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Subject: Re: [OMPI users] Rmpi installation issues
From: Sean Davis (sdavis2_at_[hidden])
Date: 2008-10-13 08:38:02


On Mon, Oct 13, 2008 at 8:14 AM, Jeff Squyres <jsquyres_at_[hidden]> wrote:
> 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.

To be explicit, try:

CC="mpicc" R CMD INSTALL Rmpi_0.5-6.tar.gz

Sean

> 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/
>> ______________________________________________________
>> _______________________________________________
>> users mailing list
>> users_at_[hidden]
>> http://www.open-mpi.org/mailman/listinfo.cgi/users
>
>
> --
> Jeff Squyres
> Cisco Systems
>
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