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.mildenber...@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.mildenber...@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@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 >
______________________________________________ R-help@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.