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Subject: [OMPI users] Rmpi installation issues
From: Simone Giannerini (sgiannerini_at_[hidden])
Date: 2008-10-13 05:22:49


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/
______________________________________________________