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.mildenber...@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.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/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@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 ______________________________________________ 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.