How to use h5fortran as a CMake dependency?

[milancurcic]

modern-fortran/neural-fortran#79 introduces h5fortran as a dependency to neural-fortran. With fpm this is easy and works well. I gave it about an hour of honest effort trying to get it to build also with CMake.

See modern-fortran/neural-fortran@69e2dbe for h5fortran-related additions to my CMakeLists.txt.

The FetchContent part seems to work correctly and it downloads the library and sets the paths. However I don't know how to tell it to build it and make it visible to my library. I tried the target_include_directories and target_link_libraries but it doesn't seem to work. Must be some obvious step I'm missing.

Thanks!

[scivision]

Thanks, this is best shown by example: https://github.com/scivision/h5fortran-fetchcontent

[milancurcic]

Thanks for the example. I think I'm getting closer, though not able to correctly link yet. I studied the example CMakeLists.txt, and although the example itself builds and runs as expected, I wasn't able to adapt the commands to my case and to reproduce correct building and linking. Specifically:

• Dependencies are not automatically built if I run make; instead, I need to do make h5fortran, make jsonfortran manually, and then make to build my project.
• Linking fails with:

...
Scanning dependencies of target test_flatten_layer
[ 50%] Building Fortran object CMakeFiles/test_flatten_layer.dir/test/test_flatten_layer.f90.o
[ 50%] Linking Fortran executable bin/test_flatten_layer
/usr/bin/ld: lib/libh5fortran.a(read.f90.o): in function `__h5fortran_MOD_hdf_check_exist':
read.f90:(.text+0x3a): undefined reference to `__h5lt_const_MOD_h5ltpath_valid_f'
/usr/bin/ld: lib/libh5fortran.a(read.f90.o): in function `__h5fortran_MOD_hdf_get_chunk':
read.f90:(.text+0x841): undefined reference to `__h5lt_const_MOD_h5ltget_dataset_ndims_f'
/usr/bin/ld: lib/libh5fortran.a(read.f90.o): in function `__h5fortran_MOD_hdf_get_shape':
read.f90:(.text+0xffd): undefined reference to `__h5lt_const_MOD_h5ltget_dataset_ndims_f'
/usr/bin/ld: read.f90:(.text+0x10ab): undefined reference to `__h5lt_const_MOD_h5ltget_dataset_info_f'
/usr/bin/ld: lib/libh5fortran.a(read.f90.o): in function `__h5fortran_MOD_hdf_get_ndim':
read.f90:(.text+0x1495): undefined reference to `__h5lt_const_MOD_h5ltget_dataset_ndims_f'
/usr/bin/ld: lib/libh5fortran.a(interface.f90.o): in function `__h5fortran_MOD_hdf_rank_check':
interface.f90:(.text+0x151): undefined reference to `__h5lt_const_MOD_h5ltget_dataset_ndims_f'
/usr/bin/ld: interface.f90:(.text+0x1a2): undefined reference to `__h5lt_const_MOD_h5ltget_dataset_info_f'
/usr/bin/ld: lib/libh5fortran.a(interface.f90.o): in function `__h5fortran_MOD_hdf_shape_check':
interface.f90:(.text+0x52f): undefined reference to `__h5lt_const_MOD_h5ltget_dataset_info_f'
/usr/bin/ld: lib/libh5fortran.a(attributes.f90.o): in function `__h5fortran.attributes_MOD_attr_shape_check':
attributes.f90:(.text+0xb0): undefined reference to `__h5lt_const_MOD_h5ltget_attribute_ndims_f'
/usr/bin/ld: attributes.f90:(.text+0x55e): undefined reference to `__h5lt_const_MOD_h5ltget_attribute_info_f'
/usr/bin/ld: lib/libh5fortran.a(attributes.f90.o): in function `__h5fortran_MOD_writeattr_num_lt':
attributes.f90:(.text+0xaf9): undefined reference to `__h5lt_const_MOD_h5ltset_attribute_float_f'
/usr/bin/ld: attributes.f90:(.text+0xbbf): undefined reference to `__h5lt_const_MOD_h5ltset_attribute_double_f'
/usr/bin/ld: attributes.f90:(.text+0xc7c): undefined reference to `__h5lt_const_MOD_h5ltset_attribute_int_f'
/usr/bin/ld: lib/libh5fortran.a(attributes.f90.o): in function `__h5fortran_MOD_writeattr_char_lt':
attributes.f90:(.text+0xda8): undefined reference to `__h5lt_const_MOD_h5ltset_attribute_string_f'
/usr/bin/ld: lib/libh5fortran.a(attributes.f90.o): in function `__h5fortran_MOD_writeattr_num':
attributes.f90:(.text+0xfa7): undefined reference to `__h5lt_const_MOD_h5ltset_attribute_float_f'
/usr/bin/ld: attributes.f90:(.text+0x105f): undefined reference to `__h5lt_const_MOD_h5ltset_attribute_double_f'
/usr/bin/ld: attributes.f90:(.text+0x10fc): undefined reference to `__h5lt_const_MOD_h5ltset_attribute_int_f'
/usr/bin/ld: lib/libh5fortran.a(attributes.f90.o): in function `__h5fortran_MOD_writeattr_char':
attributes.f90:(.text+0x1180): undefined reference to `__h5lt_const_MOD_h5ltset_attribute_string_f'
/usr/bin/ld: lib/libh5fortran.a(attributes.f90.o): in function `__h5fortran_MOD_readattr_num':
attributes.f90:(.text+0x1487): undefined reference to `__h5lt_const_MOD_h5ltget_attribute_float_f'
/usr/bin/ld: attributes.f90:(.text+0x155d): undefined reference to `__h5lt_const_MOD_h5ltget_attribute_double_f'
/usr/bin/ld: attributes.f90:(.text+0x161d): undefined reference to `__h5lt_const_MOD_h5ltget_attribute_int_f'
/usr/bin/ld: lib/libh5fortran.a(attributes.f90.o): in function `__h5fortran_MOD_readattr_char':
attributes.f90:(.text+0x19d1): undefined reference to `__h5lt_const_MOD_h5ltget_attribute_string_f'
/usr/bin/ld: lib/libh5fortran.a(read_scalar.f90.o): in function `__h5fortran_MOD_h5read_scalar':
read_scalar.f90:(.text+0x7f1): undefined reference to `__h5lt_const_MOD_h5ltread_dataset_string_f'
/usr/bin/ld: lib/libh5fortran.a(write.f90.o): in function `__h5fortran_MOD_hdf_create':
write.f90:(.text+0x1364): undefined reference to `__h5lt_const_MOD_h5ltpath_valid_f'
collect2: error: ld returned 1 exit status
make[2]: *** [CMakeFiles/test_flatten_layer.dir/build.make:106: bin/test_flatten_layer] Error 1
make[1]: *** [CMakeFiles/Makefile2:469: CMakeFiles/test_flatten_layer.dir/all] Error 2
make: *** [Makefile:166: all] Error 2

I suspect that one or more of my own CMake function calls conflicts with the new function calls, but it's not clear to me which.

Any tips would be very welcome. Here's my CMakeLists.txt.

Thanks!

[scivision]

milancurcic/neural-fortran#1

[scivision]

Also example of ExternalProject: https://github.com/scivision/h5fortran-externalproject