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Subject: Re: [OMPI users] Rmpi installation issues
From: Jeff Squyres (jsquyres_at_[hidden])
Date: 2008-10-13 08:14:45


We always recommend using the Open MPI "wrapper" compilers instead of
directly using gcc. There are very few scenarios where it is better
to use the native compilers directly.

You might want to check with the RMPI authors for more details; I'm
afraid that I don't know anything about that package.

On Oct 13, 2008, at 5:22 AM, Simone Giannerini wrote:

> Dear all,
>
> I have troubles installing rmpi 0.5-5 (or 0.5-6) on a quad opteron
> machine with OpenSUSE 11.0 and
> R 2.7.2
>
> platform x86_64-unknown-linux-gnu
> arch x86_64
> os linux-gnu
> system x86_64, linux-gnu
> status Patched
> major 2
> minor 7.2
> year 2008
> month 09
> day 18
> svn rev 46546
> language R
> version.string R version 2.7.2 Patched (2008-09-18 r46546)
>
> I tried the following
>
> # export MPI_ROOT=/usr/lib64/mpi/gcc/openmpi/
>
> # 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
> Try to find mpi.h ...
> Found in /usr/lib64/mpi/gcc/openmpi//include
> Try to find libmpi.so or libmpich.a
> checking for main in -lmpi... yes
> 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/lib64/mpi/gcc/openmpi//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/lib64/mpi/gcc/openmpi//include -DMPI2
> -DOPENMPI -fPIC -I/usr/local/include -fpic -g -O2 -c Rmpi.c -o
> Rmpi.o
> gcc -std=gnu99 -I/usr/local/lib64/R/include -DPACKAGE_NAME=\"\" -
> DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -
> DPACKAGE_BUGREPORT=\"\" -I/usr/lib64/mpi/gcc/openmpi//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/lib64/mpi/gcc/openmpi//include -DMPI2
> -DOPENMPI -fPIC -I/usr/local/include -fpic -g -O2 -c internal.c -
> o internal.o
> gcc -std=gnu99 -shared -L/usr/local/lib64 -o Rmpi.so RegQuery.o
> Rmpi.o conversion.o internal.o -L/usr/lib64/mpi/gcc/openmpi//lib -
> lmpi -lutil -lpthread -fPIC
> /usr/lib64/gcc/x86_64-suse-linux/4.3/../../../../x86_64-suse-linux/
> bin/ld: cannot find -lmpi
> collect2: ld returned 1 exit status
> make: *** [Rmpi.so] Error 1
> chmod: cannot access `/usr/local/lib64/R/library/Rmpi/libs/*': No
> such file or directory
> ERROR: compilation failed for package 'Rmpi'
> ** Removing '/usr/local/lib64/R/library/Rmpi'
>
> I also tried with
>
> R CMD INSTALL Rmpi_0.5-6.tar.gz --configure-args=--with-mpi=/usr/
> lib64/mpi/gcc/openmpi/
>
> with the same results.
> Any help would be greatly appreciated.
>
> Regards
>
> Simone Giannerini
>
>
>
> --
> ______________________________________________________
>
> Simone Giannerini
> Dipartimento di Scienze Statistiche "Paolo Fortunati"
> Universita' di Bologna
> Via delle belle arti 41 - 40126 Bologna, ITALY
> Tel: +39 051 2098262 Fax: +39 051 232153
> http://www2.stat.unibo.it/giannerini/
> ______________________________________________________
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-- 
Jeff Squyres
Cisco Systems