[R] Rmpi Segmentation fault

Dirk Eddelbuettel edd at debian.org
Fri Feb 6 21:13:18 CET 2009


On 6 February 2009 at 19:37, Paul Benton wrote:
| Dear all,
| I have used the Rmpi package many times before however this time the
| installation doesn't work :(. I've
| installed it as I always do with openMPI tar.gz file direct from the
| website. I'm installing on my ubuntu 8.10, R version 2.8.1.
| Linux 2.6.27-11-generic #1 SMP Thu Jan 29 19:28:32 UTC 2009 x86_64 GNU/Linux
| All i get is:
| > library(Rmpi)
| Segmentation fault
| :~$
| Which dumps me back into the shell, and doesn't give me much to work with.
| I've included my install of Rmpi that went fine as far as I could see. Is
| this a openMPI problem or Rmpi or even an R problem? Any help would be
| great. Also is there a way beside 'make test' to test my install of
| openMPI?

Welcome to hell!  

I have been chasing the same issue for well over a week on the same platform
(by locally rebuilding the Debian Open MPI package on Ubuntu amd64) and am
really no further.  The seg fault happens 'deep down' in the mca

I have been in contact with Hao Yu (upstream for Rmpi) and Jeff Squires and
Brian Barrett from Open MPI (after first reporting it on the ompi list
myself) who are as puzzled.  It is seems to be an intersection of amd64 and
ompi and Rmpi -- i386 works fine.

The r-sig-hpc list may be more topical, by the way.

Debugging help would be welcome!


| Cheers,
| Paul
| ------Rmpi install --------------------------
| ~$ sudo R CMD INSTALL Rmpi_0.5-6.tar.gz
| * Installing to library '/usr/local/lib64/R/library'
| * Installing *source* package 'Rmpi' ...
| checking for gcc... gcc
| checking for C compiler default output file name... a.out
| checking whether the C compiler works... yes
| checking whether we are cross compiling... no
| checking for suffix of executables...
| checking for suffix of object files... o
| checking whether we are using the GNU C compiler... yes
| checking whether gcc accepts -g... yes
| checking for gcc option to accept ISO C89... none needed
| I am here /usr/local and it is OpenMPI
| Try to find mpi.h ...
| Found in /usr/local/include
| Try to find libmpi.so or libmpich.a
| Found libmpi in /usr/local/lib
| checking for openpty in -lutil... yes
| checking for main in -lpthread... yes
| configure: creating ./config.status
| config.status: creating src/Makevars
| ** libs
| gcc -std=gnu99 -I/usr/local/lib64/R/include -DPACKAGE_NAME=\"\"
| -DPACKAGE_BUGREPORT=\"\" -I/usr/local/include -DMPI2 -DOPENMPI -fPIC
| -I/usr/local/include    -fpic  -g -O2 -c conversion.c -o conversion.o
| gcc -std=gnu99 -I/usr/local/lib64/R/include -DPACKAGE_NAME=\"\"
| -DPACKAGE_BUGREPORT=\"\" -I/usr/local/include -DMPI2 -DOPENMPI -fPIC
| -I/usr/local/include    -fpic  -g -O2 -c internal.c -o internal.o
| gcc -std=gnu99 -I/usr/local/lib64/R/include -DPACKAGE_NAME=\"\"
| -DPACKAGE_BUGREPORT=\"\" -I/usr/local/include -DMPI2 -DOPENMPI -fPIC
| -I/usr/local/include    -fpic  -g -O2 -c RegQuery.c -o RegQuery.o
| gcc -std=gnu99 -I/usr/local/lib64/R/include -DPACKAGE_NAME=\"\"
| -DPACKAGE_BUGREPORT=\"\" -I/usr/local/include -DMPI2 -DOPENMPI -fPIC
| -I/usr/local/include    -fpic  -g -O2 -c Rmpi.c -o Rmpi.o
| gcc -std=gnu99 -shared -L/usr/local/lib64 -o Rmpi.so conversion.o
| internal.o RegQuery.o Rmpi.o -L/usr/local/lib -lmpi -lutil -lpthread -fPIC
| ** R
| ** demo
| ** inst
| ** preparing package for lazy loading
| ** help
|  >>> Building/Updating help pages for package 'Rmpi'
|      Formats: text html latex example
|   hosts                             text    html    latex
|   internal                          text    html    latex
|   mpi.abort                         text    html    latex
|   mpi.apply                         text    html    latex   example
|   mpi.barrier                       text    html    latex
|   mpi.bcast                         text    html    latex
|   mpi.bcast.Robj                    text    html    latex
|   mpi.bcast.cmd                     text    html    latex
|   mpi.cart.coords                   text    html    latex   example
|   mpi.cart.create                   text    html    latex   example
|   mpi.cart.get                      text    html    latex   example
|   mpi.cart.rank                     text    html    latex   example
|   mpi.cart.shift                    text    html    latex   example
|   mpi.cartdim.get                   text    html    latex   example
|   mpi.comm                          text    html    latex   example
|   mpi.comm.disconnect               text    html    latex
|   mpi.comm.free                     text    html    latex
|   mpi.comm.inter                    text    html    latex
|   mpi.comm.set.errhandler           text    html    latex
|   mpi.comm.spawn                    text    html    latex
|   mpi.const                         text    html    latex
|   mpi.dims.create                   text    html    latex   example
|   mpi.exit                          text    html    latex
|   mpi.finalize                      text    html    latex
|   mpi.gather                        text    html    latex   example
|   mpi.gather.Robj                   text    html    latex   example
|   mpi.get.count                     text    html    latex
|   mpi.get.processor.name            text    html    latex
|   mpi.get.sourcetag                 text    html    latex
|   mpi.info                          text    html    latex
|   mpi.init.sprng                    text    html    latex
|   mpi.intercomm.merge               text    html    latex
|   mpi.parSim                        text    html    latex
|   mpi.parapply                      text    html    latex   example
|   mpi.probe                         text    html    latex
|   mpi.realloc                       text    html    latex
|   mpi.reduce                        text    html    latex
|   mpi.remote.exec                   text    html    latex   example
|   mpi.scatter                       text    html    latex   example
|   mpi.scatter.Robj                  text    html    latex   example
|   mpi.send                          text    html    latex   example
|   mpi.send.Robj                     text    html    latex
|   mpi.sendrecv                      text    html    latex   example
|   mpi.setup.rng                     text    html    latex
|   mpi.spawn.Rslaves                 text    html    latex   example
|   mpi.universe.size                 text    html    latex
|   mpi.wait                          text    html    latex
| ** building package indices ...
| * DONE (Rmpi)
| 	[[alternative HTML version deleted]]
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