Dorsal

Trilinos doesn't compile on OS X

Bug #905211 reported by Harish Narayanan
6
This bug affects 1 person
Affects Status Importance Assigned to Milestone
Dorsal
Fix Committed
Low
Johannes Ring

Bug Description

When I try to compile (py)trilinos on Lion, I receive the following error. I am just pasting it here hoping someone who's gotten trilinos to work on OS X (Johannes) can help.

[ 94%] Generating swigpyrun.h
Scanning dependencies of target pytrilinos
[ 94%] [ 95%] [ 95%] [ 95%] Building CXX object packages/PyTrilinos/src/CMakeFiles/pytrilinos.dir/PyTrilinos_NumPyImporter.cpp.o
Building CXX object packages/PyTrilinos/src/CMakeFiles/pytrilinos.dir/PyTrilinos_Util.cpp.o
Building CXX object packages/PyTrilinos/src/CMakeFiles/pytrilinos.dir/PyTrilinos_PythonException.cpp.o
Building CXX object packages/PyTrilinos/src/CMakeFiles/pytrilinos.dir/PyTrilinos_FILEstream.cpp.o
[ 95%] Building CXX object packages/PyTrilinos/src/CMakeFiles/pytrilinos.dir/PyTrilinos_Teuchos_Util.cpp.o
[ 95%] Building CXX object packages/PyTrilinos/src/CMakeFiles/pytrilinos.dir/Epetra_NumPyFEVector.cpp.o
[ 95%] Building CXX object packages/PyTrilinos/src/CMakeFiles/pytrilinos.dir/Epetra_NumPyIntSerialDenseMatrix.cpp.o
[ 95%] Building CXX object packages/PyTrilinos/src/CMakeFiles/pytrilinos.dir/Epetra_NumPyIntSerialDenseVector.cpp.o
[ 95%] Building CXX object packages/PyTrilinos/src/CMakeFiles/pytrilinos.dir/Epetra_NumPyIntVector.cpp.o
[ 95%] Building CXX object packages/PyTrilinos/src/CMakeFiles/pytrilinos.dir/Epetra_NumPyMultiVector.cpp.o
[ 95%] Building CXX object packages/PyTrilinos/src/CMakeFiles/pytrilinos.dir/Epetra_NumPySerialDenseMatrix.cpp.o
[ 95%] Building CXX object packages/PyTrilinos/src/CMakeFiles/pytrilinos.dir/Epetra_NumPySerialSymDenseMatrix.cpp.o
[ 96%] Building CXX object packages/PyTrilinos/src/CMakeFiles/pytrilinos.dir/Epetra_NumPySerialDenseVector.cpp.o
[ 96%] Building CXX object packages/PyTrilinos/src/CMakeFiles/pytrilinos.dir/Epetra_NumPyVector.cpp.o
[ 96%] [ 96%] Building CXX object packages/PyTrilinos/src/CMakeFiles/pytrilinos.dir/PyTrilinos_EpetraExt_Util.cpp.o
Building CXX object packages/PyTrilinos/src/CMakeFiles/pytrilinos.dir/PyTrilinos_Epetra_Util.cpp.o
/Users/harish/Desktop/FEniCS/dev/src/trilinos-10.8.4-Source/packages/PyTrilinos/src/PyTrilinos_EpetraExt_Util.cpp:74:15: warning: result of comparison against a string literal is unspecified (use strncmp instead)
  if (typeStr == "exact")
              ^ ~~~~~~~
/Users/harish/Desktop/FEniCS/dev/src/trilinos-10.8.4-Source/packages/PyTrilinos/src/PyTrilinos_EpetraExt_Util.cpp:76:15: warning: result of comparison against a string literal is unspecified (use strncmp instead)
  if (typeStr == "approx_deriv")
              ^ ~~~~~~~~~~~~~~
/Users/harish/Desktop/FEniCS/dev/src/trilinos-10.8.4-Source/packages/PyTrilinos/src/PyTrilinos_EpetraExt_Util.cpp:78:15: warning: result of comparison against a string literal is unspecified (use strncmp instead)
  if (typeStr == "very_approx_deriv")
              ^ ~~~~~~~~~~~~~~~~~~~
/Users/harish/Desktop/FEniCS/dev/src/trilinos-10.8.4-Source/packages/PyTrilinos/src/PyTrilinos_EpetraExt_Util.cpp:113:15: warning: result of comparison against a string literal is unspecified (use strncmp instead)
  if (typeStr == "exact")
              ^ ~~~~~~~
/Users/harish/Desktop/FEniCS/dev/src/trilinos-10.8.4-Source/packages/PyTrilinos/src/PyTrilinos_EpetraExt_Util.cpp:115:15: warning: result of comparison against a string literal is unspecified (use strncmp instead)
  if (typeStr == "approx_deriv")
              ^ ~~~~~~~~~~~~~~
/Users/harish/Desktop/FEniCS/dev/src/trilinos-10.8.4-Source/packages/PyTrilinos/src/PyTrilinos_EpetraExt_Util.cpp:117:15: warning: result of comparison against a string literal is unspecified (use strncmp instead)
  if (typeStr == "very_approx_deriv")
