[R] Rmpi installation

[Unger, Kristian, Dr.]

Hi there

I am trying to install Rmpi (version 0.5-4) on our 8-core SUSE Linux
Enterprise Server 11 SP1. I read all I could find about Rmpi installation
but still cannot get it working.

Here the last command that I used:

R CMD INSTALL
--configure.args="--with-Rmpi-include=/usr/lib64/mpi/gcc/openmpi/include \
--with-Rmpi-libpath=/usr/lib64/mpi/gcc/openmpi/lib64 \
--with-Rmpi-type=OPENMPI" Rmpi_0.5-4.tar.gz

Resulting in the following:

zytosrv01dmi:/home/unger/R_projects/OS # R CMD INSTALL
--configure-args="--with-Rmpi-include=/usr/lib64/mpi/gcc/openmpi/include
\--with-Rmpi-libpath=/usr/lib64/mpi/gcc/openmpi/lib64 \
--with-Rmpi-type=OPENMPI" Rmpi_0.5-4.tar.gz
* installing to library Œ/usr/local/lib64/R/library¹
* installing *source* package ŒRmpi¹ ...
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
checking how to run the C preprocessor... gcc -E
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking mpi.h usability... no
checking mpi.h presence... no
checking for mpi.h... no
Try to find libmpi or libmpich ...
checking for main in -lmpi... no
libmpi not found. exiting...
ERROR: configuration failed for package ŒRmpi¹
* removing Œ/usr/local/lib64/R/library/Rmpi¹

So obviously libmpi is not found. Doing a locate search for "libmpi"
(straight after updatedb) shows:

zytosrv01dmi:/home/unger/R_projects/OS # locate libmpi
/opt/mpich/ch-p4/lib64/libmpich.a
/opt/mpich/ch-p4/lib64/libmpichf90.a
/opt/mpich/ch-p4/lib64/libmpichf90nc.a
/opt/mpich/ch-p4/lib64/libmpichfarg.a
/opt/mpich/ch-p4/lib64/libmpichfsup.a
/opt/mpich/ch-p4mpd/lib64/libmpich.a
/opt/mpich/ch-p4mpd/lib64/libmpichf90.a
/opt/mpich/ch-p4mpd/lib64/libmpichf90nc.a
/opt/mpich/ch-p4mpd/lib64/libmpichfarg.a
/opt/mpich/ch-p4mpd/lib64/libmpichfsup.a
/usr/lib64/mpi/gcc/openmpi/lib64/libmpi_cxx.la
/usr/lib64/mpi/gcc/openmpi/lib64/libmpi_cxx.so
/usr/lib64/mpi/gcc/openmpi/lib64/libmpi_cxx.so.0
/usr/lib64/mpi/gcc/openmpi/lib64/libmpi_cxx.so.0.0.0
/usr/lib64/mpi/gcc/openmpi/lib64/libmpi_f77.la
/usr/lib64/mpi/gcc/openmpi/lib64/libmpi_f77.so
/usr/lib64/mpi/gcc/openmpi/lib64/libmpi_f77.so.0
/usr/lib64/mpi/gcc/openmpi/lib64/libmpi_f77.so.0.0.0
/usr/lib64/mpi/gcc/openmpi/lib64/libmpi_f90.la
/usr/lib64/mpi/gcc/openmpi/lib64/libmpi_f90.so
/usr/lib64/mpi/gcc/openmpi/lib64/libmpi_f90.so.0
/usr/lib64/mpi/gcc/openmpi/lib64/libmpi_f90.so.0.0.0
/usr/lib64/mpi/gcc/openmpi/lib64/libmpi.la
/usr/lib64/mpi/gcc/openmpi/lib64/libmpi.so
/usr/lib64/mpi/gcc/openmpi/lib64/libmpi.so.0
/usr/lib64/mpi/gcc/openmpi/lib64/libmpi.so.0.0.0

What lets me assume that the path to libmpi is
/usr/lib64/mpi/gcc/openmpi/lib64 which I already included in the options...


How can I get this working?

I would highly appreciate any help on this!

Best wishes

Kristian



________________________________________
Dr. Kristian Unger


Arbeitsgruppenleiter Integrative Biologie / Head of Integrative Biology
Group
Abteilung für Strahlenzytogenetik / Research Unit of Radiation Cytogenetics


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