[R-sig-hpc] Problems Installing Rmpi

[Hao Yu]

I am not so sure why Rmpi script doesn't supply include dir. Can you try
R CMD INSTALL Rmpi_0.5-7.tar.gz
--configure-args=--with-mpi=/usr/lib64/openmpi/1.2.7-gcc

Hao

Rick B. wrote:
> I'm running CentOS 5.3 on a dual quad core opteron 64-bit system. I've
> installed openmpi and it appears to be working:
>
> [root at rab45-1 rick]# ompi_info --all | more
> DAT Registry: sysconfdir, bad filename - /etc/ofed/dat.conf, retry
> default at /etc/dat.conf
> DAT Registry: default, bad filename - /etc/dat.conf, aborting
>                 Open MPI: 1.2.7
>    Open MPI SVN revision: r19401
>                 Open RTE: 1.2.7
>    Open RTE SVN revision: r19401
>                     OPAL: 1.2.7
> .
> .
> .
>
>                   Prefix: /usr/lib64/openmpi/1.2.7-gcc
>                   Bindir: /usr/lib64/openmpi/1.2.7-gcc/bin
>                   Libdir: /usr/lib64/openmpi/1.2.7-gcc/lib
>                   Incdir: /usr/lib64/openmpi/1.2.7-gcc/include
>                Pkglibdir: /usr/lib64/openmpi/1.2.7-gcc/lib/openmpi
>               Sysconfdir: /usr/lib64/openmpi/1.2.7-gcc/etc
>  Configured architecture: x86_64-unknown-linux-gnu
>            Configured by: mockbuild
>            Configured on: Wed Jan 21 05:20:20 EST 2009
>           Configure host: builder10.centos.org
>                 Built by: mockbuild
>                 Built on: Wed Jan 21 05:29:13 EST 2009
>               Built host: builder10.centos.org
>               C bindings: yes
>             C++ bindings: yes
>       Fortran77 bindings: yes (all)
>       Fortran90 bindings: yes
>  Fortran90 bindings size: small
>               C compiler: gcc
>      C compiler absolute: /usr/bin/gcc
>              C char size: 1
>              C bool size: 1
>             C short size: 2
>               C int size: 4
>              C long size: 8
>             C float size: 4
>            C double size: 8
>           C pointer size: 8
>             C char align: 1
>             C bool align: 1
>              C int align: 4
>            C float align: 4
>           C double align: 8
>             C++ compiler: g++
>    C++ compiler absolute: /usr/bin/g++
>       Fortran77 compiler: gfortran
>   Fortran77 compiler abs: /usr/bin/gfortran
>       Fortran90 compiler: gfortran
>
> and lots more output.
>
> When I try to install Rmpi for R version 2.8.1:
>
> [root at rab45-1 rick]# R CMD INSTALL Rmpi_0.5-7.tar.gz
> --configure-args=--with-mpi=/usr/lib64/openmpi/1.2.7-gcc/
> * Installing to library '/usr/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/openmpi/1.2.7-gcc//include
> Try to find libmpi.so or libmpich.a
> Found libmpi in /usr/lib64/openmpi/1.2.7-gcc//lib
> checking for openpty in -lutil... yes
> checking for main in -lpthread... yes
> configure: creating ./config.status
> config.status: creating src/Makevars
> ** libs
> gcc -I/usr/lib64/R/include -I/usr/lib64/openmpi/1.2.7-gcc/include/mpi.h
> -I/usr/local/include    -fpic  -O3 -g -std=gnu99 -c conversion.c -o
> conversion.o
> cc1: error: /usr/lib64/openmpi/1.2.7-gcc/include/mpi.h: not a directory
> make: *** [conversion.o] Error 1
> chmod: cannot access `/usr/lib64/R/library/Rmpi/libs/*': No such file or
> directory
> ERROR: compilation failed for package 'Rmpi'
> ** Removing '/usr/lib64/R/library/Rmpi'
>
>
> I don't understand the error message. Why does Rmpi install script send
> a file name if it really wants just the directory name?
>
> If I shorten or lengthen the mpi path or don't use configure-args at
> all, Rmpi always fails when it cannot find mpi.h.
>
> Any suggestions on fixing this will be greatly appreciated.
>
> Rick B.
>
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