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 <[EMAIL PROTECTED]> 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@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@r-project.org mailing list | https://stat.ethz.ch/mailman/listinfo/r-devel -- Three out of two people have difficulties with fractions. ______________________________________________ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel