[R] Rmpi installation

[Hugo Mildenberger]

Kristian,

I just tried that particular command here on a Gentoo system with 
openmpi-1.5.3 installed, because I wondered why the Rmpi configure 
script tests for "main" function in a shared library ... 

But I got a completly different output from configure. While the 
linker succeeds here, the package load test does not. However, on your 
system, may be the openmpi installation really is a kinda private one of 
gcc? I heard gcc makes use of openmpi internally. So is openmpi really 
installed? 

I just recognize that you are trying to use Rmpi_0.5-4.tar.gz while current 
version on  CRAN is Rmpi_0.5-9.tar.gz.

Best

Hugo

R CMD INSTALL --configure-args="--with-Rmpi-include=/usr/include  --with-Rmpi-libpath=/usr/lib64/openmpi --with-Rmpi-type=OPENMPI" 
Rmpi_0.5-9.tar.gz
* installing to library ‘/home/hm/R/x86_64-pc-linux-gnu-library/2.13’
* installing *source* package ‘Rmpi’ ...
checking for openpty in -lutil... no
checking for main in -lpthread... no
configure: creating ./config.status
config.status: creating src/Makevars
** libs
** libs
x86_64-pc-linux-gnu-gcc -std=gnu99 -I/usr/lib64/R/include -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -
DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -I/usr/include  -DMPI2 -DOPENMPI -I/usr/local/include    -fpic  -O3 -pipe -march=core2 -
mtune=core2 -ggdb -c RegQuery.c -o RegQuery.o
x86_64-pc-linux-gnu-gcc -std=gnu99 -I/usr/lib64/R/include -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -
DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -I/usr/include  -DMPI2 -DOPENMPI -I/usr/local/include    -fpic  -O3 -pipe -march=core2 -
mtune=core2 -ggdb -c Rmpi.c -o Rmpi.o
x86_64-pc-linux-gnu-gcc -std=gnu99 -I/usr/lib64/R/include -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -
DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -I/usr/include  -DMPI2 -DOPENMPI -I/usr/local/include    -fpic  -O3 -pipe -march=core2 -
mtune=core2 -ggdb -c conversion.c -o conversion.o
x86_64-pc-linux-gnu-gcc -std=gnu99 -I/usr/lib64/R/include -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -
DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -I/usr/include  -DMPI2 -DOPENMPI -I/usr/local/include    -fpic  -O3 -pipe -march=core2 -
mtune=core2 -ggdb -c internal.c -o internal.o
x86_64-pc-linux-gnu-gcc -std=gnu99 -shared -Wl,-O1 -Wl,--as-needed -o Rmpi.so RegQuery.o Rmpi.o conversion.o internal.o -L/usr/lib64/openmpi -lmpi 
-L/usr/lib64/R/lib -lR
installiert nach /home/hm/R/x86_64-pc-linux-gnu-library/2.13/Rmpi/libs
[...]
  ompi_mpi_init: orte_init failed
  --> Returned "Not found" (-13) instead of "Success" (0)