              ^ ~~~~~~~~~~~~~~~~~~~
/Users/harish/Desktop/FEniCS/dev/src/trilinos-10.8.4-Source/packages/PyTrilinos/src/PyTrilinos_EpetraExt_Util.cpp:216:17: warning: result of comparison against a string literal is unspecified (use strncmp instead)
  if (linearity == "unknown")
                ^ ~~~~~~~~~
/Users/harish/Desktop/FEniCS/dev/src/trilinos-10.8.4-Source/packages/PyTrilinos/src/PyTrilinos_EpetraExt_Util.cpp:218:17: warning: result of comparison against a string literal is unspecified (use strncmp instead)
  if (linearity == "const")
                ^ ~~~~~~~
/Users/harish/Desktop/FEniCS/dev/src/trilinos-10.8.4-Source/packages/PyTrilinos/src/PyTrilinos_EpetraExt_Util.cpp:220:17: warning: result of comparison against a string literal is unspecified (use strncmp instead)
  if (linearity == "nonconst")
                ^ ~~~~~~~~~~
/Users/harish/Desktop/FEniCS/dev/src/trilinos-10.8.4-Source/packages/PyTrilinos/src/PyTrilinos_EpetraExt_Util.cpp:224:12: warning: result of comparison against a string literal is unspecified (use strncmp instead)
  if (rank == "unknown")
           ^ ~~~~~~~~~
/Users/harish/Desktop/FEniCS/dev/src/trilinos-10.8.4-Source/packages/PyTrilinos/src/PyTrilinos_EpetraExt_Util.cpp:226:12: warning: result of comparison against a string literal is unspecified (use strncmp instead)
  if (rank == "full")
           ^ ~~~~~~
/Users/harish/Desktop/FEniCS/dev/src/trilinos-10.8.4-Source/packages/PyTrilinos/src/PyTrilinos_EpetraExt_Util.cpp:228:12: warning: result of comparison against a string literal is unspecified (use strncmp instead)
  if (rank == "deficient")
           ^ ~~~~~~~~~~~
/Users/harish/Desktop/FEniCS/dev/src/trilinos-10.8.4-Source/packages/PyTrilinos/src/PyTrilinos_EpetraExt_Util.cpp:264:17: warning: result of comparison against a string literal is unspecified (use strncmp instead)
  if (linearity == "unknown")
                ^ ~~~~~~~~~
/Users/harish/Desktop/FEniCS/dev/src/trilinos-10.8.4-Source/packages/PyTrilinos/src/PyTrilinos_EpetraExt_Util.cpp:266:17: warning: result of comparison against a string literal is unspecified (use strncmp instead)
  if (linearity == "const")
                ^ ~~~~~~~
/Users/harish/Desktop/FEniCS/dev/src/trilinos-10.8.4-Source/packages/PyTrilinos/src/PyTrilinos_EpetraExt_Util.cpp:268:17: warning: result of comparison against a string literal is unspecified (use strncmp instead)
  if (linearity == "nonconst")
                ^ ~~~~~~~~~~
/Users/harish/Desktop/FEniCS/dev/src/trilinos-10.8.4-Source/packages/PyTrilinos/src/PyTrilinos_EpetraExt_Util.cpp:272:12: warning: result of comparison against a string literal is unspecified (use strncmp instead)
  if (rank == "unknown")
           ^ ~~~~~~~~~
/Users/harish/Desktop/FEniCS/dev/src/trilinos-10.8.4-Source/packages/PyTrilinos/src/PyTrilinos_EpetraExt_Util.cpp:274:12: warning: result of comparison against a string literal is unspecified (use strncmp instead)
  if (rank == "full")
           ^ ~~~~~~
/Users/harish/Desktop/FEniCS/dev/src/trilinos-10.8.4-Source/packages/PyTrilinos/src/PyTrilinos_EpetraExt_Util.cpp:276:12: warning: result of comparison against a string literal is unspecified (use strncmp instead)
  if (rank == "deficient")
           ^ ~~~~~~~~~~~
/Users/harish/Desktop/FEniCS/dev/src/trilinos-10.8.4-Source/packages/PyTrilinos/src/PyTrilinos_EpetraExt_Util.cpp:312:17: warning: result of comparison against a string literal is unspecified (use strncmp instead)
  if (linearity == "mv_by_col")
                ^ ~~~~~~~~~~~
/Users/harish/Desktop/FEniCS/dev/src/trilinos-10.8.4-Source/packages/PyTrilinos/src/PyTrilinos_EpetraExt_Util.cpp:314:17: warning: result of comparison against a string literal is unspecified (use strncmp instead)
  if (linearity == "trans_mv_by_row")
                ^ ~~~~~~~~~~~~~~~~~
20 warnings generated.
