From mtmorgan at fhcrc.org  Fri Jun 13 01:52:50 2008
From: mtmorgan at fhcrc.org (Martin Morgan)
Date: Thu, 12 Jun 2008 16:52:50 -0700
Subject: [Rd] Rmpi segfault after install on Ubuntu Hardy Heron
In-Reply-To: <4851B4B1.2090508@ebi.ac.uk>
References: <6b93d1830806102146k1f91b723q2f7918d4a95043e6@mail.gmail.com>	<18511.50045.300225.144687@ron.nulle.part>	<6b93d1830806121538t766daad8v367290677b799993@mail.gmail.com>
	<4851B4B1.2090508@ebi.ac.uk>
Message-ID: <4851B6D2.6050503@fhcrc.org>

Oleg Sklyar wrote:
> simply cd to $R_HOME/library/Rmpi/libs and do on the command line
> 
> ldd -r Rmpi.so

I think you'll want to

R CMD ldd $R_HOME/library/Rmpi/libs/Rmpi.so

which picks up the R configuration environment, e.g., compare BLAS below:

mtmorgan at lamprey:~/> R CMD ldd $R_HOME/library/stats/libs/stats.so
         libRblas.so => 
/home/mtmorgan/arch/x86_64/R-devel/lib/libRblas.so (0x00002b543f98b000)
         libgfortran.so.2 => /usr/lib64/libgfortran.so.2 
(0x00002b543fc09000)
         libm.so.6 => /lib64/libm.so.6 (0x00002b543fec4000)
         libc.so.6 => /lib64/libc.so.6 (0x00002b5440118000)
         /lib64/ld-linux-x86-64.so.2 (0x0000555555554000)
mtmorgan at lamprey:~/s> ldd $R_HOME/library/stats/libs/stats.so
         libRblas.so => not found
         libgfortran.so.2 => /usr/lib64/libgfortran.so.2 
(0x00002aeabd923000)
         libm.so.6 => /lib64/libm.so.6 (0x00002aeabdbde000)
         libc.so.6 => /lib64/libc.so.6 (0x00002aeabde32000)
         /lib64/ld-linux-x86-64.so.2 (0x0000555555554000)

Martin

> 
> 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
>>>
>>
>>
>>
> 


-- 
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109

Location: Arnold Building M2 B169
Phone: (206) 667-2793



[Rd] Rmpi segfault after install on Ubuntu Hardy Heron
Martin Morgan