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Subject: Re: [OMPI users] Rmpi installation issues
From: Dirk Eddelbuettel (edd_at_[hidden])
Date: 2008-10-13 10:28:02


On Mon, Oct 13, 2008 at 03:56:19PM +0200, Simone Giannerini wrote:
> Dear Dirk,
>
> many thanks for your reply, please see below,

Your mail is basically unreadable / impossible to attribute what is
original and what is cited. Please follow convention and indent.
 
> On 13 October 2008 at 11:22, Simone Giannerini wrote:
> | Dear all,
> |
> | I have troubles installing rmpi 0.5-5 (or 0.5-6) on a quad opteron machine
>
> | with OpenSUSE 11.0 and
> | R 2.7.2
> |
> | platform x86_64-unknown-linux-gnu
> | arch x86_64
> | os linux-gnu
> | system x86_64, linux-gnu
> | status Patched
> | major 2
> | minor 7.2
> | year 2008
> | month 09
> | day 18
> | svn rev 46546
> | language R
> | version.string R version 2.7.2 Patched (2008-09-18 r46546)
> |
> | I tried the following
> |
> | # export MPI_ROOT=/usr/lib64/mpi/gcc/openmpi/
> |
> | # R CMD INSTALL Rmpi_0.5-6.tar.gz
>
> Where did you get 0.5-6 from? The newest, per the author's website, is
> 0.5-5.
>
> http://www.stats.uwo.ca/faculty/yu/Rmpi/download/dev

Ok, didn't see that. But please do understand that 0.5-5 is on CRAN
and released. (And yes, that is the version for which I also had to
make a fix to get it build on Debian as mentioned).

> | * 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
> | Try to find mpi.h ...
> | Found in /usr/lib64/mpi/gcc/openmpi//include
> | Try to find libmpi.so or libmpich.a
> | checking for main in -lmpi... yes
>
> At this point you have mpi.h and libmpi. Looks good.
>
> | checking for openpty in -lutil... yes
> | checking for main in -lpthread... yes
> | configure: creating ./config.status
> | config.status: creating src/Makevars
> | ** libs
> | gcc -std=gnu99 -I/usr/local/lib64/R/include -DPACKAGE_NAME=\"\"
> | -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\"
> | -DPACKAGE_BUGREPORT=\"\" -I/usr/lib64/mpi/gcc/openmpi//include -DMPI2
> | -DOPENMPI -fPIC -I/usr/local/include -fpic -g -O2 -c RegQuery.c -o
> | RegQuery.o
> | gcc -std=gnu99 -I/usr/local/lib64/R/include -DPACKAGE_NAME=\"\"
> | -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\"
> | -DPACKAGE_BUGREPORT=\"\" -I/usr/lib64/mpi/gcc/openmpi//include -DMPI2
> | -DOPENMPI -fPIC -I/usr/local/include -fpic -g -O2 -c Rmpi.c -o Rmpi.o
> | gcc -std=gnu99 -I/usr/local/lib64/R/include -DPACKAGE_NAME=\"\"
> | -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\"
> | -DPACKAGE_BUGREPORT=\"\" -I/usr/lib64/mpi/gcc/openmpi//include -DMPI2
> | -DOPENMPI -fPIC -I/usr/local/include -fpic -g -O2 -c conversion.c -o
> | conversion.o
> | gcc -std=gnu99 -I/usr/local/lib64/R/include -DPACKAGE_NAME=\"\"
> | -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\"
> | -DPACKAGE_BUGREPORT=\"\" -I/usr/lib64/mpi/gcc/openmpi//include -DMPI2
> | -DOPENMPI -fPIC -I/usr/local/include -fpic -g -O2 -c internal.c -o
> | internal.o
>
> It all compiles, thanks to mpi.h.
>
> | gcc -std=gnu99 -shared -L/usr/local/lib64 -o Rmpi.so RegQuery.o Rmpi.o
> | conversion.o internal.o -L/usr/lib64/mpi/gcc/openmpi//lib -lmpi -lutil
> | -lpthread -fPIC
> | /usr/lib64/gcc/x86_64-suse-linux/4.3/../../../../x86_64-suse-linux/bin/ld:
>
> | cannot find -lmpi
> | collect2: ld returned 1 exit status
> | make: *** [Rmpi.so] Error 1
> | chmod: cannot access `/usr/local/lib64/R/library/Rmpi/libs/*': No such
> file
> | or directory
> | ERROR: compilation failed for package 'Rmpi'
> | ** Removing '/usr/local/lib64/R/library/Rmpi'
>
> This seems to indicate that your installation of Open MPI conflicts with
> your
> setting of
> export MPI_ROOT=/usr/lib64/mpi/gcc/openmpi/
> as this directory is expected to contain include/ and lib/
>
> I am not sure I got this, Open MPI is installed in
> /usr/lib64/mpi/gcc/openmpi/ and such directory contains both include and lib
> folders:
>
> gauss:/usr/lib64/mpi/gcc/openmpi # ls -R
> bin include lib64 share

Not it does not as lib64 != lib. You probably it installed if you
create a softlink from

        /usr/lib64/mpi/gcc/openmpi/lib64
        
to

        /usr/lib64/mpi/gcc/openmpi/lib
        
Dirk

> ./bin:
> mpiCC mpicc mpiexec mpif90 mpivars.csh ompi_info opalc++
> ortec++ orted
> mpic++ mpicxx mpif77 mpirun mpivars.sh opal_wrapper opalcc
> ortecc orterun
>
> ./include:
> mpi.h mpif-common.h mpif-config.h mpif.h openmpi
>
> ./include/openmpi:
> ompi opal opal_config_bottom.h orte
> ompi_config.h opal_config.h opal_stdint.h orte_config.h
>
> [...]
>
> ./lib64:
> libmca_common_sm.la libmpi_cxx.la libmpi_f90.la
> libopen-rte.la
> libmca_common_sm.so libmpi_cxx.so libmpi_f90.so
> libopen-rte.so
> libmca_common_sm.so.0 libmpi_cxx.so.0 libmpi_f90.so.0
> libopen-rte.so.0
> libmca_common_sm.so.0.0.0 libmpi_cxx.so.0.0.0 libmpi_f90.so.0.0.0
> libopen-rte.so.0.0.0
> libmpi.la libmpi_f77.la libopen-pal.la
> mpi.mod
> libmpi.so libmpi_f77.so libopen-pal.so
> openmpi
> libmpi.so.0 libmpi_f77.so.0 libopen-pal.so.0
> libmpi.so.0.0.0 libmpi_f77.so.0.0.0 libopen-pal.so.0.0.0
>
> | I also tried with
> |
> | R CMD INSTALL Rmpi_0.5-6.tar.gz
> | --configure-args=--with-mpi=/usr/lib64/mpi/gcc/openmpi/
> |
> | with the same results.
> | Any help would be greatly appreciated.
> I'd recommend having a look at configure.ac, which is pretty
> straightforward,
> and 'helping' it with the locations you have. I had to do the same for
> Debian's Rmpi due to use also having mpich and lam.
>
> Please, could you be more explicit? Thanks, I tried to modify line 8 of the
> file configure.ac without success. BTW I had also LAM and mpich installed
> but I removed them.
>
> Thank you for your help,
>
> Kind regards
>
> Simone

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Three out of two people have difficulties with fractions.