Linking CXX shared library libpytrilinos.dylib
Undefined symbols for architecture x86_64:
  "_PyImport_ImportModule", referenced from:
      PyTrilinos::NumPyImporter::NumPyImporter() in PyTrilinos_NumPyImporter.cpp.o
  "_PyExc_ImportError", referenced from:
      PyTrilinos::NumPyImporter::NumPyImporter() in PyTrilinos_NumPyImporter.cpp.o
  "_PyErr_SetString", referenced from:
      PyTrilinos::NumPyImporter::NumPyImporter() in PyTrilinos_NumPyImporter.cpp.o
      PyTrilinos::pyDictToNewParameterList(_object*, PyTrilinos::ResponseToIllegalParameters) in PyTrilinos_Teuchos_Util.cpp.o
      PyTrilinos::updatePyDictWithParameterList(_object*, Teuchos::ParameterList const&, PyTrilinos::ResponseToIllegalParameters) in PyTrilinos_Teuchos_Util.cpp.o
      PyTrilinos::updateParameterListWithPyDict(_object*, Teuchos::ParameterList&, PyTrilinos::ResponseToIllegalParameters) in PyTrilinos_Teuchos_Util.cpp.o
      PyTrilinos::getEpetraMapPtrFromEpetraBlockMap(Epetra_BlockMap const&) in PyTrilinos_Epetra_Util.cpp.o
  "_PyObject_GetAttrString", referenced from:
      PyTrilinos::NumPyImporter::NumPyImporter() in PyTrilinos_NumPyImporter.cpp.o
      PyTrilinos::getObjectFromModule(char*, char const*) in PyTrilinos_Util.cpp.o
      PyTrilinos::objectAttrIsNone(_object*, char const*) in PyTrilinos_Util.cpp.o
      PyTrilinos::objectAttrIsTrue(_object*, char const*) in PyTrilinos_Util.cpp.o
      PyTrilinos::getBoolObjectAttr(_object*, char const*) in PyTrilinos_Util.cpp.o
      PyTrilinos::getIntObjectAttr(_object*, char const*) in PyTrilinos_Util.cpp.o
      PyTrilinos::getFloatObjectAttr(_object*, char const*) in PyTrilinos_Util.cpp.o
      ...
  "_PyExc_AttributeError", referenced from:
      PyTrilinos::NumPyImporter::NumPyImporter() in PyTrilinos_NumPyImporter.cpp.o
  "_PyCObject_Type", referenced from:
      PyTrilinos::NumPyImporter::NumPyImporter() in PyTrilinos_NumPyImporter.cpp.o
  "_PyExc_RuntimeError", referenced from:
      PyTrilinos::NumPyImporter::NumPyImporter() in PyTrilinos_NumPyImporter.cpp.o
      PyTrilinos::PythonException::PythonException() in PyTrilinos_PythonException.cpp.o
      PyTrilinos::updatePyDictWithParameterList(_object*, Teuchos::ParameterList const&, PyTrilinos::ResponseToIllegalParameters) in PyTrilinos_Teuchos_Util.cpp.o
      PyTrilinos::updateParameterListWithPyDict(_object*, Teuchos::ParameterList&, PyTrilinos::ResponseToIllegalParameters) in PyTrilinos_Teuchos_Util.cpp.o
      PyTrilinos::Epetra_NumPyFEVector::Dot(Epetra_FEVector const&) const in Epetra_NumPyFEVector.cpp.o
      PyTrilinos::Epetra_NumPyFEVector::Norm1() const in Epetra_NumPyFEVector.cpp.o
      PyTrilinos::Epetra_NumPyFEVector::Norm2() const in Epetra_NumPyFEVector.cpp.o
      ...
