[R] Rmpi Segmentation fault
Jeff Squyres
jsquyres at cisco.com
Sat Feb 7 14:00:12 CET 2009
Doh! I should have added Paul to the CC of the mail I just sent (I
don't know if my mail will go through to r-help since I'm not
subscribed)...
I'll re-send to Paul.
This *appears* to be some deep linker voodoo. Our other thread
reveals that this works for 32 bit and not for 64 bit, which is quite
mystifying...
On Feb 6, 2009, at 3:13 PM, Dirk Eddelbuettel wrote:
>
> 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.
--
Jeff Squyres
Cisco Systems
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