' aka 8.04, this may be broken as I discovered
during some testing for the HPC presentation I'll be giving at Use R. I
filed an Ubuntu bug report at

     https://bugs.launchpad.net/ubuntu/+source/binutils/+bug/234837

but no follow-up has happened.

That said, this still all works for me at 

     a) at work which is x86 and all Ubuntu machines

     b) at home where it is x86 and a mix of Debian and Ubuntu machines

_but_ only after I rebuilt openmpi_1.2.5 on an older Gutsy machine as
detailed in the bugreport. Something on Hardy breaks it. 

I am not an Ubuntu maintainer, so I am not sure who to talk to.  I'll forward
a copy of this to the Ubuntu folks.

As an aside, the Debian packages all work.

Dirk
 
| 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
| 
| 15032 Hunter Court, Westfield, IN 46074
| 
| (317) 490-5129 Work, & Mobile & VoiceMail
| (317) 663-0513 Home (no voice mail please)
| 
| ______________________________________________
| R-devel at r-project.org mailing list
| https://stat.ethz.ch/mailman/listinfo/r-devel

-- 
Three out of two people have difficulties with fractions.



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