Unable to build 1.12.1 when already installed (Error: Symbol ‘h5i_invalid_hid_f’ at (1) has no IMPLICIT type)

[thesamesam]

Hi!

This is a forward of a downstream report of a bug in Gentoo.

When hdf5 1.10.5 is already installed, one gets when building 1.12.1 with fortran support like:

FAILED: fortran/src/CMakeFiles/hdf5_fortran-static.dir/H5Lff.F90.o bin/static/h5l.mod 
/usr/bin/x86_64-pc-linux-gnu-gfortran -I/var/tmp/portage/sci-libs/hdf5-1.12.1/work/hdf5-1.12.1/fortr
an/src -I/usr/include -I/var/tmp/portage/sci-libs/hdf5-1.12.1/work/hdf5-1.12.1/fortran/src -I/var/tm
p/portage/sci-libs/hdf5-1.12.1/work/hdf5-1.12.1_build/bin/static -I/var/tmp/portage/sci-libs/hdf5-1.
12.1/work/hdf5-1.12.1_build/fortran -I/var/tmp/portage/sci-libs/hdf5-1.12.1/work/hdf5-1.12.1_build/f
ortran/src -I/var/tmp/portage/sci-libs/hdf5-1.12.1/work/hdf5-1.12.1_build/src -I/var/tmp/portage/sci
-libs/hdf5-1.12.1/work/hdf5-1.12.1/src -O2 -march=native -pipe -O2 -march=native -pipe -fdiagnostics
-urls=never -fno-diagnostics-color -Jbin/static -fPIC -Waliasing -Wall -Wcharacter-truncation -Wextr
a -Wimplicit-interface -Wsurprising -Wunderflow -pedantic -ffree-form -fimplicit-none -std=f2008 -Wa
rray-temporaries -Wintrinsics-std -Wimplicit-procedure -Wreal-q-constant -Wfunction-elimination -Wre
alloc-lhs -Wrealloc-lhs-all -Wno-c-binding-type -fpreprocessed -o fortran/src/CMakeFiles/hdf5_fortra
n-static.dir/H5Lff.F90.o -c fortran/src/CMakeFiles/hdf5_fortran-static.dir/H5Lff.F90-pp.f90
/var/tmp/portage/sci-libs/hdf5-1.12.1/work/hdf5-1.12.1/fortran/src/H5Lff.F90:49:28:
   49 |      TYPE(H5O_TOKEN_T_F) :: token
      |                            1
Error: Derived type at (1) has not been previously defined and so cannot appear in a derived type definition
/var/tmp/portage/sci-libs/hdf5-1.12.1/work/hdf5-1.12.1/fortran/src/H5Lff.F90:644:24:
  644 |     TYPE(H5O_TOKEN_T_F), INTENT(OUT), TARGET :: token ! If the link is a hard link, token specifies the object token that the link points to
      |                        1
Error: Derived type ‘h5o_token_t_f’ at (1) is being used before it is defined
/var/tmp/portage/sci-libs/hdf5-1.12.1/work/hdf5-1.12.1/fortran/src/H5Lff.F90:660:47:
[...]

The same exact build configuration works if hdf5 is uninstalled from the system first.

One of the commenters on the bug in gentoo noticed that the include order may be wrong:

Thus, according to comment #13 and comment #14, h5global.mod from system takes the precedence over the new one; looking at the generated build.ninja, is it possible that -I/usr/include appears too early in the relative INCLUDES?

[brtnfld]

Does setting CMAKE_INCLUDE_DIRECTORIES_BEFORE help?

[thesamesam]

Thanks for the tip!

It looks like CMAKE_INCLUDE_DIRECTORIES_BEFORE doesn't help, but I looked it up and I found CMAKE_INCLUDE_DIRECTORIES_PROJECT_BEFORE which does.

