[R] Rmpi Segmentation fault
Dirk Eddelbuettel
edd at debian.org
Fri Feb 6 21:13:18 CET 2009
Paul,
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
initialisation.
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!
Dirk
|
| 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)
|
| [[alternative HTML version deleted]]
|
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--
Three out of two people have difficulties with fractions.
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