mvapich, nonblocking build issue

[Wei-keng Liao]

Hi, Brent,

MPI_Get_address is an API defined in MPI2 (not in MPI version 1).
Could you check if your MPICC compiler supports MPI2?
Let us know what mvapich2 and openmpi versions you have?

A test program can be like this:

#include <mpi.h>
int main(int argc, char **argv) {
    int buf[16];
    MPI_Aint address;
    
    MPI_Init(&argc, &argv);
    MPI_Get_address(buf, &address);
    MPI_Finalize();
    return 0;
}

Please use $MPI_BIN/mpicc to compile and let us know if it passes.

Wei-keng


On Sep 12, 2011, at 12:02 PM, Brent Woodruff wrote:

> Hello all,
> 
> I am attempting to build parallel-netcdf 1.2.0 on RHEL 6.1 with mvapich 1.2.0 and am running into a problem. I have successful builds with mvapich2 and openmpi.
> 
> I should also note that I am replacing pnetcdf.h.in with this one from SVN because I intend to use this pnetcdf with netcdf 4.1.3:
> http://trac.mcs.anl.gov/projects/parallel-netcdf/export/925/trunk/src/lib/pnetcdf.h.in
> 
> Here's my procedure:
> Unpack, replace pnetcdf.h.in
> 
> export CC=gcc
> export CXX=g++
> export FC=gfortran
> export F90=gfortran
> export CFLAGS="-O2 -g -fPIC"
> export CXXFLAGS="-O2 -g -fPIC"
> export FFLAGS="-O2 -g -fPIC"
> 
>  module load gnu-mvapich # sets MPI paths
>  export MPICC=$MPI_BIN/mpicc
>  export MPICXX=$MPI_BIN/mpicxx
>  export MPIF77=$MPI_BIN/mpif77
>  export MPIF90=$MPI_BIN/mpif90
> 
>  ./configure \
>     --prefix=$MPI_HOME \
>     --includedir=$MPI_INCLUDE \
>     --libdir=$MPI_LIB \
>     --sysconfdir=$MPI_SYSCONFIG \
>     --enable-fortran \
>     --with-mpi=$MPI_HOME
> 
> The result of configure before make is:
> parallel-netCDF version 1.2.0 features:
> . parallel-netcdf configured WITH support for large files
> . parallel-netcdf configured WITH fortran bindings
> . parallel-netcdf configured WITHOUT nonblocking routines
> . parallel-netcdf configured WITH giant variable support
> 
> However, I noticed that nonblocking does get built before creating libraries. Here's the tail of make up to the error:
> 
> [ ... snip successful compiled of other objects ... ]
> /opt/hpc/gnu/mvapich/bin/mpicc -c -O2 -g -fPIC -I.    ../../../src/lib/nonblocking.c
> /opt/hpc/gnu/mvapich/bin/mpicc -c -O2 -g -fPIC -I.    ../../../src/lib/malloc.c
> ar cru libpnetcdf.a mpinetcdf.o header.o mpincio.o attr.o dim.o error.o nc.o ncx.o string.o var.o ncmpidtype.o convert_swap.o filetype.o getput_var.o getput_var1.o getput_vara.o getput_vars.o getput_varm.o i_getput_var.o i_getput_var1.o i_getput_vara.o i_getput_vars.o i_getput_varm.o m_getput_varx.o nonblocking.o malloc.o
> ranlib libpnetcdf.a
> m4 -B10000 -DAPI=C ../../../src/lib/../../man/netcdf.m4 >pnetcdf.3  || rm pnetcdf.3
> m4: Warning: `m4 -B' may be removed in a future release
> /opt/hpc/gnu/mvapich/bin/mpicc -c -O2 -g -fPIC -I.    ../../../src/lib/validator.c
> /opt/hpc/gnu/mvapich/bin/mpicc -o ncvalid -O2 -g -fPIC  validator.o libpnetcdf.a
> libpnetcdf.a(nonblocking.o): In function `ncmpii_mgetput':
> /mnt/devel/BUILD/parallel-netcdf-1.2.0/gnu-mvapich/src/lib/../../../src/lib/nonblocking.c:727: undefined reference to `MPI_Get_address'
> /mnt/devel/BUILD/parallel-netcdf-1.2.0/gnu-mvapich/src/lib/../../../src/lib/nonblocking.c:733: undefined reference to `MPI_Get_address'
> collect2: ld returned 1 exit status
> make[3]: *** [ncvalid] Error 1
> make[3]: Leaving directory `/mnt/devel/BUILD/parallel-netcdf-1.2.0/gnu-mvapich/src/lib'
> make[2]: *** [all] Error 2
> make[2]: Leaving directory `/mnt/devel/BUILD/parallel-netcdf-1.2.0/gnu-mvapich/src'
> make[1]: *** [subdir_target] Error 1
> make[1]: Leaving directory `/mnt/devel/BUILD/parallel-netcdf-1.2.0/gnu-mvapich'
> make: *** [src/lib/all] Error 2
> 
> Any suggestions would be appreciated!
> 
> Brent W.