[R] Rmpi installation

Unger, Kristian, Dr. unger at helmholtz-muenchen.de
Wed Jun 15 17:45:41 CEST 2011 

Dear Hugo

I ran the command with the verbose switch and get the following output:

> mpicc mtest.c -ov mtest
mtest: In function `_start':
/usr/src/packages/BUILD/glibc-2.11.1/csu/../sysdeps/x86_64/elf/start.S:65:
multiple definition of `_start'
/usr/lib64/gcc/x86_64-suse-linux/4.3/../../../../lib64/crt1.o:/usr/src/pack
ages/BUILD/glibc-2.11.1/csu/../sysdeps/x86_64/elf/start.S:65: first
defined here
mtest: In function `_fini':
(.fini+0x0): multiple definition of `_fini'
/usr/lib64/gcc/x86_64-suse-linux/4.3/../../../../lib64/crti.o:initfini.c:(.
fini+0x0): first defined here
mtest:(.rodata+0x0): multiple definition of `_IO_stdin_used'
/usr/lib64/gcc/x86_64-suse-linux/4.3/../../../../lib64/crt1.o:(.rodata.cst4
+0x0): first defined here
mtest: In function `__data_start':
(.data+0x0): multiple definition of `__data_start'
/usr/lib64/gcc/x86_64-suse-linux/4.3/../../../../lib64/crt1.o:(.data+0x0):
first defined here
mtest: In function `main':
(.text+0xec): multiple definition of `main'
/tmp/ccUyk8e9.o:mtest.c:(.text+0x0): first defined here
mtest: In function `_init':
(.init+0x0): multiple definition of `_init'
/usr/lib64/gcc/x86_64-suse-linux/4.3/../../../../lib64/crti.o:initfini.c:(.
init+0x0): first defined here
/usr/lib64/gcc/x86_64-suse-linux/4.3/../../../../x86_64-suse-linux/bin/ld:
error in mtest(.eh_frame); no .eh_frame_hdr table will be created.
collect2: ld returned 1 exit status

Not sure if this makes any sense?


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 17:25 schrieb "Hugo Mildenberger" unter
<Hugo.Mildenberger at web.de>:

>Kristian,
>
>these are the usual problems with binary distributions.
>
>Regarding
>
>         >  --with-Rmpi-include=/usr/lib64/mpi/gcc/openmpi/include
>
>and configure output
>
>         > checking for mpi.h... no
>
>... so does "/usr/lib64/mpi/gcc/openmpi/include" really exist? At least,
>that appears to be a very unusual place to look for mpi.h (normally
>to be found in "/usr/include" ).
>
>And if you try to compile & link the attached demo program: does
>the link phase succeed? Compile & link using
>
>    $ mpicc mtest.c -o mtest
>
>Presumably you have already tried to run install.packages("Rmpi").
>
>
>Kind regards
>
>Hugo
>
>
>
>On Wednesday 15 June 2011 16:22:07 Unger, Kristian, Dr. wrote:
>> 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/inclu
>>>>>de
>> >> >--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/incl
>>>>>>ud
>> >>>>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/includ
>>>>e
>> >> >> \--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
>>


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

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