From osklyar at ebi.ac.uk  Fri Jun 13 01:43:45 2008
From: osklyar at ebi.ac.uk (Oleg Sklyar)
Date: Fri, 13 Jun 2008 00:43:45 +0100
Subject: [Rd] Rmpi segfault after install on Ubuntu Hardy Heron
In-Reply-To: <6b93d1830806121538t766daad8v367290677b799993@mail.gmail.com>
References: <6b93d1830806102146k1f91b723q2f7918d4a95043e6@mail.gmail.com>	<18511.50045.300225.144687@ron.nulle.part>
	<6b93d1830806121538t766daad8v367290677b799993@mail.gmail.com>
Message-ID: <4851B4B1.2090508@ebi.ac.uk>

simply cd to $R_HOME/library/Rmpi/libs and do on the command line

ldd -r Rmpi.so

this will display you a list of dependencies of Rmpi.so and you can see 
if you find there the libraries that you expected to link against, or 
there will be some libraries from unexpected paths or missing ones

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?
> 
> 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
>>
> 
> 
> 

-- 
Dr Oleg Sklyar * EBI-EMBL, Cambridge CB10 1SD, UK * +44-1223-494466



[Rd] Rmpi segfault after install on Ubuntu Hardy Heron
Oleg Sklyar