FindNetCDF: linking wrong HDF5 version if multiple were found

[MuellerSeb]

We ran into a problem, where this script linked a wrong HDF5 version and the executable, that was linked against NetCDF::NetCDF_Fortran, crashed with a HDF5 version warning.

There were two HDF5 versions present on our system, which is now resolved.

But: Other scripts like https://github.com/geospace-code/nc4fortran/blob/main/cmake/Modules/FindNetCDF.cmake were able to provide a correctly linkable netcdf-fortran library.

I don't know at which point stuff went wrong, but still wanted to draw attention to this issue.

Cheers,
Sebastian

[MuellerSeb]

When executing, we got the following error:

Warning! ***HDF5 library version mismatched error***
The HDF5 header files used to compile this application do not match
the version used by the HDF5 library to which this application is linked.
Data corruption or segmentation faults may occur if the application continues.
This can happen when an application was compiled by one version of HDF5 but
linked with a different version of static or shared HDF5 library.
You should recompile the application or check your shared library related
settings such as 'LD_LIBRARY_PATH'.
You can, at your own risk, disable this warning by setting the environment
variable 'HDF5_DISABLE_VERSION_CHECK' to a value of '1'.
Setting it to 2 or higher will suppress the warning messages totally.
Headers are 1.10.2, library is 1.8.12
	    SUMMARY OF THE HDF5 CONFIGURATION
	    =================================

General Information:
-------------------
		   HDF5 Version: 1.8.12
		  Configured on: Thu Sep 16 02:22:24 UTC 2021
		  Configured by: [email protected]
		 Configure mode: production
		    Host system: x86_64-redhat-linux-gnu
	      Uname information: Linux buildhw-x86-14.iad2.fedoraproject.org 5.12.14-300.fc34.x86_64 #1 SMP Wed Jun 30 18:30:21 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux
		       Byte sex: little-endian
		      Libraries: static, shared
	     Installation point: /usr

Compiling Options:
------------------
               Compilation Mode: production
                     C Compiler: /usr/bin/gcc ( gcc (GCC) 4.8.5 20150623 )
                         CFLAGS: -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic
                      H5_CFLAGS: -std=c99 -pedantic -Wall -Wextra -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wcast-qual -Wcast-align -Wwrite-strings -Wconversion -Waggregate-return -Wstrict-prototypes -Wmissing-prototypes -Wmissing-declarations -Wredundant-decls -Wnested-externs -Winline -Wfloat-equal -Wmissing-format-attribute -Wmissing-noreturn -Wpacked -Wdisabled-optimization -Wformat=2 -Wunreachable-code -Wendif-labels -Wdeclaration-after-statement -Wold-style-definition -Winvalid-pch -Wvariadic-macros -Winit-self -Wmissing-include-dirs -Wswitch-default -Wswitch-enum -Wunused-macros -Wunsafe-loop-optimizations -Wc++-compat -Wstrict-overflow -Wlogical-op -Wlarger-than=2048 -Wvla -Wsync-nand -Wframe-larger-than=16384 -Wpacked-bitfield-compat -Wstrict-overflow=5 -Wjump-misses-init -Wunsuffixed-float-constants -Wdouble-promotion -Wsuggest-attribute=const -Wtrampolines -Wstack-usage=8192 -Wvector-operation-performance -Wsuggest-attribute=pure -Wsuggest-attribute=noreturn -Wsuggest-attribute=format -O3 -fomit-frame-pointer -finline-functions
                      AM_CFLAGS: 
                       CPPFLAGS: 
                    H5_CPPFLAGS: -D_POSIX_C_SOURCE=199506L   -DNDEBUG -UH5_DEBUG_API
                    AM_CPPFLAGS: -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_BSD_SOURCE 
               Shared C Library: yes
               Static C Library: yes
  Statically Linked Executables: no
                        LDFLAGS: -Wl,-z,relro 
                     H5_LDFLAGS: 
                     AM_LDFLAGS: 
 	 	Extra libraries:  -lsz -lz -ldl -lm 
 		       Archiver: ar
 		 	 Ranlib: ranlib
 	      Debugged Packages: 
		    API Tracing: no

Languages:
----------
                        Fortran: yes
               Fortran Compiler: /usr/bin/gfortran ( GNU Fortran (GCC) 4.8.5 20150623 )
          Fortran 2003 Compiler: yes
                  Fortran Flags: -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic -I/usr/lib64/gfortran/modules
               H5 Fortran Flags:  
               AM Fortran Flags: 
         Shared Fortran Library: yes
         Static Fortran Library: yes

                            C++: yes
                   C++ Compiler: /usr/bin/g++ ( g++ (GCC) 4.8.5 20150623 )
                      C++ Flags: -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic
                   H5 C++ Flags:  
                   AM C++ Flags: 
             Shared C++ Library: yes
             Static C++ Library: yes

Features:
---------
                  Parallel HDF5: no
             High Level library: yes
                   Threadsafety: no
            Default API Mapping: v18
 With Deprecated Public Symbols: yes
         I/O filters (external): deflate(zlib),szip(encoder)
         I/O filters (internal): shuffle,fletcher32,nbit,scaleoffset
                            MPE: no
                     Direct VFD: no
                        dmalloc: no
Clear file buffers before write: yes
           Using memory checker: no
         Function Stack Tracing: no
                           GPFS: no
      Strict File Format Checks: no
   Optimization Instrumentation: no
       Large File Support (LFS): yes
Bye...

Also, the NAG Fortran compiler complained during compilation:

/software/easybuild-broadwell/software/Compiler/GCCcore/7.3.0/binutils/2.30/bin/ld: warning: libhdf5_hl.so.100, needed by /software/netcdf-fortran/4.4.5-1/lib/libnetcdff.so, may conflict with libhdf5_hl.so.8
/software/easybuild-broadwell/software/Compiler/GCCcore/7.3.0/binutils/2.30/bin/ld: warning: libhdf5.so.101, needed by /software/netcdf-fortran/4.4.5-1/lib/libnetcdff.so, may conflict with libhdf5.so.8