Fix HDF5 OSX intermediate group creation errors #1741

dweindl · 2022-03-25T09:07:06Z

Still not sure what the original problem was, but going through the HDF5 C++ API seems to fix the following error occurring in amici::hdf5::hdf5CreateGroup with recent HDF5 versions on OSX:

>       return _amici.writeSolverSettingsToHDF5(*args)
E       RuntimeError: Failed to create group in hdf5CreateGroup: ssettings

../sdist/amici/amici.py:6129: RuntimeError
----------------------------- Captured stderr call -----------------------------
HDF5-DIAG: Error detected in HDF5 (1.10.8) thread 0:
  #000: H5Plcpl.c line 152 in H5Pset_create_intermediate_group(): can't find object for ID
    major: Object atom
    minor: Unable to find atom information (already closed?)
  #001: H5Pint.c line 3805 in H5P_object_verify(): property list is not a member of the class
    major: Property lists
    minor: Unable to register new atom
  #002: H5Pint.c line 3756 in H5P_isa_class(): not a property list
    major: Invalid arguments to routine
    minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.10.8) thread 0:
  #000: H5G.c line 288 in H5Gcreate2(): not link creation property list
    major: Invalid arguments to routine
    minor: Inappropriate type
  #001: H5Pint.c line 3756 in H5P_isa_class(): not a property list
    major: Invalid arguments to routine
    minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.10.8) thread 0:
  #000: H5P.c line 1488 in H5Pclose(): not a property list
    major: Invalid arguments to routine
    minor: Inappropriate type

H5::LinkCreatPropList::setCreateIntermediateGroup was only added in HDF5 1.10.6, but current Ubuntu LTS still comes with HDF5 1.10.4. Therefore we still need to keep the C version.

codecov · 2022-03-25T09:20:56Z

Codecov Report

Merging #1741 (177e804) into develop (9b13330) will increase coverage by 1.13%.
The diff coverage is n/a.

@@             Coverage Diff             @@
##           develop    #1741      +/-   ##
===========================================
+ Coverage    77.87%   79.01%   +1.13%     
===========================================
  Files           73       73              
  Lines        11364    11364              
===========================================
+ Hits          8850     8979     +129     
+ Misses        2514     2385     -129

Flag	Coverage Δ
cpp	`74.80% <ø> (+0.04%)`	⬆️
petab	`62.51% <ø> (ø)`
python	`71.32% <ø> (+3.11%)`	⬆️

Flags with carried forward coverage won't be shown. Click here to find out more.

Impacted Files	Coverage Δ
src/hdf5.cpp	`90.51% <ø> (ø)`
src/solver_cvodes.cpp	`69.53% <0.00%> (+0.18%)`	⬆️
src/exception.cpp	`80.64% <0.00%> (+6.45%)`	⬆️
python/amici/conserved_moieties.py	`90.41% <0.00%> (+24.65%)`	⬆️