opensuse build fails

[junghans]

-- HDF5 C compiler wrapper is unable to compile a minimal HDF5 program.
CMake Error at /usr/share/cmake/Modules/FindPackageHandleStandardArgs.cmake:[23](https://github.com/espressopp/espressopp/runs/5429930182?check_suite_focus=true#step:6:23)0 (message):
-- Configuring incomplete, errors occurred!
  Could NOT find HDF5 (missing: HDF5_LIBRARIES HDF5_INCLUDE_DIRS
See also "/__w/espressopp/espressopp/build/CMakeFiles/CMakeOutput.log".
  HDF5_HL_LIBRARIES C HL) (found version "")
Call Stack (most recent call first):
  /usr/share/cmake/Modules/FindPackageHandleStandardArgs.cmake:594 (_FPHSA_FAILURE_MESSAGE)
  cmake/FindHDF5.cmake:1001 (find_package_handle_standard_args)
  CMakeLists.txt:70 (find_package)

[junghans]

I guess we need to add a path here: https://github.com/espressopp/buildenv/blob/1826da1ffc6685bcf6c70844f067323e99277226/opensuse#L20

[XzzX]

pipeline which is failing: https://github.com/espressopp/espressopp/actions/runs/2007092318

[junghans]

Now it fails in a different way: https://github.com/espressopp/espressopp/runs/5879274758?check_suite_focus=true

[XzzX]

I know this problem: XzzX/mrmd@a520795

Release version of HDF5 enforces _FORTIFY_SOURCE on all its dependencies. And _FORTIFY_SOURCE requires optimizations flags. Therefore, it produces warnings when build in debug mode without optimization. Do we have debug libraries for HDF5?

[junghans]

https://build.opensuse.org/request/show/967624 should fix that!

[junghans]

@XzzX

and another issue on Fedora:

[ 32%] Building CXX object src/CMakeFiles/_espressopp.dir/esutil/GammaVariate.cpp.o
cd /__w/espressopp/espressopp/build/src && /usr/lib64/ccache/clang++ -DGMX_DOUBLE=0 -DHAS_GROMACS -D_espressopp_EXPORTS -I/__w/espressopp/espressopp/src -I/__w/espressopp/espressopp/src/include -I/__w/espressopp/espressopp/build/src -isystem /usr/include/python3.10 -isystem /usr/include/openmpi-x86_64 -g -fPIC -Werror -fopenmp=libomp -std=c++17 -MD -MT src/CMakeFiles/_espressopp.dir/esutil/GammaVariate.cpp.o -MF CMakeFiles/_espressopp.dir/esutil/GammaVariate.cpp.o.d -o CMakeFiles/_espressopp.dir/esutil/GammaVariate.cpp.o -c /__w/espressopp/espressopp/src/esutil/GammaVariate.cpp
/__w/espressopp/espressopp/src/esutil/Collectives.cpp:38:35: error: 'binary_function<int, int, int>' is deprecated [-Werror,-Wdeprecated-declarations]
struct UniqueReduce : public std::binary_function<int, int, int>
                                  ^
/usr/bin/../lib/gcc/x86_64-redhat-linux/12/../../../../include/c++/12/bits/stl_function.h:141:7: note: 'binary_function<int, int, int>' has been explicitly marked deprecated here
    } _GLIBCXX11_DEPRECATED;
      ^

[XzzX]

Wild guess, just remove the inheritance. I will try that.

[junghans]

@XzzX next one:

In file included from /__w/espressopp/espressopp/src/interaction/LJcos.cpp:25:
/__w/espressopp/espressopp/src/interaction/VerletListAdressInteractionTemplate.hpp:1091:25: error: 'bind2nd<std::divides<double>, double>' is deprecated: use 'std::bind' instead [-Werror,-Wdeprecated-declarations]
                   std::bind2nd(std::divides<real>(), Volume));
                        ^
/usr/bin/../lib/gcc/x86_64-redhat-linux/12/../../../../include/c++/12/backward/binders.h:170:5: note: 'bind2nd<std::divides<double>, double>' has been explicitly marked deprecated here
    _GLIBCXX11_DEPRECATED_SUGGEST("std::bind")
    ^

[XzzX]

#428

[XzzX]

Next round:
https://github.com/espressopp/espressopp/runs/6274009088?check_suite_focus=true

h5py was built without MPI support, can't use mpio driver

@junghans Did you change anything about the h5py installation? This is an old test from the previous H5MD interface. It explicitly selects mpio.

[junghans]

I saw that, I was hoping espressopp/buildenv#62 would fix that...but apparently not.

I will look into this later this week.

[junghans]

In the ubuntu container:

$ ipython3
import pyh5md
pyh5md.File('file.txt', "w",driver='mpio')

ValueError: h5py was built without MPI support, can't use mpio driver

[junghans]

I think the problem is in usr/lib/python3/dist-packages/h5py/__init__.py:

_OPENMPI_MULTIPROC = os_getenv('OMPI_COMM_WORLD_SIZE') is not None
_MPICH_MULTIPROC = os_getenv('MPI_LOCALNRANKS') is not None
_MPI_USE_ALWAYS = os_getenv('H5PY_ALWAYS_USE_MPI') is not None

_MPI_ACTIVE = _OPENMPI_MULTIPROC or _MPICH_MULTIPROC or _MPI_USE_ALWAYS

if _MPI_ACTIVE:
    try:
        from . import _debian_h5py_mpi as _h5py
    except:
        from . import _debian_h5py_serial as _h5py
else:
    from . import _debian_h5py_serial as _h5py

I guess we have to set H5PY_ALWAYS_USE_MPI.

[junghans]

espressopp/buildenv@9687442

[junghans]

I made some progress: https://github.com/espressopp/espressopp/actions/runs/2267132297

ubuntu_devel is broken due to some rebuild they currently do.....
see: https://github.com/espressopp/buildenv/runs/6281675179?check_suite_focus=true