[R] Problem installing Rmpi with lam on SGI SLES9

[Hendrik Fuß]

Hi,

I've been trying here to install Rmpi on an SGI IA-64 machine with 64
processors, running SuSE Linux Enterprise Server 9, R 2.4.0 and
lam-mpi 7.1.3. While I've read of similar problems on this list, I
think I've got an entirely new set of error messages to contribute
(see below). I'm not sure what the actual error is and what the @gprel
relocation message is about. Any help greatly appreciated.

thanks
Hendrik


behemoth:~/Rmpi # R CMD INSTALL /home/hfuss/build/Rmpi_0.5-3.tar.gz
--configure-args=--with-mpi=/usr/local/lam-mpi
* Installing *source* package 'Rmpi' ...
Try to find mpi.h ...
Found in /usr/local/lam-mpi/include
Try to find libmpi or libmpich ...
Found libmpi in /usr/local/lam-mpi/lib
Try to find liblam ...
Found liblam in /usr/local/lam-mpi/lib
checking for openpty in -lutil... no
checking for main in -lpthread... no
configure: creating ./config.status
config.status: creating src/Makevars
** libs
gcc -I/usr/local/lib/R/include -I/usr/local/lib/R/include
-DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\"
-DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\"
-I/usr/local/lam-mpi/include -DMPI2 -I/usr/local/include    -fpic  -g
-O2 -std=gnu99 -c RegQuery.c -o RegQuery.o
gcc -I/usr/local/lib/R/include -I/usr/local/lib/R/include
-DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\"
-DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\"
-I/usr/local/lam-mpi/include -DMPI2 -I/usr/local/include    -fpic  -g
-O2 -std=gnu99 -c Rmpi.c -o Rmpi.o
gcc -I/usr/local/lib/R/include -I/usr/local/lib/R/include
-DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\"
-DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\"
-I/usr/local/lam-mpi/include -DMPI2 -I/usr/local/include    -fpic  -g
-O2 -std=gnu99 -c conversion.c -o conversion.o
gcc -I/usr/local/lib/R/include -I/usr/local/lib/R/include
-DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\"
-DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\"
-I/usr/local/lam-mpi/include -DMPI2 -I/usr/local/include    -fpic  -g
-O2 -std=gnu99 -c internal.c -o internal.o
gcc -shared -L/usr/local/lib -o Rmpi.so RegQuery.o Rmpi.o conversion.o
internal.o -L/usr/local/lam-mpi/lib -lmpi -llam
/usr/lib/gcc-lib/ia64-suse-linux/3.3.3/../../../../ia64-suse-linux/bin/ld:
/usr/local/lam-mpi/lib/libmpi.a(laminit.o): @gprel relocation against
dynamic symbol lam_comms
/usr/lib/gcc-lib/ia64-suse-linux/3.3.3/../../../../ia64-suse-linux/bin/ld:
/usr/local/lam-mpi/lib/libmpi.a(laminit.o): @gprel relocation against
dynamic symbol lam_argv0
/usr/lib/gcc-lib/ia64-suse-linux/3.3.3/../../../../ia64-suse-linux/bin/ld:
/usr/local/lam-mpi/lib/libmpi.a(laminit.o): @gprel relocation against
dynamic symbol lam_mpi_ao
/usr/lib/gcc-lib/ia64-suse-linux/3.3.3/../../../../ia64-suse-linux/bin/ld:
/usr/local/lam-mpi/lib/libmpi.a(laminit.o): @gprel relocation against
dynamic symbol lam_ger
/usr/lib/gcc-lib/ia64-suse-linux/3.3.3/../../../../ia64-suse-linux/bin/ld:
/usr/local/lam-mpi/lib/libmpi.a(laminit.o): @gprel relocation against
dynamic symbol lam_c2c
/usr/lib/gcc-lib/ia64-suse-linux/3.3.3/../../../../ia64-suse-linux/bin/ld:
/usr/local/lam-mpi/lib/libmpi.a(laminit.o): @gprel relocation against
dynamic symbol lam_appnum
/usr/lib/gcc-lib/ia64-suse-linux/3.3.3/../../../../ia64-suse-linux/bin/ld:
/usr/local/lam-mpi/lib/libmpi.a(laminit.o): @gprel relocation against
dynamic symbol lam_universe_size
/usr/lib/gcc-lib/ia64-suse-linux/3.3.3/../../../../ia64-suse-linux/bin/ld:
/usr/local/lam-mpi/lib/libmpi.a(laminit.o): @gprel relocation against
dynamic symbol lam_jobid
/usr/lib/gcc-lib/ia64-suse-linux/3.3.3/../../../../ia64-suse-linux/bin/ld:
/usr/local/lam-mpi/lib/libmpi.a(laminit.o): @gprel relocation against
dynamic symbol lam_jobid
/usr/lib/gcc-lib/ia64-suse-linux/3.3.3/../../../../ia64-suse-linux/bin/ld:
/usr/local/lam-mpi/lib/libmpi.a(laminit.o): @gprel relocation against
dynamic symbol lam_mpi_ao
/usr/lib/gcc-lib/ia64-suse-linux/3.3.3/../../../../ia64-suse-linux/bin/ld:
/usr/local/lam-mpi/lib/libmpi.a(laminit.o): @gprel relocation against
dynamic symbol lam_ger
/usr/lib/gcc-lib/ia64-suse-linux/3.3.3/../../../../ia64-suse-linux/bin/ld:
/usr/local/lam-mpi/lib/libmpi.a(laminit.o): @gprel relocation against
dynamic symbol lam_c2c
/usr/lib/gcc-lib/ia64-suse-linux/3.3.3/../../../../ia64-suse-linux/bin/ld:
/usr/local/lam-mpi/lib/libmpi.a(laminit.o): @gprel relocation against
dynamic symbol lam_appnum
/usr/lib/gcc-lib/ia64-suse-linux/3.3.3/../../../../ia64-suse-linux/bin/ld:
/usr/local/lam-mpi/lib/libmpi.a(laminit.o): @gprel relocation against
dynamic symbol lam_universe_size
/usr/lib/gcc-lib/ia64-suse-linux/3.3.3/../../../../ia64-suse-linux/bin/ld:
/usr/local/lam-mpi/lib/libmpi.a(laminit.o): @gprel relocation against
dynamic symbol lam_mpi_ao
/usr/lib/gcc-lib/ia64-suse-linux/3.3.3/../../../../ia64-suse-linux/bin/ld:
/usr/local/lam-mpi/lib/libmpi.a(laminit.o): @gprel relocation against
dynamic symbol lam_clockskew
collect2: ld returned 1 exit status
make: *** [Rmpi.so] Error 1
chmod: cannot access `/usr/local/lib/R/library/Rmpi/libs/*': No such
file or directory
ERROR: compilation failed for package 'Rmpi'
** Removing '/usr/local/lib/R/library/Rmpi'


-- 
Hendrik Fuß
PhD student
Systems Biology Research Group

University of Ulster, School of Biomedical Sciences
Cromore Road, Coleraine, BT52 1SA, Northern Ireland