  "_PyCObject_AsVoidPtr", referenced from:
      PyTrilinos::NumPyImporter::NumPyImporter() in PyTrilinos_NumPyImporter.cpp.o
  "_PyErr_Format", referenced from:
      PyTrilinos::NumPyImporter::NumPyImporter() in PyTrilinos_NumPyImporter.cpp.o
      PyTrilinos::getClassFromModule(char*, char const*) in PyTrilinos_Util.cpp.o
      PyTrilinos::getBoolObjectAttr(_object*, char const*) in PyTrilinos_Util.cpp.o
      PyTrilinos::getTupleObjectAttr(_object*, char const*) in PyTrilinos_Util.cpp.o
      PyTrilinos::updatePyDictWithParameterList(_object*, Teuchos::ParameterList const&, PyTrilinos::ResponseToIllegalParameters) in PyTrilinos_Teuchos_Util.cpp.o
      PyTrilinos::updateParameterListWithPyDict(_object*, Teuchos::ParameterList&, PyTrilinos::ResponseToIllegalParameters) in PyTrilinos_Teuchos_Util.cpp.o
      PyTrilinos::Epetra_NumPyFEVector::Dot(Epetra_FEVector const&) const in Epetra_NumPyFEVector.cpp.o
      ...
  "_PyErr_Print", referenced from:
      PyTrilinos::NumPyImporter::NumPyImporter() in PyTrilinos_NumPyImporter.cpp.o
      PyTrilinos::convertInArgsToPython(EpetraExt::ModelEvaluator::InArgs const&) in PyTrilinos_EpetraExt_Util.cpp.o
  "_PyErr_Fetch", referenced from:
      PyTrilinos::PythonException::PythonException() in PyTrilinos_PythonException.cpp.o
  "_PyObject_Str", referenced from:
      PyTrilinos::PythonException::PythonException() in PyTrilinos_PythonException.cpp.o
  "_PyString_AsString", referenced from:
      PyTrilinos::PythonException::PythonException() in PyTrilinos_PythonException.cpp.o
      PyTrilinos::getStringObjectAttr(_object*, char const*) in PyTrilinos_Util.cpp.o
      PyTrilinos::getStringItemObjectAttr(_object*, char const*, int) in PyTrilinos_Util.cpp.o
      PyTrilinos::setPythonParameter(Teuchos::ParameterList&, std::string const&, _object*) in PyTrilinos_Teuchos_Util.cpp.o
      PyTrilinos::isEquivalent(_object*, Teuchos::ParameterList const&) in PyTrilinos_Teuchos_Util.cpp.o
      PyTrilinos::updateParameterListWithPyDict(_object*, Teuchos::ParameterList&, PyTrilinos::ResponseToIllegalParameters) in PyTrilinos_Teuchos_Util.cpp.o
      _SwigPyObject_print in PyTrilinos_Teuchos_Util.cpp.o
      ...
  "_PyString_FromString", referenced from:
      PyTrilinos::PythonException::PythonException() in PyTrilinos_PythonException.cpp.o
      PyTrilinos::setPythonParameter(Teuchos::ParameterList&, std::string const&, _object*) in PyTrilinos_Teuchos_Util.cpp.o
      PyTrilinos::getPythonParameter(Teuchos::ParameterList const&, std::string const&) in PyTrilinos_Teuchos_Util.cpp.o
      _SwigPyObject_str in PyTrilinos_Teuchos_Util.cpp.o
      _SwigPyObject_format in PyTrilinos_Teuchos_Util.cpp.o
      _SWIG_Python_NewPointerObj in PyTrilinos_Epetra_Util.cpp.o
      _SWIG_Python_ConvertPtrAndOwn in PyTrilinos_Epetra_Util.cpp.o
      ...
  "_PyErr_Restore", referenced from:
      PyTrilinos::PythonException::restore() in PyTrilinos_PythonException.cpp.o
  "_Py_BuildValue", referenced from:
      PyTrilinos::getObjectFromModule(char*, char const*) in PyTrilinos_Util.cpp.o
      PyTrilinos::getPythonParameter(Teuchos::ParameterList const&, std::string const&) in PyTrilinos_Teuchos_Util.cpp.o
      PyTrilinos::updatePyDictWithParameterList(_object*, Teuchos::ParameterList const&, PyTrilinos::ResponseToIllegalParameters) in PyTrilinos_Teuchos_Util.cpp.o
      PyTrilinos::Epetra_NumPyMultiVector::getArray(_object*) in Epetra_NumPyMultiVector.cpp.o
  "_PyImport_ImportModuleLevel", referenced from:
      PyTrilinos::getObjectFromModule(char*, char const*) in PyTrilinos_Util.cpp.o
  "_PyExc_TypeError", referenced from:
      PyTrilinos::getClassFromModule(char*, char const*) in PyTrilinos_Util.cpp.o
      PyTrilinos::getBoolObjectAttr(_object*, char const*) in PyTrilinos_Util.cpp.o
      PyTrilinos::getTupleObjectAttr(_object*, char const*) in PyTrilinos_Util.cpp.o
      PyTrilinos::updatePyDictWithParameterList(_object*, Teuchos::ParameterList const&, PyTrilinos::ResponseToIllegalParameters) in PyTrilinos_Teuchos_Util.cpp.o
      PyTrilinos::updateParameterListWithPyDict(_object*, Teuchos::ParameterList&, PyTrilinos::ResponseToIllegalParameters) in PyTrilinos_Teuchos_Util.cpp.o
      PyTrilinos::getEpetraMapPtrFromEpetraBlockMap(Epetra_BlockMap const&) in PyTrilinos_Epetra_Util.cpp.o
      PyTrilinos::getEpetraVectorObjectAttr(_object*, char const*) in PyTrilinos_Epetra_Util.cpp.o
      ...
