[R-sig-hpc] installing Rmpi

[Hao Yu]

Markus,

Can you try to take -fPIC flag out in Rmpi (comment out the line
PKG_LIBS="${MPI_LIBS} -fPIC" in configure.ac)? The flag -fPIC was added
due to the same reason.

Hao

Markus Schmidberger wrote:
> Hi,
>
> I have R 2.9.2 compiled with gcc.
> Now I try to INSTALL Rmpi, linked to the correct header files. The
> configure-file finds everything correct, but than fails.
>
> Any idea?
>
>  R CMD INSTALL Rmpi_0.5-7.tar.gz
> --configure-args=--with-mpi=/lrz/sys/parallel/openmpi/1.3.0/altix_shm
> * Installing to library '/home/hlrb2/pr32di/lu57waf2/ia64/Rlibrary'
> * 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 /lrz/sys/parallel/openmpi/1.3.0/altix_shm/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/lrz/sys/applications/R/2.8.1gccO3//lib/R/include
> -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DP
> ACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\"
> -I/lrz/sys/parallel/openmpi/1.3.0/altix_shm/in                   clude
> -DMPI2 -DOPENMPI -fPIC -I/usr/local/include    -fPIC  -O3 -c
> conversion.c -o conversion.o
> gcc -std=gnu99 -I/lrz/sys/applications/R/2.8.1gccO3//lib/R/include
> -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DP
> ACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\"
> -I/lrz/sys/parallel/openmpi/1.3.0/altix_shm/in                   clude
> -DMPI2 -DOPENMPI -fPIC -I/usr/local/include    -fPIC  -O3 -c internal.c
> -o internal.o
> gcc -std=gnu99 -I/lrz/sys/applications/R/2.8.1gccO3//lib/R/include
> -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DP
> ACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\"
> -I/lrz/sys/parallel/openmpi/1.3.0/altix_shm/in                   clude
> -DMPI2 -DOPENMPI -fPIC -I/usr/local/include    -fPIC  -O3 -c RegQuery.c
> -o RegQuery.o
> gcc -std=gnu99 -I/lrz/sys/applications/R/2.8.1gccO3//lib/R/include
> -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DP
> ACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\"
> -I/lrz/sys/parallel/openmpi/1.3.0/altix_shm/in                   clude
> -DMPI2 -DOPENMPI -fPIC -I/usr/local/include    -fPIC  -O3 -c Rmpi.c -o
> Rmpi.o
> gcc -std=gnu99 -shared  -o Rmpi.so conversion.o internal.o RegQuery.o
> Rmpi.o -L/lrz/sys/parallel/openmpi/1.3.0/al
> tix_shm/lib -lmpi -lutil -lpthread -fPIC
> -L/lrz/sys/applications/R/2.8.1gccO3//lib/R/lib -lR
> /usr/lib/gcc/ia64-suse-linux/4.1.2/../../../../ia64-suse-linux/bin/ld:
> /lrz/sys/parallel/openmpi/1.3.0/altix_shm/
> lib/libmpi.a(ad_init.o): @gprel relocation against dynamic symbol
> ADIOI_Flatlist
> /usr/lib/gcc/ia64-suse-linux/4.1.2/../../../../ia64-suse-linux/bin/ld:
> final link failed: Nonrepresentable sectio                   n on output
> collect2: ld returned 1 exit status
> make: *** [Rmpi.so] Error 1
> chmod: cannot access
> `/home/hlrb2/pr32di/lu57waf2/ia64/Rlibrary/Rmpi/libs/*': No such file or
> directory
> ERROR: compilation failed for package 'Rmpi'
> ** Removing '/home/hlrb2/pr32di/lu57waf2/ia64/Rlibrary/Rmpi'
> ** Restoring previous '/home/hlrb2/pr32di/lu57waf2/ia64/Rlibrary/Rmpi'
>
> Thanks
> Markus
>
>
> --
> Dipl.-Tech. Math. Markus Schmidberger
>
> Ludwig-Maximilians-Universität München
> IBE - Institut für medizinische Informationsverarbeitung,
> Biometrie und Epidemiologie
> Marchioninistr. 15, D-81377 Muenchen
> URL: http://www.ibe.med.uni-muenchen.de
> Mail: Markus.Schmidberger [at] ibe.med.uni-muenchen.de
> Tel: +49 (089) 7095 - 4497
>


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