HDF5 not properly linked on Windows + Bash + Ninja

[tdegeus]

I am trying to link HDF5 using CMake as follows:

set(test_name "unit-tests")
set(HIGHFIVE_USE_BOOST 0)
set(HIGHFIVE_USE_XTENSOR 1)
find_package(HighFive REQUIRED)
target_link_libraries(${test_name} PRIVATE HighFive)

Then, on my GitHub action:

    defaults:
      run:
        shell: bash -l {0}

    name: "${{ matrix.runs-on }} • x64 ${{ matrix.args }}"
    runs-on: ${{ matrix.runs-on }}

    steps:

    ...

    - name: Configure using CMake
      run: cmake -Bbuild -G Ninja

    - name: Build C++
      working-directory: build
      run: cmake --build .

With this I'm getting the error that

Linking CXX executable test\unit-tests.exe
FAILED: test/unit-tests.exe 
cmd.exe /C "cd . && C:\Miniconda\envs\myenv\Library\bin\clang++.exe -fuse-ld=lld-link -nostartfiles -nostdlib -O3 -DNDEBUG -D_DLL -D_MT -Xclang --dependent-lib=msvcrt  test/CMakeFiles/unit-tests.dir/main.cpp.obj test/CMakeFiles/unit-tests.dir/Redraw.cpp.obj test/CMakeFiles/unit-tests.dir/Static.cpp.obj -o test\unit-tests.exe -Xlinker /implib:test\unit-tests.lib -Xlinker /pdb:test\unit-tests.pdb -Xlinker /version:0.0   C:/Miniconda/envs/myenv/Library/lib/libhdf5.lib  -lkernel32 -luser32 -lgdi32 -lwinspool -lshell32 -lole32 -loleaut32 -luuid -lcomdlg32 -ladvapi32 -loldnames && cd ."
lld-link: error: undefined symbol: __declspec(dllimport) H5Pclose

(and many more of these linker errors).

For full reference : tdegeus/QPot#19

[PhilipDeegan]

You might be able to get around this by adding a define for

-DH5_BUILT_AS_DYNAMIC_LIB=1

https://github.com/HDFGroup/hdf5/blob/2ea165efd095d8876639814dc615dd01a2ec34e6/src/H5api_adpt.h#L23

[tdegeus]

Thanks for the suggestion @PhilipDeegan , but unfortunately that did not fix... But it does suggest that I might be understanding things incorrectly. I thought that HDF5 might not be linked correctly, but your suggestion implies that it might be linked correctly, but that it might be missing some symbols because of the way HDF5 was coded?

[tdegeus]

What is a bit strange is that I don't find something like -lhdf5 as argument, wheres the HighFive target clear does something (resulting in arguments like -DH5_USE_XTENSOR -DMPI_NO_CPPBIND):

