Fix CMake

[scivision]

This provides several fixes to CMake with regard to finding and linking HDF5 as well as canonical specification of compiler options. Now it's stuck on not finding json_module.mod from JsonFortran, I didn't look into that.

A key distinction is find_package(HDF5 ...) uses my FindHDF5.cmake in h5fortran, which works for more scenarios and generally is more robust than factory CMake FindHDF5.

[scivision]

I didn't look at if you wanted to make HDF5 optional etc. that would probably also be possible (may switch source files depending if HDF5 found or similar)

[milancurcic]

Interesting, I still have the same issue with your patch:

(venv) milan@mars:~/Work/neural-fortran/neural-fortran_scivision/build$ cmake .. -DSERIAL=1
-- The C compiler identification is GNU 9.4.0
-- The Fortran compiler identification is GNU 9.4.0
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /usr/bin/cc - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- Detecting Fortran compiler ABI info
-- Detecting Fortran compiler ABI info - done
-- Check for working Fortran compiler: /usr/bin/gfortran - skipped
-- Configuring build for serial execution
-- h5fortran 4.6.3  CMake 3.22.5
-- checking that C and Fortran compilers can link
-- checking that C and Fortran compilers can link - OK
-- Looking for H5_HAVE_FILTER_SZIP
-- Looking for H5_HAVE_FILTER_SZIP - found
-- Looking for H5_HAVE_FILTER_DEFLATE
-- Looking for H5_HAVE_FILTER_DEFLATE - found
-- Looking for H5_HAVE_PARALLEL
-- Looking for H5_HAVE_PARALLEL - not found
-- Found ZLIB: /usr/lib/x86_64-linux-gnu/libz.so (found version "1.2.11") 
-- Found SZIP: /usr/lib/x86_64-linux-gnu/libsz.so  
-- Looking for pthread.h
-- Looking for pthread.h - found
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Failed
-- Looking for pthread_create in pthreads
-- Looking for pthread_create in pthreads - not found
-- Looking for pthread_create in pthread
-- Looking for pthread_create in pthread - found
-- Found Threads: TRUE  
-- Performing Test HDF5_C_links
-- Performing Test HDF5_C_links - Success
-- Performing Test HDF5_Fortran_links
-- Performing Test HDF5_Fortran_links - Success
-- Found HDF5: /usr/lib/x86_64-linux-gnu/hdf5/serial/lib/libhdf5_hl.so;/usr/lib/x86_64-linux-gnu/hdf5/serial/lib/libhdf5.so (found suitable version "1.10.4", minimum required is "1.8.7") found components: Fortran HL 
CMake Deprecation Warning at build/_deps/jsonfortran-src/CMakeLists.txt:12 (cmake_minimum_required):
  Compatibility with CMake < 2.8.12 will be removed from a future version of
  CMake.

  Update the VERSION argument <min> value or use a ...<max> suffix to tell
  CMake that the project does not need compatibility with older versions.