  "__Py_NoneStruct", referenced from:
      PyTrilinos::objectAttrIsNone(_object*, char const*) in PyTrilinos_Util.cpp.o
      PyTrilinos::setPythonParameter(Teuchos::ParameterList&, std::string const&, _object*) in PyTrilinos_Teuchos_Util.cpp.o
      PyTrilinos::getPythonParameter(Teuchos::ParameterList const&, std::string const&) in PyTrilinos_Teuchos_Util.cpp.o
      _SwigPyObject_disown in PyTrilinos_Teuchos_Util.cpp.o
      _SwigPyObject_acquire in PyTrilinos_Teuchos_Util.cpp.o
      _SwigPyObject_own in PyTrilinos_Teuchos_Util.cpp.o
      _SwigPyObject_append in PyTrilinos_Teuchos_Util.cpp.o
      ...
  "__Py_TrueStruct", referenced from:
      PyTrilinos::objectAttrIsTrue(_object*, char const*) in PyTrilinos_Util.cpp.o
      PyTrilinos::getBoolObjectAttr(_object*, char const*) in PyTrilinos_Util.cpp.o
      PyTrilinos::setPythonParameter(Teuchos::ParameterList&, std::string const&, _object*) in PyTrilinos_Teuchos_Util.cpp.o
      PyTrilinos::Epetra_NumPyFEVector::getArray(Epetra_BlockMap const&, _object*) in Epetra_NumPyFEVector.cpp.o
      PyTrilinos::Epetra_NumPyVector::getArray(Epetra_BlockMap const&, _object*) in Epetra_NumPyVector.cpp.o
      PyTrilinos::convertDerivativePropertiesToPython(EpetraExt::ModelEvaluator::DerivativeProperties const&) in PyTrilinos_EpetraExt_Util.cpp.o
  "_PyBool_Type", referenced from:
      PyTrilinos::getBoolObjectAttr(_object*, char const*) in PyTrilinos_Util.cpp.o
      PyTrilinos::setPythonParameter(Teuchos::ParameterList&, std::string const&, _object*) in PyTrilinos_Teuchos_Util.cpp.o
      PyTrilinos::Epetra_NumPyFEVector::getArray(Epetra_BlockMap const&, _object*) in Epetra_NumPyFEVector.cpp.o
      PyTrilinos::Epetra_NumPyIntVector::getArray(Epetra_BlockMap const&, _object*) in Epetra_NumPyIntVector.cpp.o
      PyTrilinos::Epetra_NumPySerialDenseMatrix::getArray(_object*, int) in Epetra_NumPySerialDenseMatrix.cpp.o
      PyTrilinos::Epetra_NumPyVector::getArray(Epetra_BlockMap const&, _object*) in Epetra_NumPyVector.cpp.o
  "_PyInt_AsLong", referenced from:
      PyTrilinos::getIntObjectAttr(_object*, char const*) in PyTrilinos_Util.cpp.o
      PyTrilinos::setPythonParameter(Teuchos::ParameterList&, std::string const&, _object*) in PyTrilinos_Teuchos_Util.cpp.o
      PyTrilinos::Epetra_NumPyIntSerialDenseVector::getArray(_object*) in Epetra_NumPyIntSerialDenseVector.cpp.o
      PyTrilinos::Epetra_NumPyMultiVector::getArray(Epetra_BlockMap const&, _object*) in Epetra_NumPyMultiVector.cpp.o
      PyTrilinos::Epetra_NumPySerialDenseMatrix::getArray(_object*, int) in Epetra_NumPySerialDenseMatrix.cpp.o
      PyTrilinos::Epetra_NumPySerialSymDenseMatrix::getArray(_object*) in Epetra_NumPySerialSymDenseMatrix.cpp.o
      PyTrilinos::Epetra_NumPySerialDenseVector::getArray(_object*) in Epetra_NumPySerialDenseVector.cpp.o
      ...
