[R] Rmpi Segmentation fault

hpbenton at scripps.edu hpbenton at scripps.edu
Fri Feb 6 20:35:18 CET 2009


Dear all,

I have used the Rmpi package many times before however this time 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 doens'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?

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_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\"
-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_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\"
-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_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\"
-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_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\"
-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)



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