Rmpi installation
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Rmpi installation
 
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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 ______________________________________________ [hidden email] 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. |
Re: Rmpi installation
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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 > > ______________________________________________ > [hidden email] 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. ______________________________________________ [hidden email] 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. |
Re: Rmpi installation
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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 <[hidden email]>: >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 >> >> ______________________________________________ >> [hidden email] 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 ______________________________________________ [hidden email] 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. |
Re: Rmpi installation
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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 > <[hidden email]>: > > >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 > >> > >> ______________________________________________ > >> [hidden email] 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 > ______________________________________________ [hidden email] 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. |
Re: Rmpi installation
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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 <[hidden email]>: >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 >> <[hidden email]>: >> >> >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 >> >> >> >> ______________________________________________ >> >> [hidden email] 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 ______________________________________________ [hidden email] 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. |
Re: Rmpi installation
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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 > <[hidden email]>: > > >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 > >> <[hidden email]>: > >> > >> >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 > >> >> > >> >> ______________________________________________ > >> >> [hidden email] 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 > [hidden email] 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. |
Re: Rmpi installation
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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 <[hidden email]>: >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 >> <[hidden email]>: >> >> >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 >> >> <[hidden email]>: >> >> >> >> >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 >> >> >> >> >> >> ______________________________________________ >> >> >> [hidden email] 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 ______________________________________________ [hidden email] 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. |
Re: Rmpi installation
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Dear Kristian,
please run exactly mpicc mtest.c -o mtest If you really need it, add -v separately. mpicc is nothing but a compiler wrapper. The "-o" switch specifies the outfile name, which has to follow immediately after "-o", with or without a blank character in between. I'm not sure about what happens with -ov mtest. Probably an output file named "v" is produced on disk, in addition to the file mtest stemming from a previous with "-o mtest" Depending on mpicc's, gcc's and ld's version, gcc may instruct the linker to link the previously produced executable "mtest" with the object newly compiled from mtest.c plus several implicit libraries and startup objects, and output the result to "v". ld would then be faced with duplicate defined symbols and output a list of these doublets. My proposal was meant as a test for an else correct openmpi installation, perhaps I should have said this. On successful completion, no message should be printed, but an executable named "mtest" should have been produced, which could then be run typing ./mtest . If the link process failed, then the openmpi installation was inconsistent. Kind regards Hugo On Wednesday 15 June 2011 17:45:41 Unger, Kristian, Dr. wrote: > 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 > <[hidden email]>: > > >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 > >> <[hidden email]>: > >> > >> >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 > >> >> <[hidden email]>: > >> >> > >> >> >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 > >> >> >> > >> >> >> ______________________________________________ > >> >> >> [hidden email] 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 > ______________________________________________ [hidden email] 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. |
Re: Rmpi installation
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Hi Hugo