  "_PyErr_Occurred", referenced from:
      PyTrilinos::getIntObjectAttr(_object*, char const*) in PyTrilinos_Util.cpp.o
      PyTrilinos::getFloatObjectAttr(_object*, char const*) in PyTrilinos_Util.cpp.o
      PyTrilinos::getStringObjectAttr(_object*, char const*) in PyTrilinos_Util.cpp.o
      PyTrilinos::getStringItemObjectAttr(_object*, char const*, int) in PyTrilinos_Util.cpp.o
      PyTrilinos::setPythonParameter(Teuchos::ParameterList&, std::string const&, _object*) in PyTrilinos_Teuchos_Util.cpp.o
      __ZL14SWIG_TypeQueryPKc in PyTrilinos_Teuchos_Util.cpp.o
      __ZL14SWIG_TypeQueryPKc in PyTrilinos_Epetra_Util.cpp.o
      ...
  "_PyFloat_AsDouble", referenced from:
      PyTrilinos::getFloatObjectAttr(_object*, char const*) in PyTrilinos_Util.cpp.o
      PyTrilinos::setPythonParameter(Teuchos::ParameterList&, std::string const&, _object*) in PyTrilinos_Teuchos_Util.cpp.o
  "_PyTuple_GetItem", referenced from:
      PyTrilinos::getStringItemObjectAttr(_object*, char const*, int) in PyTrilinos_Util.cpp.o
      PyTrilinos::getConstEpetraVectorItemObjectAttr(_object*, char const*, int) in PyTrilinos_Epetra_Util.cpp.o
      PyTrilinos::getEvaluationItemObjectAttr(_object*, char const*, int) in PyTrilinos_EpetraExt_Util.cpp.o
      PyTrilinos::getDerivativeSupportItemObjectAttr(_object*, char const*, int) in PyTrilinos_EpetraExt_Util.cpp.o
      PyTrilinos::getDerivativePropertiesItemObjectAttr(_object*, char const*, int) in PyTrilinos_EpetraExt_Util.cpp.o
      PyTrilinos::getDerivativeItemObjectAttr(_object*, char const*, int) in PyTrilinos_EpetraExt_Util.cpp.o
  "_PyFloat_Type", referenced from:
      PyTrilinos::setPythonParameter(Teuchos::ParameterList&, std::string const&, _object*) in PyTrilinos_Teuchos_Util.cpp.o
  "_PyType_IsSubtype", referenced from:
      PyTrilinos::setPythonParameter(Teuchos::ParameterList&, std::string const&, _object*) in PyTrilinos_Teuchos_Util.cpp.o
  "_PyType_Ready", referenced from:
      PyTrilinos::setPythonParameter(Teuchos::ParameterList&, std::string const&, _object*) in PyTrilinos_Teuchos_Util.cpp.o
      PyTrilinos::getPythonParameter(Teuchos::ParameterList const&, std::string const&) in PyTrilinos_Teuchos_Util.cpp.o
      _SwigPyObject_dealloc in PyTrilinos_Teuchos_Util.cpp.o
      _SwigPyObject_append in PyTrilinos_Teuchos_Util.cpp.o
      _SWIG_Python_NewPointerObj in PyTrilinos_Epetra_Util.cpp.o
      _SWIG_Python_ConvertPtrAndOwn in PyTrilinos_Epetra_Util.cpp.o
      _SwigPyObject_dealloc in PyTrilinos_Epetra_Util.cpp.o
      ...
