[R] Rmpi on Linux x86_64 GNU/Linux

[Martin Morgan]

Hi Brian --

Prof. Ripley's reply to an earlier question

http://tolstoy.newcastle.edu.au/R/e2/help/07/08/24306.html

points to the need for mpi to be compiled as a shared library. Hope
that helps,

Martin

"Brian O'Gorman" <Brian.O'Gorman at noaa.gov> writes:

> I'm having trouble with R CMD INSTALL Rmpi_0.5-5.tar.gz
> --configure-args=~/lam
>
> lam is is installed locally.
> lamboot  -d (or lamboot-d and also recon) works. make -k check from
> the lamtest suite passes all tests.
> Is this is problem with the -fPIC compiler as in the message? Should
> it be modified in the Makefile?
> Any help or comments are appreciated, thanks.
>
>
> * Installing to library
> /u1/uaf/ogorman/R/x86_64-unknown-linux-gnu-library/2.6'
> * 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 /import/home/u1/uaf/ogorman/lam/include
> Try to find libmpi.so or libmpich.a
> checking for main in -lmpi... yes
> Try to find liblam.so ...
> checking for main in -llam... 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/pkg/r/r-2.6.1/lib64/R/include
> -I/usr/local/pkg/r/r-2.6.1/lib64/R/include -DPACKAGE_NAME=\"\"
> -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\"
> -DPACKAGE_BUGREPORT=\"\" -I/import/home/u1/uaf/ogorman/lam/include
> -DMPI2 -DLAM -fPIC -I/usr/local/include    -fpic  -g -O2 -c
> conversion.c -o conversion.o
> gcc -std=gnu99 -I/usr/local/pkg/r/r-2.6.1/lib64/R/include
> -I/usr/local/pkg/r/r-2.6.1/lib64/R/include -DPACKAGE_NAME=\"\"
> -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\"
> -DPACKAGE_BUGREPORT=\"\" -I/import/home/u1/uaf/ogorman/lam/include
> -DMPI2 -DLAM -fPIC -I/usr/local/include    -fpic  -g -O2 -c internal.c
> -o internal.o
> gcc -std=gnu99 -I/usr/local/pkg/r/r-2.6.1/lib64/R/include
> -I/usr/local/pkg/r/r-2.6.1/lib64/R/include -DPACKAGE_NAME=\"\"
> -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\"
> -DPACKAGE_BUGREPORT=\"\" -I/import/home/u1/uaf/ogorman/lam/include
> -DMPI2 -DLAM -fPIC -I/usr/local/include    -fpic  -g -O2 -c RegQuery.c
> -o RegQuery.o
> gcc -std=gnu99 -I/usr/local/pkg/r/r-2.6.1/lib64/R/include
> -I/usr/local/pkg/r/r-2.6.1/lib64/R/include -DPACKAGE_NAME=\"\"
> -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\"
> -DPACKAGE_BUGREPORT=\"\" -I/import/home/u1/uaf/ogorman/lam/include
> -DMPI2 -DLAM -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/import/home/u1/uaf/ogorman/lam/lib
> -lmpi -llam -lutil -lpthread -fPIC
> /usr/lib64/gcc-lib/x86_64-suse-linux/3.3.3/../../../../x86_64-suse-linux/bin/ld:
> /import/home/u1/uaf/ogorman/lam/lib/libmpi.a(abort.o): relocation
> R_X86_64_32 can not be used when making a shared object; recompile
> with -fPIC
> /import/home/u1/uaf/ogorman/lam/lib/libmpi.a: could not read symbols:
> Bad value
> collect2: ld returned 1 exit status
> make: *** [Rmpi.so] Error 1
> chmod: cannot access
> /import/home/u1/uaf/ogorman/R/x86_64-unknown-linux-gnu-library/2.6/Rmpi/libs/*':
> No such file or directory
> ERROR: compilation failed for package 'Rmpi'
> ** Removing
> /import/home/u1/uaf/ogorman/R/x86_64-unknown-linux-gnu-library/2.6/Rmpi'
>
> -- 
> "The struggle for today, is not altogether for today - it is for a vast future also."
> 	-- Abraham Linclon, December 3, 1861
>
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-- 
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109

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