undefined reference due to --no-allow-shlib-undefined: H5get_libversion

[yurivict]

When cmake is called with:

-DCMAKE_C_COMPILER:STRING="cc"  
-DCMAKE_CXX_COMPILER:STRING="c++"  
-DCMAKE_C_FLAGS:STRING="-O2 -pipe  -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing "  
-DCMAKE_C_FLAGS_DEBUG:STRING="-O2 -pipe  -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing "  
-DCMAKE_C_FLAGS_RELEASE:STRING="-O2 -pipe  -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing  
-DNDEBUG"  
-DCMAKE_CXX_FLAGS:STRING="-O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing  -isystem /usr/local/include "  
-DCMAKE_CXX_FLAGS_DEBUG:STRING="-O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing  -isystem /usr/local/include "  
-DCMAKE_CXX_FLAGS_RELEASE:STRING="-O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing  -isystem /usr/local/include  
-DNDEBUG"  
-DCMAKE_EXE_LINKER_FLAGS:STRING=" -Wl,-rpath=/usr/local/lib/gcc13  -L/usr/local/lib/gcc13 -fstack-protector-strong -L/usr/local/lib " 
 -DCMAKE_MODULE_LINKER_FLAGS:STRING=" -Wl,-rpath=/usr/local/lib/gcc13  -L/usr/local/lib/gcc13 -fstack-protector-strong -L/usr/local/lib "  
-DCMAKE_SHARED_LINKER_FLAGS:STRING=" -Wl,-rpath=/usr/local/lib/gcc13  -L/usr/local/lib/gcc13 -fstack-protector-strong -L/usr/local/lib "  
-DCMAKE_INSTALL_PREFIX:PATH="/usr/local"  
-DCMAKE_AUTOGEN_PARALLEL:STRING="7"  
-DCMAKE_BUILD_TYPE:STRING="Release"  
-DTHREADS_HAVE_PTHREAD_ARG:BOOL=YES  
-DCMAKE_INSTALL_RPATH_USE_LINK_PATH=YES  
-DCMAKE_VERBOSE_MAKEFILE:BOOL=ON  
-DFETCHCONTENT_FULLY_DISCONNECTED:BOOL=ON 
-DSeacas_ENABLE_ALL_PACKAGES:BOOL=ON 
-DSeacas_ENABLE_ALL_OPTIONAL_PACKAGES:BOOL=ON 
-DSeacas_ENABLE_SECONDARY_TESTED_CODE:BOOL=ON 
-DBUILD_SHARED_LIBS:BOOL=ON 
-DPython_ADDITIONAL_VERSIONS=3.11 
-DPython_EXECUTABLE:FILEPATH="/usr/local/bin/python3.11" 
-DPython3_EXECUTABLE:FILEPATH="/usr/local/bin/python3.11" 
-DBOOST_PYTHON_SUFFIX:STRING=311

the build fails due to missing -lhdf5:

cd /usr/ports/science/seacas/work/.build/packages/seacas/applications/epu && /usr/local/libexec/ccache/c++ -DFMT_SHARED -I/usr/ports/science/seacas/work/.build -I/usr/ports/science/seacas/work/seacas-2024-08-15/packages/seacas/applications/epu -I/usr/ports/science/seacas/work/seacas-2024-08-15/packages/seacas/libraries/exodus/include -I/usr/ports/science/seacas/work/.build/packages/seacas/libraries/exodus -I/usr/ports/science/seacas/work/seacas-2024-08-15/packages/seacas/libraries/suplib_c -I/usr/ports/science/seacas/work/seacas-2024-08-15/packages/seacas/libraries/suplib_cpp -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing  -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing  -isystem /usr/local/include  -DNDEBUG -std=c++17 -MD -MT packages/seacas/applications/epu/CMakeFiles/epu.dir/EP_ParallelDisks.C.o -MF CMakeFiles/epu.dir/EP_ParallelDisks.C.o.d -o CMakeFiles/epu.dir/EP_ParallelDisks.C.o -c /usr/ports/science/seacas/work/seacas-2024-08-15/packages/seacas/applications/epu/EP_ParallelDisks.C
--- packages/seacas/applications/conjoin/CMakeFiles/conjoin.dir/all ---
ld: error: undefined reference due to --no-allow-shlib-undefined: H5get_libversion

Adding -lhdf5 solves this problem.

Version: 2024-08-15
clang-18
FreeBSD 14.1

[gsjaardema]

The -lhdf5 should already be being added by the netCDF shared library dependency. Not sure why that is somehow getting lost...

During the cmake configuration, it should show that it has found the netCDF library and show whether it depends on hdf5 and it then adds the dependency at that point.

If that is not what is happening, then you can send the output from the CMake configuration and we can see what it shows related to hdf5.