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 ?/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? 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 f?r Strahlenzytogenetik / Research Unit of Radiation Cytogenetics Helmholtz Zentrum M?nchen Deutsches Forschungszentrum f?r Gesundheit und Umwelt (GmbH) Ingolst?dter Landstr. 1 85764 Neuherberg www.helmholtz-muenchen.de Aufsichtsratsvorsitzende: MinDir?in B?rbel Brumme-Bothe Gesch?ftsf?hrer: Prof. Dr. G?nther Wess und Dr. Nikolaus Blum Registergericht: Amtsgericht M?nchen HRB 6466 USt-IdNr: DE 129521671
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 ?/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? > > 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 f?r Strahlenzytogenetik / Research Unit of Radiation Cytogenetics > > > Helmholtz Zentrum M?nchen > Deutsches Forschungszentrum f?r Gesundheit und Umwelt (GmbH) > Ingolst?dter Landstr. 1 > 85764 Neuherberg > www.helmholtz-muenchen.de > Aufsichtsratsvorsitzende: MinDir?in B?rbel Brumme-Bothe > Gesch?ftsf?hrer: Prof. Dr. G?nther Wess und Dr. Nikolaus Blum > Registergericht: Amtsgericht M?nchen 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.
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 f?r 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/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 ?/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? >> >> 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 f?r Strahlenzytogenetik / Research Unit of Radiation >>Cytogenetics >> >> >> Helmholtz Zentrum M?nchen >> Deutsches Forschungszentrum f?r Gesundheit und Umwelt (GmbH) >> Ingolst?dter Landstr. 1 >> 85764 Neuherberg >> www.helmholtz-muenchen.de >> Aufsichtsratsvorsitzende: MinDir?in B?rbel Brumme-Bothe >> Gesch?ftsf?hrer: Prof. Dr. G?nther Wess und Dr. Nikolaus Blum >> Registergericht: Amtsgericht M?nchen 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 M?nchen Deutsches Forschungszentrum f?r Gesundheit und Umwelt (GmbH) Ingolst?dter Landstr. 1 85764 Neuherberg www.helmholtz-muenchen.de Aufsichtsratsvorsitzende: MinDir?in B?rbel Brumme-Bothe Gesch?ftsf?hrer: Prof. Dr. G?nther Wess und Dr. Nikolaus Blum Registergericht: Amtsgericht M?nchen HRB 6466 USt-IdNr: DE 129521671
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 f?r 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/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 ?/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? > >> > >> 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 f?r Strahlenzytogenetik / Research Unit of Radiation > >>Cytogenetics > >> > >> > >> Helmholtz Zentrum M?nchen > >> Deutsches Forschungszentrum f?r Gesundheit und Umwelt (GmbH) > >> Ingolst?dter Landstr. 1 > >> 85764 Neuherberg > >> www.helmholtz-muenchen.de > >> Aufsichtsratsvorsitzende: MinDir?in B?rbel Brumme-Bothe > >> Gesch?ftsf?hrer: Prof. Dr. G?nther Wess und Dr. Nikolaus Blum > >> Registergericht: Amtsgericht M?nchen 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 M?nchen > Deutsches Forschungszentrum f?r Gesundheit und Umwelt (GmbH) > Ingolst?dter Landstr. 1 > 85764 Neuherberg > www.helmholtz-muenchen.de > Aufsichtsratsvorsitzende: MinDir?in B?rbel Brumme-Bothe > Gesch?ftsf?hrer: Prof. Dr. G?nther Wess und Dr. Nikolaus Blum > Registergericht: Amtsgericht M?nchen HRB 6466 > USt-IdNr: DE 129521671 >
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 f?r 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 f?r 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 ?/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? >> >> >> >> 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 f?r Strahlenzytogenetik / Research Unit of Radiation >> >>Cytogenetics >> >> >> >> >> >> Helmholtz Zentrum M?nchen >> >> Deutsches Forschungszentrum f?r Gesundheit und Umwelt (GmbH) >> >> Ingolst?dter Landstr. 1 >> >> 85764 Neuherberg >> >> www.helmholtz-muenchen.de >> >> Aufsichtsratsvorsitzende: MinDir?in B?rbel Brumme-Bothe >> >> Gesch?ftsf?hrer: Prof. Dr. G?nther Wess und Dr. Nikolaus Blum >> >> Registergericht: Amtsgericht M?nchen 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 M?nchen >> Deutsches Forschungszentrum f?r Gesundheit und Umwelt (GmbH) >> Ingolst?dter Landstr. 1 >> 85764 Neuherberg >> www.helmholtz-muenchen.de >> Aufsichtsratsvorsitzende: MinDir?in B?rbel Brumme-Bothe >> Gesch?ftsf?hrer: Prof. Dr. G?nther Wess und Dr. Nikolaus Blum >> Registergericht: Amtsgericht M?nchen HRB 6466 >> USt-IdNr: DE 129521671 >>Helmholtz Zentrum M?nchen Deutsches Forschungszentrum f?r Gesundheit und Umwelt (GmbH) Ingolst?dter Landstr. 1 85764 Neuherberg www.helmholtz-muenchen.de Aufsichtsratsvorsitzende: MinDir?in B?rbel Brumme-Bothe Gesch?ftsf?hrer: Prof. Dr. G?nther Wess und Dr. Nikolaus Blum Registergericht: Amtsgericht M?nchen HRB 6466 USt-IdNr: DE 129521671
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 f?r 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 f?r 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 ?/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?
> >> >>
> >> >> 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 f?r Strahlenzytogenetik / Research Unit of
Radiation
> >> >>Cytogenetics
> >> >>
> >> >>
> >> >> Helmholtz Zentrum M?nchen
> >> >> Deutsches Forschungszentrum f?r Gesundheit und Umwelt
(GmbH)
> >> >> Ingolst?dter Landstr. 1
> >> >> 85764 Neuherberg
> >> >> www.helmholtz-muenchen.de
> >> >> Aufsichtsratsvorsitzende: MinDir?in B?rbel Brumme-Bothe
> >> >> Gesch?ftsf?hrer: Prof. Dr. G?nther Wess und Dr. Nikolaus
Blum
> >> >> Registergericht: Amtsgericht M?nchen 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 M?nchen
> >> Deutsches Forschungszentrum f?r Gesundheit und Umwelt (GmbH)
> >> Ingolst?dter Landstr. 1
> >> 85764 Neuherberg
> >> www.helmholtz-muenchen.de
> >> Aufsichtsratsvorsitzende: MinDir?in B?rbel Brumme-Bothe
> >> Gesch?ftsf?hrer: Prof. Dr. G?nther Wess und Dr. Nikolaus Blum
> >> Registergericht: Amtsgericht M?nchen HRB 6466
> >> USt-IdNr: DE 129521671
> >>
>
>
> Helmholtz Zentrum M?nchen
> Deutsches Forschungszentrum f?r Gesundheit und Umwelt (GmbH)
> Ingolst?dter Landstr. 1
> 85764 Neuherberg
> www.helmholtz-muenchen.de
> Aufsichtsratsvorsitzende: MinDir?in B?rbel Brumme-Bothe
> Gesch?ftsf?hrer: Prof. Dr. G?nther Wess und Dr. Nikolaus Blum
> Registergericht: Amtsgericht M?nchen HRB 6466
> USt-IdNr: DE 129521671
>