  "_PyInstance_Type", referenced from:
      PyTrilinos::setPythonParameter(Teuchos::ParameterList&, std::string const&, _object*) in PyTrilinos_Teuchos_Util.cpp.o
      _SWIG_Python_ConvertPtrAndOwn in PyTrilinos_Epetra_Util.cpp.o
  "__PyInstance_Lookup", referenced from:
      PyTrilinos::setPythonParameter(Teuchos::ParameterList&, std::string const&, _object*) in PyTrilinos_Teuchos_Util.cpp.o
      _SWIG_Python_ConvertPtrAndOwn in PyTrilinos_Epetra_Util.cpp.o
  "__PyObject_GetDictPtr", referenced from:
      PyTrilinos::setPythonParameter(Teuchos::ParameterList&, std::string const&, _object*) in PyTrilinos_Teuchos_Util.cpp.o
      PyTrilinos::getPythonParameter(Teuchos::ParameterList const&, std::string const&) in PyTrilinos_Teuchos_Util.cpp.o
      _SWIG_Python_NewPointerObj in PyTrilinos_Epetra_Util.cpp.o
      _SWIG_Python_ConvertPtrAndOwn in PyTrilinos_Epetra_Util.cpp.o
  "_PyDict_GetItem", referenced from:
      PyTrilinos::setPythonParameter(Teuchos::ParameterList&, std::string const&, _object*) in PyTrilinos_Teuchos_Util.cpp.o
      _SWIG_Python_ConvertPtrAndOwn in PyTrilinos_Epetra_Util.cpp.o
  "__PyWeakref_ProxyType", referenced from:
      PyTrilinos::setPythonParameter(Teuchos::ParameterList&, std::string const&, _object*) in PyTrilinos_Teuchos_Util.cpp.o
      _SWIG_Python_ConvertPtrAndOwn in PyTrilinos_Epetra_Util.cpp.o
  "__PyWeakref_CallableProxyType", referenced from:
      PyTrilinos::setPythonParameter(Teuchos::ParameterList&, std::string const&, _object*) in PyTrilinos_Teuchos_Util.cpp.o
      _SWIG_Python_ConvertPtrAndOwn in PyTrilinos_Epetra_Util.cpp.o
  "_PyObject_GetAttr", referenced from:
      PyTrilinos::setPythonParameter(Teuchos::ParameterList&, std::string const&, _object*) in PyTrilinos_Teuchos_Util.cpp.o
      _SWIG_Python_ConvertPtrAndOwn in PyTrilinos_Epetra_Util.cpp.o
  "_PyErr_Clear", referenced from:
      PyTrilinos::setPythonParameter(Teuchos::ParameterList&, std::string const&, _object*) in PyTrilinos_Teuchos_Util.cpp.o
      __ZL14SWIG_TypeQueryPKc in PyTrilinos_Teuchos_Util.cpp.o
      __ZL14SWIG_TypeQueryPKc in PyTrilinos_Epetra_Util.cpp.o
      _SWIG_Python_ConvertPtrAndOwn in PyTrilinos_Epetra_Util.cpp.o
      EpetraExt::convertOutArgsFromPython(_object*) in PyTrilinos_EpetraExt_Util.cpp.o
  "_PyCapsule_Import", referenced from:
      __ZL14SWIG_TypeQueryPKc in PyTrilinos_Teuchos_Util.cpp.o
      __ZL14SWIG_TypeQueryPKc in PyTrilinos_Epetra_Util.cpp.o
  "_PyExc_ValueError", referenced from:
      PyTrilinos::pyDictToNewParameterList(_object*, PyTrilinos::ResponseToIllegalParameters) in PyTrilinos_Teuchos_Util.cpp.o
      PyTrilinos::updatePyDictWithParameterList(_object*, Teuchos::ParameterList const&, PyTrilinos::ResponseToIllegalParameters) in PyTrilinos_Teuchos_Util.cpp.o
      PyTrilinos::updateParameterListWithPyDict(_object*, Teuchos::ParameterList&, PyTrilinos::ResponseToIllegalParameters) in PyTrilinos_Teuchos_Util.cpp.o
      PyTrilinos::Epetra_NumPyFEVector::ReplaceGlobalValues(_object*, _object*) in Epetra_NumPyFEVector.cpp.o
      PyTrilinos::Epetra_NumPyFEVector::SumIntoGlobalValues(_object*, _object*) in Epetra_NumPyFEVector.cpp.o
      PyTrilinos::Epetra_NumPyIntSerialDenseMatrix::Shape(int, int) in Epetra_NumPyIntSerialDenseMatrix.cpp.o
      PyTrilinos::Epetra_NumPyIntSerialDenseMatrix::Reshape(int, int) in Epetra_NumPyIntSerialDenseMatrix.cpp.o
      ...