One step closer! I added the path to libmpi to ld.so.conf and ran ldconfig (see http://www.linuxforums.org/forum/programming-scripting/80405-linking-shared -libraries.html). Compiling the code you sent me works but running the file gets stuck with the following message: ./mtest librdmacm: couldn't read ABI version. librdmacm: assuming: 4 libibverbs: Fatal: couldn't read uverbs ABI version. CMA: unable to open /dev/infiniband/rdma_cm -------------------------------------------------------------------------- WARNING: Failed to open "OpenIB-cma" [DAT_INTERNAL_ERROR:]. This may be a real error or it may be an invalid entry in the uDAPL Registry which is contained in the dat.conf file. Contact your local System Administrator to confirm the availability of the interfaces in the dat.conf file. -------------------------------------------------------------------------- Any suggestions? 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 19:25 schrieb "Hugo Mildenberger" unter <[hidden email]>: >Dear Kristian, > > please run exactly > > mpicc mtest.c -o mtest > > If you really need it, add -v separately. mpicc is nothing but a >compiler wrapper. > The "-o" switch specifies the outfile name, which has to follow >immediately after "-o", > with or without a blank character in between. I'm not sure about what >happens > with -ov mtest. Probably an output file named "v" is produced on disk, >in addition to > the file mtest stemming from a previous with "-o mtest" Depending on > mpicc's, gcc's and ld's version, gcc may instruct the linker to link >the previously > produced executable "mtest" with the object newly compiled from mtest.c >plus > several implicit libraries and startup objects, and output the result >to "v". > ld would then be faced with duplicate defined symbols and output a list >of these > doublets. > > My proposal was meant as a test for an else correct openmpi >installation, perhaps > I should have said this. On successful completion, no message should be >printed, but > an executable named "mtest" should have been produced, which could then > be run typing ./mtest . If the link process failed, then the openmpi >installation was > inconsistent. > >Kind regards > >Hugo > >On Wednesday 15 June 2011 17:45:41 Unger, Kristian, Dr. wrote: >> 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/pa >>ck >> 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.cs >>t4 >> +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 >> <[hidden email]>: >> >> >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 >> >> <[hidden email]>: >> >> >> >> >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/includ >>>>e >> >> >> --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 >> >> >> <[hidden email]>: >> >> >> >> >> >> >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/inc >>>>>>>lu >> >>>>>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/in >>>>>>>>cl >> >>>>>>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/incl >>>>>>ud >> >>>>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 >> >> >> >> >> >> >> >> ______________________________________________ >> >> >> >> [hidden email] 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 >> 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 ______________________________________________ [hidden email] 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. |
Re: Rmpi installation
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In reply to this post by Hugo Mildenberger
Another update: I ditched the pre-installed version of openmpi and
installed openmpi from source (./configure --without-openib). Compiling and running your test programme gives me the following error: unger@zytosrv01dmi:~/R_projects/OS> ./mtest [zytosrv01dmi:6094] *** An error occurred in MPI_Send [zytosrv01dmi:6094] *** on communicator MPI_COMM_WORLD [zytosrv01dmi:6094] *** MPI_ERR_RANK: invalid rank [zytosrv01dmi:6094] *** MPI_ERRORS_ARE_FATAL (your MPI job will now abort) However, Rmpi installs happily and it is also possible to call the package in R. When it comes to running a job under snowfall sfInit( parallel=TRUE,type="MPI", cpus=8) the job is split into eight separate processes which all run on the same CPU. So it seems that the processes are not distributed across the 8 CPUs available. Best wishes Kristian Am 15.06.11 19:25 schrieb "Hugo Mildenberger" unter <[hidden email]>: >Dear Kristian, > > please run exactly > > mpicc mtest.c -o mtest > > If you really need it, add -v separately. mpicc is nothing but a >compiler wrapper. > The "-o" switch specifies the outfile name, which has to follow >immediately after "-o", > with or without a blank character in between. I'm not sure about what >happens > with -ov mtest. Probably an output file named "v" is produced on disk, >in addition to > the file mtest stemming from a previous with "-o mtest" Depending on > mpicc's, gcc's and ld's version, gcc may instruct the linker to link >the previously > produced executable "mtest" with the object newly compiled from mtest.c >plus > several implicit libraries and startup objects, and output the result >to "v". > ld would then be faced with duplicate defined symbols and output a list >of these > doublets. > > My proposal was meant as a test for an else correct openmpi >installation, perhaps > I should have said this. On successful completion, no message should be >printed, but > an executable named "mtest" should have been produced, which could then > be run typing ./mtest . If the link process failed, then the openmpi >installation was > inconsistent. > >Kind