[R-sig-hpc] installing Rmpi

[Markus Schmidberger]

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