[R-sig-hpc] Problems Installing Rmpi

[Hao Yu]

Rick, please use
###################################
AC_INIT(DESCRIPTION)

AC_PROG_CC

AC_ARG_WITH(mpi,
[   --with-mpi=/opt/lib32/usr/lib          Location of MPI library.],
[   if test "${withval}" != no; then
        MPI_ROOT=${withval}
        MPI_INCLUDE="-I${MPI_ROOT}/include"
        LDFLAGS="$LDFLAGS -L${withval}/lib"
        CFLAGS="$CFLAGS -I${withval}/include"
    fi  ]
)
MPITYPE="OPENMPI"
MPI_DEPS="-DMPI2"
AC_CHECK_LIB(util, openpty, [ MPI_LIBS="$MPI_LIBS -lutil" ])
AC_CHECK_LIB(pthread, main, [ MPI_LIBS="$MPI_LIBS -lpthread" ])

PKG_LIBS="${MPI_LIBS} -fPIC"
PKG_CPPFLAGS="${MPI_INCLUDE} ${MPI_DEPS} -D${MPITYPE} -fPIC"

AC_SUBST(PKG_LIBS)
AC_SUBST(PKG_CPPFLAGS)
AC_SUBST(DEFS)

AC_OUTPUT(src/Makevars)
###################################
to replace the original configure.ac completely. It is completely bypass
checking mpi.h and mpi.so. In this way, OS will not append mpi.h to
${MPI_INCLUDE} (hopefully).

Hao


Rick B. wrote:
>
> On Wed, 2009-05-13 at 10:53 -0400, Rowe, Brian Lee Yung (Portfolio
> Analytics) wrote:
>> Hi Rick,
>>
>> I just got Rmpi installed on a 16 CPU RHEL 4 box with OpenMPI. It took
>> quite a bit of fiddling of environment variables, but I did manage to
>> get it to work using mpicc (which incidentally does make life a bit
>> easier than trying to use gcc directly).
>>
>> For the error below, what I had to do was explicitly add my MPI
>> include library to C_INCLUDE_PATH. The other thing I had to do was set
>> MPI_ROOT explicitly to the location of my OpenMPI installation. I only
>> figured this out by looking at Rmpi's configure.ac and looking at the
>> configure output at the 'Try to find mpi.h ...' stage, no echo was
>> output meaning that it was falling back to the default. I think this
>> has to do with the behavior/interoperability of mpicc and Rmpi.
>>
>> In short, if you set your C_INCLUDE_PATH and MPI_ROOT (and
>> LD_LIBRARY_PATH if you haven't done that), you should be able to get
>> it to compile.
>>
>> HTH,
>> Brian
>>
>>
>> On Mon, 2009-05-11 at 10:09 -0400, Sean Davis wrote:
>> > Did you try:
>> >
>> > # assumes that mpicc is in the PATH
>> > CC=mpicc R CMD INSTALL Rmpi_0.5-7.tar.gz
>> >
>> > This has worked for me on openSUSE in the past.
>> >
>> > Sean
>>
>>
>> Thanks. mpicc is in the path, but this fails -  it cannot find mpi.h.
>> If
>> I include "--configure-args=--with-mpi=/usr/lib64/openmpi/1.2.7-gcc"
>> it
>> fails the same way as before.
>>
>> Why is the Rmpi script asking for a directory but passing a file name?
>>
>> Rick B.
>
>
> It had no problem finding mpi.h. The problem now is that the configure
> generates an incorrect compile command:
>
> 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'
>
> mpi.h is appendend to the -I/usr/lib64/openmpi/1.2.7-gcc/include and the
> compile fails because it just wants the folder, not the file.
>
> Rick B.
>
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