regards > >Hugo > >On Wednesday 15 June 2011 17:45:41 Unger, Kristian, Dr. wrote: >> 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/pa >>ck >> 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.cs >>t4 >> +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 >> <[hidden email]>: >> >> >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 >> >> <[hidden email]>: >> >> >> >> >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/includ >>>>e >> >> >> --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 >> >> >> <[hidden email]>: >> >> >> >> >> >> >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/inc >>>>>>>lu >> >>>>>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/in >>>>>>>>cl >> >>>>>>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/incl >>>>>>ud >> >>>>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 >> >> >> >> >> >> >> >> ______________________________________________ >> >> >> >> [hidden email] 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 >> 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 ______________________________________________ [hidden email] 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. |
Re: Rmpi installation
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Kristian,
> Another update: I ditched the pre-installed version of openmpi and > installed openmpi from source (./configure --without-openib). A very reasonable approach. Remembering my own struggles with SuSE years ago, I did not dare to propose that procedure. > Compiling and running your test programme gives me the following error: > > unger@zytosrv01dmi:~/R_projects/OS> ./mtest > [zytosrv01dmi:6094] *** An error occurred in MPI_Send > [zytosrv01dmi:6094] *** on communicator MPI_COMM_WORLD > [zytosrv01dmi:6094] *** MPI_ERR_RANK: invalid rank > [zytosrv01dmi:6094] *** MPI_ERRORS_ARE_FATAL (your MPI job will now abort) Same here. For the moment I can't figure out why this happens, also because the parameters of the openmpi functions are scarcely documented. Try one of the demo programs in the openmpi "examples" directory instead, e.g. the attached one > However, Rmpi installs happily and it is also possible to call the package > in R. When it comes to running a job under snowfall > > sfInit( parallel=TRUE,type="MPI", cpus=8) the job is split into eight > separate processes which all run on the same CPU. So it seems that the > processes are not distributed across the 8 CPUs available. sfSetMaxCPUs(number=8) should fix at least the thread distribution. However, on my notebook all cores are kept busy with 100% load after sfInit(), with nothing obvious to compute. I don't know if this has to be considered a bug or a feature. Kind regards Hugo > Best wishes > > Kristian > > > > > > > > > Am 15.06.11 19:25 schrieb "Hugo Mildenberger" unter > <[hidden email]>: > > >Dear Kristian, > > > > please run exactly > > > > mpicc mtest.c -o mtest > > > > If you really need it, add -v separately. mpicc is nothing but a > >compiler wrapper. > > The "-o" switch specifies the outfile name, which has to follow > >immediately after "-o", > > with or without a blank character in between. I'm not sure about what > >happens > > with -ov mtest. Probably an output file named "v" is produced on disk, > >in addition to > > the file mtest stemming from a previous with "-o mtest" Depending on > > mpicc's, gcc's and ld's version, gcc may instruct the linker to link > >the previously > > produced executable "mtest" with the object newly compiled from mtest.c > >plus > > several implicit libraries and startup objects, and output the result > >to "v". > > ld would then be faced with duplicate defined symbols and output a list > >of these > > doublets. > > > > My proposal was meant as a test for an else correct openmpi > >installation, perhaps > > I should have said this. On successful completion, no message should be > >printed, but > > an executable named "mtest" should have been produced, which could then > > be run typing ./mtest . If the link process failed, then the openmpi > >installation was > > inconsistent. > > > >Kind regards > > > >Hugo > > > >On Wednesday 15 June 2011 17:45:41 Unger, Kristian, Dr. wrote: > >> 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/pa > >>ck > >> 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.cs > >>t4 > >> +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 > >> <[hidden email]>: > >> > >> >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 > >> >> <[hidden email]>: > >> >> > >> >> >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/includ > >>>>e > >> >> >> --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 > >> >> >> <[hidden email]>: > >> >> >> > >> >> >> >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/inc > >>>>>>>lu > >> >>>>>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/in > >>>>>>>>cl > >> >>>>>>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/incl > >>>>>>ud > >> >>>>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 > >> >> >> >> > >> >> >> >> ______________________________________________ > >> >> >> >> [hidden email] 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 > >> > > > 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 ______________________________________________ [hidden email] 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. |
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