Re: [netcdfgroup] undefined reference to `H5Pset_fapl_http' and `H5FD_http_init'

• To: Vesselin Kolev <vlk@xxxxxxxxxxxxxxxxx>
• Subject: Re: [netcdfgroup] undefined reference to `H5Pset_fapl_http' and `H5FD_http_init'
• From: Wei-Keng Liao <wkliao@xxxxxxxxxxxxxxxx>
• Date: Sun, 10 Oct 2021 19:37:05 +0000
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Your HDF5 was configured to be installed under folder:
> /opt/software/hdf/5/1.10.7-gcc_11-zlib_1-api_v18-mpich_3

But you are using a different folder in your NetCDF configuration.
> /opt/software/hdf/5/1.10.7-gcc_11-zlib_1-api_v18-nojava

In addition, your HDF5 was built using mpicc/mpifort, but
you are using gcc to build NetCDF. I suggest you to use the
same compilers.

Wei-keng

> On Oct 10, 2021, at 4:17 AM, Vesselin Kolev via netcdfgroup 
> <netcdfgroup@xxxxxxxxxxxxxxxx> wrote:
> 
> Hello Everyone,
> 
> I face very strange problem when compiling NetCDF-C 4.8.0 against HDF5-1.10.7 
> and HDF5-1.12.1.
> 
> Note that HDF5 is compiled in the following manner:
> 
> LDFLAGS="-L/opt/software/zlib/1.2.11/lib" 
> CFLAGS="-I/opt/software/zlib/1.2.11/include" 
> CXXFLAGS="-I/opt/software/zlib/1.2.11/include" 
> FCLAGS="-I/opt/software/zlib/1.2.11/include" 
> ZLIB_ROOT=/opt/software/zlib/1.2.11 FC=mpifort FCFLAGS="-Ofast" CC=mpicc 
> CFLAGS="-Ofast" CXX=mpic++ CXXFLAGS="-Ofast" cmake .. 
> -DCMAKE_INSTALL_PREFIX=/opt/software/hdf/5/1.10.7-gcc_11-zlib_1-api_v18-mpich_3
>  -DHDF5_ENABLE_THREADSAFE=OFF -DHDF5_BUILD_CPP_LIB=OFF 
> -DHDF5_BUILD_FORTRAN=ON -DHDF5_BUILD_HL_LIB=ON -DHDF5_BUILD_JAVA=OFF 
> -DHDF5_ENABLE_Z_LIB_SUPPORT=ON -DBUILD_SHARED_LIBS=ON 
> -DDEFAULT_API_VERSION=v18 -DHDF5_ENABLE_PARALLEL=ON
> 
> using GCC 11.0.3. Also note, that the HDF5 compilation passed the 
> post-compilation tests without any fail.
> 
> But if I try to compile NetCDF-C agains that particular compilation of HDF5:
> 
> LDFLAGS="-L/opt/software/hdf/5/1.10.7-gcc_11-zlib_1-api_v18-nojava/lib" 
> CC=gcc CFLAGS="-Ofast 
> -I/opt/software/hdf/5/1.10.7-gcc_11-zlib_1-api_v18-nojava/include" 
> ./configure --prefix=/opt/software/netcdf-c/4/4.8.0-gcc_11_hdf5_1.10.7 
> --enable-mmap --enable-byterange
> 
> I get the following error:
> 
> ../liblib/.libs/libnetcdf.so: undefined reference to `H5Pset_fapl_http'
> ../liblib/.libs/libnetcdf.so: undefined reference to `H5FD_http_init'
> 
> Any suggestions where to look for the source of the problem are greatly 
> welcomed.
> 
> Thank you very much in advance!
> 
> Best,
> 
> Vesselin Kolev
> 
> 
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  • Re: [netcdfgroup] undefined reference to `H5Pset_fapl_http' and `H5FD_http_init'
    • From: Vesselin Kolev

• References:
  • [netcdfgroup] undefined reference to `H5Pset_fapl_http' and `H5FD_http_init'
    • From: Vesselin Kolev