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.
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/
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--
Jeff Squyres
Cisco Systems
