[R] Rmpi installation

Hugo Mildenberger Hugo.Mildenberger at web.de
Wed Jun 15 15:12:49 CEST 2011


Hmm, 

looks like there was a trailing blank after the backslash and before end of line, 
resulting in --with-Rmpi-libpath possibly not recognised: 

  > \--with-Rmpi-libpath=/usr/lib64/mpi/gcc/openmpi/lib64 \

I also doubt there is real need to escape newlines within a string. But another 
possible problem source is that according to R CMD INSTALL --help, the parameter 
is called  "--configure-args", not "configure.args". 


$ 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

Best



On Wednesday 15 June 2011 14:25:46 Unger, Kristian, Dr. wrote:
> 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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