[R-sig-hpc] Problem installing Rmpi on SuSE 64 bit system: does compile but does not load

[Rainer M Krug]

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Hi

I am having problems installing Rmpi on a 64 bit system running SuSE
(version not known to me at the moment).

R is compiled from source in my home directory, and everything works fine.

I do the following:

#Make sure that R-12.2.0 is used
> export PATH=/home/rkrug/R/R/R-2.12.0/bin/:$PATH

# load module for openmpi-1.4.2
> module load  openmpi-1.4.2

# Check that it is loaded
> mpirun --version
mpirun (Open MPI) 1.4.2r22761-ct8.2.1c-b11a-r31

Report bugs to http://www.open-mpi.org/community/help/

# OK - fine

# Try to install Rmpi
> R  CMD INSTALL --configure.args="--with-mpi=/usr/src/openmpi-1.4.2"
R/packages/Rmpi_0.5-8.tar.gz
Warning: unknown option ‘--configure.args=--with-mpi=/usr/src/openmpi-1.4.2’
* installing to library ‘/home/rkrug/R/R/R-2.12.0/library’
* installing *source* package ‘Rmpi’ ...
checking for gcc... gcc -std=gnu99
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 -std=gnu99 accepts -g... yes
checking for gcc -std=gnu99 option to accept ISO C89... none needed
I am here /usr
Trying to find mpi.h ...
Found in /usr/include
Trying 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/home/rkrug/R/R/R-2.12.0/include -DPACKAGE_NAME=\"\"
- -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\"
- -DPACKAGE_BUGREPORT=\"\" -I/usr/include  -DMPI2 -DOPENMPI
- -I/usr/local/include    -fpic  -march=core2 -O3 -c RegQuery.c -o
RegQuery.o
gcc -std=gnu99 -I/home/rkrug/R/R/R-2.12.0/include -DPACKAGE_NAME=\"\"
- -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\"
- -DPACKAGE_BUGREPORT=\"\" -I/usr/include  -DMPI2 -DOPENMPI
- -I/usr/local/include    -fpic  -march=core2 -O3 -c Rmpi.c -o Rmpi.o
gcc -std=gnu99 -I/home/rkrug/R/R/R-2.12.0/include -DPACKAGE_NAME=\"\"
- -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\"
- -DPACKAGE_BUGREPORT=\"\" -I/usr/include  -DMPI2 -DOPENMPI
- -I/usr/local/include    -fpic  -march=core2 -O3 -c conversion.c -o
conversion.o
gcc -std=gnu99 -I/home/rkrug/R/R/R-2.12.0/include -DPACKAGE_NAME=\"\"
- -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\"
- -DPACKAGE_BUGREPORT=\"\" -I/usr/include  -DMPI2 -DOPENMPI
- -I/usr/local/include    -fpic  -march=core2 -O3 -c internal.c -o
internal.o
gcc -std=gnu99 -lpthread -shared -Bdirect,--hash-style=both,-Wl,-O1 -o
Rmpi.so RegQuery.o Rmpi.o conversion.o internal.o -L/usr/lib -lmpi
- -lutil -lpthread -L/home/rkrug/R/R/R-2.12.0/lib -lR
/usr/lib64/gcc/x86_64-suse-linux/4.3/../../../../x86_64-suse-linux/bin/ld:
skipping incompatible /usr/lib/libpthread.so when searching for -lpthread
/usr/lib64/gcc/x86_64-suse-linux/4.3/../../../../x86_64-suse-linux/bin/ld:
skipping incompatible /usr/lib/libpthread.a when searching for -lpthread
/usr/lib64/gcc/x86_64-suse-linux/4.3/../../../../x86_64-suse-linux/bin/ld:
skipping incompatible /usr/lib/libutil.so when searching for -lutil
/usr/lib64/gcc/x86_64-suse-linux/4.3/../../../../x86_64-suse-linux/bin/ld:
skipping incompatible /usr/lib/libutil.a when searching for -lutil
/usr/lib64/gcc/x86_64-suse-linux/4.3/../../../../x86_64-suse-linux/bin/ld:
skipping incompatible /usr/lib/libpthread.so when searching for -lpthread
/usr/lib64/gcc/x86_64-suse-linux/4.3/../../../../x86_64-suse-linux/bin/ld:
skipping incompatible /usr/lib/libpthread.a when searching for -lpthread
/usr/lib64/gcc/x86_64-suse-linux/4.3/../../../../x86_64-suse-linux/bin/ld:
skipping incompatible /usr/lib/libc.so when searching for -lc
/usr/lib64/gcc/x86_64-suse-linux/4.3/../../../../x86_64-suse-linux/bin/ld:
skipping incompatible /usr/lib/libc.a when searching for -lc
installing to /home/rkrug/R/R/R-2.12.0/library/Rmpi/libs
** R
** demo
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded
/home/rkrug/R/R/R-2.12.0/bin/exec/R: symbol lookup error:
/usr/lib64/openmpi/mca_paffinity_linux.so: undefined symbol:
mca_base_param_reg_int


So - what is happening here? As I understand it, it is compiling, but
can not be loaded, as "undefined symbol".

Could anyone please shed some light on this issue, as I am stuck.

Thanks,

Rainer


- -- 
Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation
Biology, UCT), Dipl. Phys. (Germany)

Centre of Excellence for Invasion Biology
Natural Sciences Building
Office Suite 2039
Stellenbosch University
Main Campus, Merriman Avenue
Stellenbosch
South Africa

Tel:        +33 - (0)9 53 10 27 44
Cell:       +27 - (0)8 39 47 90 42
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Fax (FR):   +33 - (0)9 58 10 27 44
email:      Rainer at krugs.de

Skype:      RMkrug
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