[R] Rmpi installation

[Unger, Kristian, Dr.]

Thank you very much Hugo. Using the command as suggested results exactly
the same error:

# 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 ‘/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
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 ‘Rmpi’
* removing ‘/usr/local/lib64/R/library/Rmpi’


Best wishes

Kristian

________________________________________
Dr. Kristian Unger


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

Tel.: +49-89-3187-3515

Mob.: +49-160-90641879





Am 15.06.11 15:12 schrieb "Hugo Mildenberger" unter
<Hugo.Mildenberger at web.de>:

>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
>>
>>
>> Helmholtz Zentrum München
>> Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH)
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>>
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Helmholtz Zentrum München
Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH)
Ingolstädter Landstr. 1
85764 Neuherberg
www.helmholtz-muenchen.de
Aufsichtsratsvorsitzende: MinDir´in Bärbel Brumme-Bothe
Geschäftsführer: Prof. Dr. Günther Wess und Dr. Nikolaus Blum
Registergericht: Amtsgericht München HRB 6466
USt-IdNr: DE 129521671