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

• To: Wei-Keng Liao <wkliao@xxxxxxxxxxxxxxxx>
• Subject: Re: [netcdfgroup] undefined reference to `H5Pset_fapl_http' and `H5FD_http_init'
• From: Vesselin Kolev <vlk@xxxxxxxxxxxxxxxxx>
• Date: Mon, 11 Oct 2021 08:10:38 +0300
• Authentication-results: directory.dce.uni-sofia.bg; dkim=pass (2048-bit key; unprotected) header.d=lcpe.uni-sofia.bg header.i=@lcpe.uni-sofia.bg header.a=rsa-sha256 header.s=2020021300 header.b=UHRkA6qN

Hello Liao and thank you for the replay!

I still get the same error while trying to compile NetCDF-c.:

../liblib/.libs/libnetcdf.so: undefined reference to `H5Pset_fapl_http'
../liblib/.libs/libnetcdf.so: undefined reference to `H5FD_http_init'

https://fossies.org/dox/netcdf-c-4.8.0/H5FDhttp_8c.html

nm libhdf5/.libs/libnchdf5.a | grep http
                 U H5Pset_fapl_http
                 U H5FD_http_init

and it seems like H5FDhttp.c goes into the set of compiled files:

nm libhdf5/.libs/libnchdf5.a | grep ".o" | grep http
libnchdf5_la-H5FDhttp.o:

Thank you very much in advance for your answer.


Best,

Vesselin Kolev

On 10/10/2021 22:37, Wei-Keng Liao wrote:

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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• Follow-Ups:
  • Re: [netcdfgroup] undefined reference to `H5Pset_fapl_http' and `H5FD_http_init'
    • From: Dennis Heimbigner

• References:
  • [netcdfgroup] undefined reference to `H5Pset_fapl_http' and `H5FD_http_init'
    • From: Vesselin Kolev
  • Re: [netcdfgroup] undefined reference to `H5Pset_fapl_http' and `H5FD_http_init'
    • From: Wei-Keng Liao