fatal error: hdf5.h: No such file or directory

[sliptonic]

I just rebased my development branch off master and tried to rebuild.

This is based on master commit: b503d55299483f6c7cf36856cea31bdfe79a4b58
from 11/27/2016

I'm getting this error:
MED_Common.hxx:32:18: fatal error: hdf5.h: No such file or directory

[wmayer]

At which point in the build process do you get the failure?

[sliptonic]

At which point in the build process do you get the failure?

About 2%:

Code: Select all

[  2%] Building CXX object src/3rdParty/salomesmesh/CMakeFiles/SMESH.dir/src/SMESH/SMESH_ProxyMesh.cpp.o
In file included from /usr/lib/x86_64-linux-gnu/oce-0.17/../../../include/oce/TColStd_SequenceOfReal.hxx:112:0,
                 from /usr/lib/x86_64-linux-gnu/oce-0.17/../../../include/oce/TColStd_HSequenceOfReal.hxx:13,
                 from /home/brad/FreeCAD/src/3rdParty/salomesmesh/inc/SMESH_MeshEditor.hxx:41,
                 from /home/brad/FreeCAD/src/3rdParty/salomesmesh/inc/SMESH_MesherHelper.hxx:32,
                 from /home/brad/FreeCAD/src/3rdParty/salomesmesh/src/SMESH/SMESH_ProxyMesh.cpp:27:
/usr/lib/x86_64-linux-gnu/oce-0.17/../../../include/oce/TCollection_Sequence.lxx: In copy constructor ‘TColStd_SequenceOfReal::TColStd_SequenceOfReal(const TColStd_SequenceOfReal&)’:
/usr/lib/x86_64-linux-gnu/oce-0.17/../../../include/oce/TCollection_Sequence.lxx:31:8: warning: base class ‘class TCollection_BaseSequence’ should be explicitly initialized in the copy constructor [-Wextra]
 inline TCollection_Sequence::TCollection_Sequence(const TCollection_Sequence& theOther)
        ^
In file included from /home/brad/FreeCAD/src/3rdParty/salomesmesh/inc/SMESH_MesherHelper.hxx:32:0,
                 from /home/brad/FreeCAD/src/3rdParty/salomesmesh/src/SMESH/SMESH_ProxyMesh.cpp:27:
/home/brad/FreeCAD/src/3rdParty/salomesmesh/inc/SMESH_MeshEditor.hxx: At global scope:
/home/brad/FreeCAD/src/3rdParty/salomesmesh/inc/SMESH_MeshEditor.hxx:268:16: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   typedef std::auto_ptr< std::list<int> > PGroupIDs;
                ^
In file included from /usr/include/c++/5/memory:81:0,
                 from /usr/include/boost/config/no_tr1/memory.hpp:21,
                 from /usr/include/boost/smart_ptr/shared_ptr.hpp:23,
                 from /usr/include/boost/shared_ptr.hpp:17,
                 from /home/brad/FreeCAD/src/3rdParty/salomesmesh/inc/SMDS_ElemIterator.hxx:33,
                 from /home/brad/FreeCAD/src/3rdParty/salomesmesh/inc/SMDS_MeshElement.hxx:34,
                 from /home/brad/FreeCAD/src/3rdParty/salomesmesh/inc/SMESH_ProxyMesh.hxx:29,
                 from /home/brad/FreeCAD/src/3rdParty/salomesmesh/src/SMESH/SMESH_ProxyMesh.cpp:23:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from /usr/lib/x86_64-linux-gnu/oce-0.17/../../../include/oce/Extrema_SequenceOfPOnSurf.hxx:112:0,
                 from /usr/lib/x86_64-linux-gnu/oce-0.17/../../../include/oce/Extrema_FuncExtPS.hxx:17,
                 from /usr/lib/x86_64-linux-gnu/oce-0.17/../../../include/oce/Extrema_GenExtPS.hxx:19,
                 from /usr/lib/x86_64-linux-gnu/oce-0.17/../../../include/oce/Extrema_ExtPS.hxx:16,
                 from /usr/lib/x86_64-linux-gnu/oce-0.17/../../../include/oce/ShapeAnalysis_Surface.hxx:15,
                 from /home/brad/FreeCAD/src/3rdParty/salomesmesh/inc/SMESH_MesherHelper.hxx:37,
                 from /home/brad/FreeCAD/src/3rdParty/salomesmesh/src/SMESH/SMESH_ProxyMesh.cpp:27:
/usr/lib/x86_64-linux-gnu/oce-0.17/../../../include/oce/TCollection_Sequence.lxx: In copy constructor ‘Extrema_SequenceOfPOnSurf::Extrema_SequenceOfPOnSurf(const Extrema_SequenceOfPOnSurf&)’:
/usr/lib/x86_64-linux-gnu/oce-0.17/../../../include/oce/TCollection_Sequence.lxx:31:8: warning: base class ‘class TCollection_BaseSequence’ should be explicitly initialized in the copy constructor [-Wextra]
 inline TCollection_Sequence::TCollection_Sequence(const TCollection_Sequence& theOther)
        ^
[  2%] Building CXX object src/3rdParty/salomesmesh/CMakeFiles/SMESH.dir/src/SMESH/MED_Algorithm.cpp.o
In file included from /home/brad/FreeCAD/src/3rdParty/salomesmesh/inc/MED_Structures.hxx:26:0,
                 from /home/brad/FreeCAD/src/3rdParty/salomesmesh/inc/MED_Algorithm.hxx:26,
                 from /home/brad/FreeCAD/src/3rdParty/salomesmesh/src/SMESH/MED_Algorithm.cpp:22:
/home/brad/FreeCAD/src/3rdParty/salomesmesh/inc/MED_Common.hxx:32:18: fatal error: hdf5.h: No such file or directory
compilation terminated.

[wmayer]

I can't see that this is related to the recent changes since nothing in smesh has changed. Can you post the git hash of your last successful build, please?

[sliptonic]

It affects me building master itself as well. I seem to have some kind of perfect storm of problems stemming from a recent ubuntu update, and the OCC version detection changes. Python-vtk suddenly disappeared (now reinstalled) and I'm chasing one missing package after another.

Clearly on my side. I'll report back if I find a root cause.

[sliptonic]

I'm still getting the problem and have narrowed it down.

Commit: cf22852ee31921adfb0284622cbb5017ce0a9798 appears to build fine (I'm still building but well past the 2% failure point.)

Commit af62262021cc4ade42f232d86e8b96b553307691 fails

[wmayer]

Try adding vtkhdf5 to the list:

Code: Select all

list(APPEND VTK_COMPONENTS vtkIOMPIParallel vtkParallelMPI)

[sliptonic]

Yes! That worked. Thank you.