[R] Rmpi installation

Unger, Kristian, Dr. unger at helmholtz-muenchen.de
Wed Jun 15 16:22:07 CEST 2011 

Thanks Hugo.

I am pretty sure openmpi is installed:

# zypper se openmpi
Loading repository data...
Reading installed packages...

S | Name          | Summary                         | Type
--+---------------+---------------------------------+-----------
i | openmpi       | A powerful implementaion of MPI | package
  | openmpi       | A powerful implementaion of MPI | srcpackage
i | openmpi-devel | A powerful implementaion of MPI | package



I got the same error message with the latest version available. The reason
why I took the somewhat older version is that I wanted to make sure that
it is not related to any libraries used by the newest version.

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 16:16 schrieb "Hugo Mildenberger" unter
<Hugo.Mildenberger at web.de>:

>Kristian,
>
>I just tried that particular command here on a Gentoo system with
>openmpi-1.5.3 installed, because I wondered why the Rmpi configure
>script tests for "main" function in a shared library ...
>
>But I got a completly different output from configure. While the
>linker succeeds here, the package load test does not. However, on your
>system, may be the openmpi installation really is a kinda private one of
>gcc? I heard gcc makes use of openmpi internally. So is openmpi really
>installed?
>
>I just recognize that you are trying to use Rmpi_0.5-4.tar.gz while
>current
>version on  CRAN is Rmpi_0.5-9.tar.gz.
>
>Best
>
>Hugo
>
>R CMD INSTALL --configure-args="--with-Rmpi-include=/usr/include
>--with-Rmpi-libpath=/usr/lib64/openmpi --with-Rmpi-type=OPENMPI"
>Rmpi_0.5-9.tar.gz
>* installing to library ‘/home/hm/R/x86_64-pc-linux-gnu-library/2.13’
>* installing *source* package ‘Rmpi’ ...
>checking for openpty in -lutil... no
>checking for main in -lpthread... no
>configure: creating ./config.status
>config.status: creating src/Makevars
>** libs
>** libs
>x86_64-pc-linux-gnu-gcc -std=gnu99 -I/usr/lib64/R/include
>-DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -
>DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -I/usr/include  -DMPI2
>-DOPENMPI -I/usr/local/include    -fpic  -O3 -pipe -march=core2 -
>mtune=core2 -ggdb -c RegQuery.c -o RegQuery.o
>x86_64-pc-linux-gnu-gcc -std=gnu99 -I/usr/lib64/R/include
>-DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -
>DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -I/usr/include  -DMPI2
>-DOPENMPI -I/usr/local/include    -fpic  -O3 -pipe -march=core2 -
>mtune=core2 -ggdb -c Rmpi.c -o Rmpi.o
>x86_64-pc-linux-gnu-gcc -std=gnu99 -I/usr/lib64/R/include
>-DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -
>DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -I/usr/include  -DMPI2
>-DOPENMPI -I/usr/local/include    -fpic  -O3 -pipe -march=core2 -
>mtune=core2 -ggdb -c conversion.c -o conversion.o
>x86_64-pc-linux-gnu-gcc -std=gnu99 -I/usr/lib64/R/include
>-DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -
>DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -I/usr/include  -DMPI2
>-DOPENMPI -I/usr/local/include    -fpic  -O3 -pipe -march=core2 -
>mtune=core2 -ggdb -c internal.c -o internal.o
>x86_64-pc-linux-gnu-gcc -std=gnu99 -shared -Wl,-O1 -Wl,--as-needed -o
>Rmpi.so RegQuery.o Rmpi.o conversion.o internal.o -L/usr/lib64/openmpi
>-lmpi
>-L/usr/lib64/R/lib -lR
>installiert nach /home/hm/R/x86_64-pc-linux-gnu-library/2.13/Rmpi/libs
>[...]
>  ompi_mpi_init: orte_init failed
>  --> Returned "Not found" (-13) instead of "Success" (0)
>
>
>On Wednesday 15 June 2011 15:19:22 Unger, Kristian, Dr. wrote:
>> 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/includ
>>>>e
>> >>\
>> >> --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)
>> >> 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
>> >>
>> >> ______________________________________________
>> >> R-help at r-project.org mailing list
>> >> https://stat.ethz.ch/mailman/listinfo/r-help
>> >> PLEASE do read the posting guide
>> >>http://www.R-project.org/posting-guide.html
>> >> and provide commented, minimal, self-contained, reproducible code.
>>
>>
>> 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
>>


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

More information about the R-help mailing list