[netcdf-hdf] errors building netcdf4 for parallel I/O

• To: netcdf-hdf@xxxxxxxxxxxxxxxx
• Subject: [netcdf-hdf] errors building netcdf4 for parallel I/O
• From: robl@xxxxxxxxxxx (Robert Latham)
• Date: Wed, 12 Sep 2007 12:36:18 -0500

Hi

My apologies if netcdf-hdf is just for high-level design and
coordination.  I didn't think this was apropriate for netcdf-group but
if that's the better venue, I'll repost there.

I know netcdf4 is still in beta, but I'm looking to just play around
with the interface and libraries to see what's new.

I'm trying to build netcdf4 on linux (ubuntu 7.04) with gcc-4.1.2 and
MPICH2 (1.0.6pre1). 

I've built hdf5-1.8.0-beta3 with MPICH2: 

CC=${HOME}/work/soft/mpich2/bin/mpicc ../configure \
        --prefix=/home/robl/work/soft/hdf5-1.8.0-beta3

then tried to build
netcdf4-beta1:  

CC=${HOME}/work/soft/mpich2/bin/mpicc FC=${HOME}/work/soft/mpich2/bin/mpif77 \
        ../configure --with-hdf5=${HOME}/work/soft/hdf5-1.8.0-beta3 \
        --prefix=${HOME}/work/soft/netcdf-4.0-beta1 --disable-f90 \
        --enable-netcdf-4

Compilation fails with this error message:

libtool: compile:  /home/robl/work/soft/mpich2/bin/mpicc -DHAVE_CONFIG_H -I. 
-I../../libsrc4 -I.. -I../fortran -I../../libsrc4 -I../../libsrc 
-I/home/robl/work/soft/hdf5-1.8.0-beta3/include 
-I/home/robl/work/soft/hdf5-1.8.0-beta3/include -g -O2 -MT nc4attr.lo -MD -MP 
-MF .deps/nc4attr.Tpo -c ../../libsrc4/nc4attr.c -o nc4attr.o
In file included from 
/home/robl/work/soft/hdf5-1.8.0-beta3/include/H5public.h:58,
                 from /home/robl/work/soft/hdf5-1.8.0-beta3/include/hdf5.h:25,
                 from ../../libsrc4/nc4internal.h:18,
                 from ../../libsrc4/nc4attr.c:18:
/home/robl/work/soft/mpich2/include/mpi.h:94: error: two or more data types in 
declaration specifiers
/home/robl/work/soft/mpich2/include/mpi.h:94: warning: useless type name in 
empty declaration
/home/robl/work/soft/mpich2/include/mpi.h:279: error: two or more data types in 
declaration specifiers
/home/robl/work/soft/mpich2/include/mpi.h:279: warning: useless type name in 
empty declaration
make[2]: *** [nc4attr.lo] Error 1
make[2]: Leaving directory `/home/robl/work/netcdf-4.0-beta1/build/libsrc4'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/home/robl/work/netcdf-4.0-beta1/build'
make: *** [all] Error 2

line 94 of mpi.h is simply
typedef int MPI_Comm;
likewise line 279 is just
typedef int MPI_Info;


I see the NCO folks have encountered this same problem
(http://nco.sf.net/TODO, nco643).  

Has anybody else seen this?  I could be doing something odd. If so,
please steer me back on course.   I'll be happy to provide any
additional information. 

==rob

-- 
Rob Latham
Mathematics and Computer Science Division    A215 0178 EA2D B059 8CDF
Argonne National Lab, IL USA                 B29D F333 664A 4280 315B

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  • Re: [netcdf-hdf] errors building netcdf4 for parallel I/O
    • From: Elena Pourmal