Rmpi segfault after install on Ubuntu Hardy Heron
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.
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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)