-- CMake build configuration for JSON-Fortran 8.3.0
-- Dynamically computing FORD output information...
-- Running FORD to dynamically compute documentation outputs, this could take a while...
-- Caching FORD outputs
-- Done dynamically computing FORD outputs.
-- Found HDF5: /usr/lib/x86_64-linux-gnu/hdf5/serial/lib/libhdf5_hl.so;/usr/lib/x86_64-linux-gnu/hdf5/serial/lib/libhdf5.so (found version "1.10.4") found components: Fortran 
-- Configuring to build with -fcoarray=single
-- Configuring done
-- Generating done
-- Build files have been written to: /home/milan/Work/neural-fortran/neural-fortran_scivision/build
(venv) milan@mars:~/Work/neural-fortran/neural-fortran_scivision/build$ make
Scanning dependencies of target neural
[  0%] Building Fortran object CMakeFiles/neural.dir/src/nf/nf_datasets_mnist.f90.o
[  2%] Building Fortran object CMakeFiles/neural.dir/src/nf/nf_activation.f90.o
[  2%] Building Fortran object CMakeFiles/neural.dir/src/nf/nf_base_layer.f90.o
[  4%] Building Fortran object CMakeFiles/neural.dir/src/nf/nf_layer.f90.o
[  6%] Building Fortran object CMakeFiles/neural.dir/src/nf/nf_layer_constructors.f90.o
[  8%] Building Fortran object CMakeFiles/neural.dir/src/nf/nf_optimizers.f90.o
[ 10%] Building Fortran object CMakeFiles/neural.dir/src/nf/nf_network.f90.o
[ 10%] Building Fortran object CMakeFiles/neural.dir/src/nf.f90.o
[ 10%] Building Fortran object CMakeFiles/neural.dir/src/nf/io/nf_io_binary.f90.o
[ 12%] Building Fortran object CMakeFiles/neural.dir/src/nf/io/nf_io_binary_submodule.f90.o
[ 12%] Building Fortran object CMakeFiles/neural.dir/src/nf/io/nf_io_hdf5.f90.o
[ 14%] Building Fortran object CMakeFiles/neural.dir/src/nf/io/nf_io_hdf5_submodule.f90.o
f951: Fatal Error: Module file ‘h5fortran.mod’ has not been generated, either because the module does not contain a MODULE PROCEDURE or there is an error in the module.
compilation terminated.
make[2]: *** [CMakeFiles/neural.dir/build.make:569: CMakeFiles/neural.dir/src/nf/io/nf_io_hdf5_submodule.f90.o] Error 1
make[1]: *** [CMakeFiles/Makefile2:251: CMakeFiles/neural.dir/all] Error 2
make: *** [Makefile:166: all] Error 2

[scivision]

Thanks I pushed a fix for linking for GNU Make. It stops build again at missing json_module.mod

[scivision]

OK I see jsonfortran has a older style CMake. It may be more expedient to simply control it from this Cmake script. I'll give it a quick try (ignoring the jsonfortran/CMakeLists.txt and using this project's code to control it).

[milancurcic]

Thanks a lot. As you can probably guess, I'm OK with any one approach that will just work. What I really hope to avoid is dropping CMake support.

[scivision]

OK give that a try, it works for me with GCC and Intel oneAPI

[milancurcic]

Thanks, Michael, that works like a charm. You rock as usual. If you agree, I'll merge these. And these new cmake files you added seem like nice examples for me to study.

[scivision]

Yes it's ready to merge. I didn't add in the JsonFortran Coarray features but that can be done separately if needed.

[milancurcic]

Well UTF-8 support in JSON now breaks the code because my fields are ASCII. I'd prefer to keep them ASCII if possible. Any good reason to do UTF-8?

[ 52%] Building Fortran object CMakeFiles/neural.dir/src/nf/nf_keras_submodule.f90.o
/home/milan/Work/neural-fortran/neural-fortran_scivision/src/nf/nf_keras_submodule.f90:40:15:

   40 |       call json % get(layer_json, 'class_name', res(n) % class)
      |               1
Error: Found no matching specific binding for the call to the GENERIC ‘get’ at (1)
/home/milan/Work/neural-fortran/neural-fortran_scivision/src/nf/nf_keras_submodule.f90:46:15:

   46 |       call json % get(layer_config_json, 'name', res(n) % name)
      |               1
Error: Found no matching specific binding for the call to the GENERIC ‘get’ at (1)
/home/milan/Work/neural-fortran/neural-fortran_scivision/src/nf/nf_keras_submodule.f90:59:19:

   59 |           call json % get(layer_config_json, 'activation', res(n) % activation)
      |                   1
Error: Found no matching specific binding for the call to the GENERIC ‘get’ at (1)
make[2]: *** [CMakeFiles/neural.dir/build.make:322: CMakeFiles/neural.dir/src/nf/nf_keras_submodule.f90.o] Error 1
make[1]: *** [CMakeFiles/Makefile2:238: CMakeFiles/neural.dir/all] Error 2
make: *** [Makefile:166: all] Error 2

[scivision]

OK this is fixed

[milancurcic]

Perfect, thanks again, I'll merge.