With CMAKE_INCLUDE_DIRECTORIES_BEFORE (doesn't work; you can see it's kind of there but it's still injecting /usr/include too early):

[946/993] /usr/bin/x86_64-pc-linux-gnu-gfortran -I/tmp/portage/sci-libs/hdf5-1.12.1-r1/work/hdf5-1.12.1/fortran/src -I/usr/include -I/tmp/portage/sci-libs/hdf5-1.12.1-r1/work/hdf5-1.12.1/fortran/src -I/tmp/portage/sci-libs/hdf5-1.12.1-r1/work/hdf5-1.12.1_build/bin/shared -I/tmp/portage/sci-libs/hdf5-1.12.1-r1/work/hdf5-1.12.1_build/fortran -I/tmp/portage/sci-libs/hdf5-1.12.1-r1/work/hdf5-1.12.1_build/fortran/src -I/tmp/portage/sci-libs/hdf5-1.12.1-r1/work/hdf5-1.12.1_build/src -I/tmp/portage/sci-libs/hdf5-1.12.1-r1/work/hdf5-1.12.1/src -O2 -pipe -march=native -fdiagnostics-color=always -frecord-gcc-switches   -ggdb3 -O2 -pipe -march=native -fdiagnostics-color=always -frecord-gcc-switches     -ggdb3 -fdiagnostics-urls=never -fno-diagnostics-color -Jbin/shared -fPIC -Waliasing -Wall -Wcharacter-truncation -Wextra -Wimplicit-interface -Wsurprising -Wunderflow -pedantic -ffree-form -fimplicit-none -std=f2008 -Warray-temporaries -Wintrinsics-std -Wimplicit-procedure -Wreal-q-constant -Wfunction-elimination -Wrealloc-lhs -Wrealloc-lhs-all -Wno-c-binding-type -fpreprocessed -o fortran/src/CMakeFiles/hdf5_fortran-shared.dir/H5fortkit.F90.o -c fortran/src/CMakeFiles/hdf5_fortran-shared.dir/H5fortkit.F90-pp.f90

And with CMAKE_INCLUDE_DIRECTORIES_PROJECT_BEFORE (works):

[946/993] /usr/bin/x86_64-pc-linux-gnu-gfortran -I/tmp/portage/sci-libs/hdf5-1.12.1-r1/work/hdf5-1.12.1/fortran/src -I/tmp/portage/sci-libs/hdf5-1.12.1-r1/work/hdf5-1.12.1/fortran/src -I/tmp/portage/sci-libs/hdf5-1.12.1-r1/work/hdf5-1.12.1_build/bin/shared -I/tmp/portage/sci-libs/hdf5-1.12.1-r1/work/hdf5-1.12.1_build/fortran -I/tmp/portage/sci-libs/hdf5-1.12.1-r1/work/hdf5-1.12.1_build/fortran/src -I/tmp/portage/sci-libs/hdf5-1.12.1-r1/work/hdf5-1.12.1_build/src -I/tmp/portage/sci-libs/hdf5-1.12.1-r1/work/hdf5-1.12.1/src -I/usr/include -O2 -pipe -march=native -fdiagnostics-color=always -frecord-gcc-switches   -ggdb3 -O2 -pipe -march=native -fdiagnostics-color=always -frecord-gcc-switches     -ggdb3 -fdiagnostics-urls=never -fno-diagnostics-color -Jbin/shared -fPIC -Waliasing -Wall -Wcharacter-truncation -Wextra -Wimplicit-interface -Wsurprising -Wunderflow -pedantic -ffree-form -fimplicit-none -std=f2008 -Warray-temporaries -Wintrinsics-std -Wimplicit-procedure -Wreal-q-constant -Wfunction-elimination -Wrealloc-lhs -Wrealloc-lhs-all -Wno-c-binding-type -fpreprocessed -o fortran/src/CMakeFiles/hdf5_fortran-shared.dir/H5fortkit.F90.o -c fortran/src/CMakeFiles/hdf5_fortran-shared.dir/H5fortkit.F90-pp.f90

[brtnfld]

Everything related to this issue has been resolved, so I will close it. Thanks for your help!