[R] Rmpi installation

Hugo Mildenberger Hugo.Mildenberger at web.de
Wed Jun 15 19:25:31 CEST 2011 

Dear Kristian,

   please run exactly

    mpicc mtest.c -o mtest 
 
  If you really need it, add -v separately. mpicc is nothing but a compiler wrapper. 
  The "-o" switch specifies the outfile name, which has to follow immediately after "-o", 
  with or without a blank character in between. I'm not sure about what happens 
  with -ov mtest. Probably an output file named "v" is produced on disk, in addition to 
  the file mtest stemming from a previous with "-o mtest" Depending on 
  mpicc's, gcc's and ld's version, gcc may instruct the linker to link the previously 
  produced executable "mtest" with the object newly compiled from mtest.c plus 
  several implicit libraries and startup objects, and output the result to "v". 
  ld would then be faced with duplicate defined symbols and output a list of these 
  doublets.
  
  My proposal was meant as a test for an else correct openmpi installation, perhaps
  I should have said this. On successful completion, no message should be printed, but
  an executable named "mtest" should have been produced, which could then
  be run typing ./mtest    . If the link process failed, then the openmpi installation was 
  inconsistent. 

Kind regards

Hugo
 
On Wednesday 15 June 2011 17:45:41 Unger, Kristian, Dr. wrote:
> 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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