[1/4] C:\Miniconda\envs\myenv\Library\bin\clang++.exe -DDH5_BUILT_AS_DYNAMIC_LIB -DH5_BUILT_AS_DYNAMIC_LIB -DH5_USE_XTENSOR -DMPI_NO_CPPBIND -DQPOT_ENABLE_ASSERT -DUSE_HDF5 -I../include -isystem C:/Miniconda/envs/myenv/Library/include -O3 -DNDEBUG -D_DLL -D_MT -Xclang --dependent-lib=msvcrt -Wall -Wextra -pedantic -Wno-unknown-pragmas -MD -MT test/CMakeFiles/unit-tests.dir/Static.cpp.obj -MF test\CMakeFiles\unit-tests.dir\Static.cpp.obj.d -o test/CMakeFiles/unit-tests.dir/Static.cpp.obj -c ../test/Static.cpp
[2/4] C:\Miniconda\envs\myenv\Library\bin\clang++.exe -DDH5_BUILT_AS_DYNAMIC_LIB -DH5_BUILT_AS_DYNAMIC_LIB -DH5_USE_XTENSOR -DMPI_NO_CPPBIND -DQPOT_ENABLE_ASSERT -DUSE_HDF5 -I../include -isystem C:/Miniconda/envs/myenv/Library/include -O3 -DNDEBUG -D_DLL -D_MT -Xclang --dependent-lib=msvcrt -Wall -Wextra -pedantic -Wno-unknown-pragmas -MD -MT test/CMakeFiles/unit-tests.dir/main.cpp.obj -MF test\CMakeFiles\unit-tests.dir\main.cpp.obj.d -o test/CMakeFiles/unit-tests.dir/main.cpp.obj -c ../test/main.cpp
[3/4] C:\Miniconda\envs\myenv\Library\bin\clang++.exe -DDH5_BUILT_AS_DYNAMIC_LIB -DH5_BUILT_AS_DYNAMIC_LIB -DH5_USE_XTENSOR -DMPI_NO_CPPBIND -DQPOT_ENABLE_ASSERT -DUSE_HDF5 -I../include -isystem C:/Miniconda/envs/myenv/Library/include -O3 -DNDEBUG -D_DLL -D_MT -Xclang --dependent-lib=msvcrt -Wall -Wextra -pedantic -Wno-unknown-pragmas -MD -MT test/CMakeFiles/unit-tests.dir/Redraw.cpp.obj -MF test\CMakeFiles\unit-tests.dir\Redraw.cpp.obj.d -o test/CMakeFiles/unit-tests.dir/Redraw.cpp.obj -c ../test/Redraw.cpp
[4/4] cmd.exe /C "cd . && C:\Miniconda\envs\myenv\Library\bin\clang++.exe -fuse-ld=lld-link -nostartfiles -nostdlib -O3 -DNDEBUG -D_DLL -D_MT -Xclang --dependent-lib=msvcrt  test/CMakeFiles/unit-tests.dir/main.cpp.obj test/CMakeFiles/unit-tests.dir/Redraw.cpp.obj test/CMakeFiles/unit-tests.dir/Static.cpp.obj -o test\unit-tests.exe -Xlinker /implib:test\unit-tests.lib -Xlinker /pdb:test\unit-tests.pdb -Xlinker /version:0.0   C:/Miniconda/envs/myenv/Library/lib/libhdf5.lib  -lkernel32 -luser32 -lgdi32 -lwinspool -lshell32 -lole32 -loleaut32 -luuid -lcomdlg32 -ladvapi32 -loldnames && cd ."
FAILED: test/unit-tests.exe 
cmd.exe /C "cd . && C:\Miniconda\envs\myenv\Library\bin\clang++.exe -fuse-ld=lld-link -nostartfiles -nostdlib -O3 -DNDEBUG -D_DLL -D_MT -Xclang --dependent-lib=msvcrt  test/CMakeFiles/unit-tests.dir/main.cpp.obj test/CMakeFiles/unit-tests.dir/Redraw.cpp.obj test/CMakeFiles/unit-tests.dir/Static.cpp.obj -o test\unit-tests.exe -Xlinker /implib:test\unit-tests.lib -Xlinker /pdb:test\unit-tests.pdb -Xlinker /version:0.0   C:/Miniconda/envs/myenv/Library/lib/libhdf5.lib  -lkernel32 -luser32 -lgdi32 -lwinspool -lshell32 -lole32 -loleaut32 -luuid -lcomdlg32 -ladvapi32 -loldnames && cd ."
lld-link: error: undefined symbol: __declspec(dllimport) H5Pclose

[PhilipDeegan]

you have

C:/Miniconda/envs/myenv/Library/lib/libhdf5.lib

if you have no dll, you might only have a static library version of hdf5

[tdegeus]

The problems curiously disappeared from me. This might be due to a HDF5 and/or CMake update

[tdegeus]

And curiously reappeared here: tdegeus/XDMFWrite_HighFive#11

[1uc]

@tdegeus Is this still an issue or can we close this?

[1uc]

We've rewritten the HighFive CMake related code for v3 and are close to of have merge the changes. I'm closing this issue as outdated. Please open a new Issue if the problem persists after #897 got merged.