[R] Rmpi installation

Hugo Mildenberger Hugo.Mildenberger at web.de
Wed Jun 15 17:25:41 CEST 2011 

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/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
>

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