On Wednesday 15 June 2011 15:19:22 Unger, Kristian, Dr. wrote:
> Thank you very much Hugo. Using the command as suggested results exactly
> the same error:
> 
> # R CMD INSTALL
> --configure-args="--with-Rmpi-include=/usr/lib64/mpi/gcc/openmpi/include
> --with-Rmpi-libpath=/usr/lib64/mpi/gcc/openmpi/lib64
> --with-Rmpi-type=OPENMPI" Rmpi_0.5-4.tar.gz
> * installing to library ‘/usr/local/lib64/R/library’
> * installing *source* package ‘Rmpi’ ...
> checking for gcc... gcc
> checking for C compiler default output file name... a.out
> checking whether the C compiler works... yes
> checking whether we are cross compiling... no
> checking for suffix of executables...
> checking for suffix of object files... o
> checking whether we are using the GNU C compiler... yes
> checking whether gcc accepts -g... yes
> checking for gcc option to accept ISO C89... none needed
> checking how to run the C preprocessor... gcc -E
> checking for grep that handles long lines and -e... /usr/bin/grep
> checking for egrep... /usr/bin/grep -E
> checking for ANSI C header files... yes
> checking for sys/types.h... yes
> checking for sys/stat.h... yes
> checking for stdlib.h... yes
> checking for string.h... yes
> checking for memory.h... yes
> checking for strings.h... yes
> checking for inttypes.h... yes
> checking for stdint.h... yes
> checking for unistd.h... yes
> checking mpi.h usability... no
> checking mpi.h presence... no
> checking for mpi.h... no
> Try to find libmpi or libmpich ...
> checking for main in -lmpi... no
> libmpi not found. exiting...
> ERROR: configuration failed for package ‘Rmpi’
> * removing ‘/usr/local/lib64/R/library/Rmpi’
> 
> 
> Best wishes
> 
> Kristian
> 
> ________________________________________
> Dr. Kristian Unger
> 
> 
> Arbeitsgruppenleiter Integrative Biologie / Head of Integrative Biology
> Group
> Abteilung für Strahlenzytogenetik / Research Unit of Radiation
> Cytogenetics
> 
> Tel.: +49-89-3187-3515
> 
> Mob.: +49-160-90641879
> 
> 
> 
> 
> 
> Am 15.06.11 15:12 schrieb "Hugo Mildenberger" unter
> <Hugo.Mildenberger at web.de>:
> 
> >Hmm,
> >
> >looks like there was a trailing blank after the backslash and before end
> >of line,
> >resulting in --with-Rmpi-libpath possibly not recognised:
> >
> >  > \--with-Rmpi-libpath=/usr/lib64/mpi/gcc/openmpi/lib64 \
> >
> >I also doubt there is real need to escape newlines within a string. But
> >another
> >possible problem source is that according to R CMD INSTALL --help, the
> >parameter
> >is called  "--configure-args", not "configure.args".
> >
> >
> >$ R CMD INSTALL
> >--configure-args="--with-Rmpi-include=/usr/lib64/mpi/gcc/openmpi/include
> >--with-Rmpi-libpath=/usr/lib64/mpi/gcc/openmpi/lib64 --
> >with-Rmpi-type=OPENMPI" Rmpi_0.5-4.tar.gz
> >
> >Best
> >
> >
> >
> >On Wednesday 15 June 2011 14:25:46 Unger, Kristian, Dr. wrote:
> >> Hi there
> >>
> >> I am trying to install Rmpi (version 0.5-4) on our 8-core SUSE Linux
> >> Enterprise Server 11 SP1. I read all I could find about Rmpi
> >>installation
> >> but still cannot get it working.
> >>
> >> Here the last command that I used:
> >>
> >> R CMD INSTALL
> >>
> >>--configure.args="--with-Rmpi-include=/usr/lib64/mpi/gcc/openmpi/include
> >>\
> >> --with-Rmpi-libpath=/usr/lib64/mpi/gcc/openmpi/lib64 \
> >> --with-Rmpi-type=OPENMPI" Rmpi_0.5-4.tar.gz
> >>
> >> Resulting in the following:
> >>
> >> zytosrv01dmi:/home/unger/R_projects/OS # R CMD INSTALL
> >> --configure-args="--with-Rmpi-include=/usr/lib64/mpi/gcc/openmpi/include
> >> \--with-Rmpi-libpath=/usr/lib64/mpi/gcc/openmpi/lib64 \
> >> --with-Rmpi-type=OPENMPI" Rmpi_0.5-4.tar.gz
> >> * installing to library Œ/usr/local/lib64/R/library¹
> >> * installing *source* package ŒRmpi¹ ...
> >> checking for gcc... gcc
> >> checking for C compiler default output file name... a.out
> >> checking whether the C compiler works... yes
> >> checking whether we are cross compiling... no
