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/include > >>\ > >> --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 > ______________________________________________ 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.