> >> checking for suffix of executables...
> >> checking for suffix of object files... o
> >> checking whether we are using the GNU C compiler... yes
> >> checking whether gcc accepts -g... yes
> >> checking for gcc option to accept ISO C89... none needed
> >> checking how to run the C preprocessor... gcc -E
> >> checking for grep that handles long lines and -e... /usr/bin/grep
> >> checking for egrep... /usr/bin/grep -E
> >> checking for ANSI C header files... yes
> >> checking for sys/types.h... yes
> >> checking for sys/stat.h... yes
> >> checking for stdlib.h... yes
> >> checking for string.h... yes
> >> checking for memory.h... yes
> >> checking for strings.h... yes
> >> checking for inttypes.h... yes
> >> checking for stdint.h... yes
> >> checking for unistd.h... yes
> >> checking mpi.h usability... no
> >> checking mpi.h presence... no
> >> checking for mpi.h... no
> >> Try to find libmpi or libmpich ...
> >> checking for main in -lmpi... no
> >> libmpi not found. exiting...
> >> ERROR: configuration failed for package ŒRmpi¹
> >> * removing Œ/usr/local/lib64/R/library/Rmpi¹
> >>
> >> So obviously libmpi is not found. Doing a locate search for "libmpi"
> >> (straight after updatedb) shows:
> >>
> >> zytosrv01dmi:/home/unger/R_projects/OS # locate libmpi
> >> /opt/mpich/ch-p4/lib64/libmpich.a
> >> /opt/mpich/ch-p4/lib64/libmpichf90.a
> >> /opt/mpich/ch-p4/lib64/libmpichf90nc.a
> >> /opt/mpich/ch-p4/lib64/libmpichfarg.a
> >> /opt/mpich/ch-p4/lib64/libmpichfsup.a
> >> /opt/mpich/ch-p4mpd/lib64/libmpich.a
> >> /opt/mpich/ch-p4mpd/lib64/libmpichf90.a
> >> /opt/mpich/ch-p4mpd/lib64/libmpichf90nc.a
> >> /opt/mpich/ch-p4mpd/lib64/libmpichfarg.a
> >> /opt/mpich/ch-p4mpd/lib64/libmpichfsup.a
> >> /usr/lib64/mpi/gcc/openmpi/lib64/libmpi_cxx.la
> >> /usr/lib64/mpi/gcc/openmpi/lib64/libmpi_cxx.so
> >> /usr/lib64/mpi/gcc/openmpi/lib64/libmpi_cxx.so.0
> >> /usr/lib64/mpi/gcc/openmpi/lib64/libmpi_cxx.so.0.0.0
> >> /usr/lib64/mpi/gcc/openmpi/lib64/libmpi_f77.la
> >> /usr/lib64/mpi/gcc/openmpi/lib64/libmpi_f77.so
> >> /usr/lib64/mpi/gcc/openmpi/lib64/libmpi_f77.so.0
> >> /usr/lib64/mpi/gcc/openmpi/lib64/libmpi_f77.so.0.0.0
> >> /usr/lib64/mpi/gcc/openmpi/lib64/libmpi_f90.la
> >> /usr/lib64/mpi/gcc/openmpi/lib64/libmpi_f90.so
> >> /usr/lib64/mpi/gcc/openmpi/lib64/libmpi_f90.so.0
> >> /usr/lib64/mpi/gcc/openmpi/lib64/libmpi_f90.so.0.0.0
> >> /usr/lib64/mpi/gcc/openmpi/lib64/libmpi.la
> >> /usr/lib64/mpi/gcc/openmpi/lib64/libmpi.so
> >> /usr/lib64/mpi/gcc/openmpi/lib64/libmpi.so.0
> >> /usr/lib64/mpi/gcc/openmpi/lib64/libmpi.so.0.0.0
> >>
> >> What lets me assume that the path to libmpi is
> >> /usr/lib64/mpi/gcc/openmpi/lib64 which I already included in the
> >>options...
> >>
> >>
> >> How can I get this working?
> >>
> >> I would highly appreciate any help on this!
> >>
> >> Best wishes
> >>
> >> Kristian
> >>
> >>
> >>
> >> ________________________________________
> >> Dr. Kristian Unger
> >>
> >>
> >> Arbeitsgruppenleiter Integrative Biologie / Head of Integrative Biology
> >> Group
> >> Abteilung für Strahlenzytogenetik / Research Unit of Radiation
> >>Cytogenetics
> >>
> >>
> >> Helmholtz Zentrum München
> >> Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH)
> >> Ingolstädter Landstr. 1
> >> 85764 Neuherberg
> >> www.helmholtz-muenchen.de
> >> Aufsichtsratsvorsitzende: MinDir´in Bärbel Brumme-Bothe
> >> Geschäftsführer: Prof. Dr. Günther Wess und Dr. Nikolaus Blum
> >> Registergericht: Amtsgericht München HRB 6466
> >> USt-IdNr: DE 129521671
> >>
> >> ______________________________________________
> >> R-help at r-project.org mailing list
> >> https://stat.ethz.ch/mailman/listinfo/r-help
> >> PLEASE do read the posting guide
> >>http://www.R-project.org/posting-guide.html
> >> and provide commented, minimal, self-contained, reproducible code.
> 
> 
> Helmholtz Zentrum 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
>