  "_PyBool_FromLong", referenced from:
      PyTrilinos::getPythonParameter(Teuchos::ParameterList const&, std::string const&) in PyTrilinos_Teuchos_Util.cpp.o
      _SwigPyObject_richcompare in PyTrilinos_Teuchos_Util.cpp.o
      _SwigPyObject_own in PyTrilinos_Teuchos_Util.cpp.o
      _SwigPyObject_richcompare in PyTrilinos_Epetra_Util.cpp.o
      _SwigPyObject_own in PyTrilinos_Epetra_Util.cpp.o
  "_PyInt_FromLong", referenced from:
      PyTrilinos::getPythonParameter(Teuchos::ParameterList const&, std::string const&) in PyTrilinos_Teuchos_Util.cpp.o
      PyTrilinos::convertArrayOfIntToPython(Teuchos::Array<int> const&) in PyTrilinos_EpetraExt_Util.cpp.o
  "_PyFloat_FromDouble", referenced from:
      PyTrilinos::getPythonParameter(Teuchos::ParameterList const&, std::string const&) in PyTrilinos_Teuchos_Util.cpp.o
      PyTrilinos::convertInArgsToPython(EpetraExt::ModelEvaluator::InArgs const&) in PyTrilinos_EpetraExt_Util.cpp.o
  "__PyObject_New", referenced from:
      PyTrilinos::getPythonParameter(Teuchos::ParameterList const&, std::string const&) in PyTrilinos_Teuchos_Util.cpp.o
      _SWIG_Python_NewPointerObj in PyTrilinos_Epetra_Util.cpp.o
  "_PyObject_Malloc", referenced from:
      PyTrilinos::getPythonParameter(Teuchos::ParameterList const&, std::string const&) in PyTrilinos_Teuchos_Util.cpp.o
      _SwigPyObject_dealloc in PyTrilinos_Teuchos_Util.cpp.o
      _SWIG_Python_NewPointerObj in PyTrilinos_Epetra_Util.cpp.o
      _SwigPyObject_dealloc in PyTrilinos_Epetra_Util.cpp.o
  "_PyObject_Init", referenced from:
      PyTrilinos::getPythonParameter(Teuchos::ParameterList const&, std::string const&) in PyTrilinos_Teuchos_Util.cpp.o
      _SwigPyObject_dealloc in PyTrilinos_Teuchos_Util.cpp.o
      _SWIG_Python_NewPointerObj in PyTrilinos_Epetra_Util.cpp.o
      _SwigPyObject_dealloc in PyTrilinos_Epetra_Util.cpp.o
  "_PyObject_Call", referenced from:
      PyTrilinos::getPythonParameter(Teuchos::ParameterList const&, std::string const&) in PyTrilinos_Teuchos_Util.cpp.o
      _SWIG_Python_NewPointerObj in PyTrilinos_Epetra_Util.cpp.o
  "_PyDict_New", referenced from:
      PyTrilinos::getPythonParameter(Teuchos::ParameterList const&, std::string const&) in PyTrilinos_Teuchos_Util.cpp.o
      PyTrilinos::updatePyDictWithParameterList(_object*, Teuchos::ParameterList const&, PyTrilinos::ResponseToIllegalParameters) in PyTrilinos_Teuchos_Util.cpp.o
      PyTrilinos::parameterListToNewPyDict(Teuchos::ParameterList const&, PyTrilinos::ResponseToIllegalParameters) in PyTrilinos_Teuchos_Util.cpp.o
      _SWIG_Python_NewPointerObj in PyTrilinos_Epetra_Util.cpp.o
  "_PyDict_SetItem", referenced from:
      PyTrilinos::getPythonParameter(Teuchos::ParameterList const&, std::string const&) in PyTrilinos_Teuchos_Util.cpp.o
      _SWIG_Python_NewPointerObj in PyTrilinos_Epetra_Util.cpp.o
  "_PyInstance_NewRaw", referenced from:
      PyTrilinos::getPythonParameter(Teuchos::ParameterList const&, std::string const&) in PyTrilinos_Teuchos_Util.cpp.o
      _SWIG_Python_NewPointerObj in PyTrilinos_Epetra_Util.cpp.o
  "_PyDict_Next", referenced from:
      PyTrilinos::isEquivalent(_object*, Teuchos::ParameterList const&) in PyTrilinos_Teuchos_Util.cpp.o
      PyTrilinos::updateParameterListWithPyDict(_object*, Teuchos::ParameterList&, PyTrilinos::ResponseToIllegalParameters) in PyTrilinos_Teuchos_Util.cpp.o
  "_PyDict_GetItemString", referenced from:
      PyTrilinos::isEquivalent(_object*, Teuchos::ParameterList const&) in PyTrilinos_Teuchos_Util.cpp.o
      PyTrilinos::updatePyDictWithParameterList(_object*, Teuchos::ParameterList const&, PyTrilinos::ResponseToIllegalParameters) in PyTrilinos_Teuchos_Util.cpp.o
  "_PyObject_RichCompareBool", referenced from:
      PyTrilinos::isEquivalent(_object*, Teuchos::ParameterList const&) in PyTrilinos_Teuchos_Util.cpp.o
  "_PyDict_SetItemString", referenced from:
      PyTrilinos::updatePyDictWithParameterList(_object*, Teuchos::ParameterList const&, PyTrilinos::ResponseToIllegalParameters) in PyTrilinos_Teuchos_Util.cpp.o
  "_PySequence_Concat", referenced from:
      PyTrilinos::updatePyDictWithParameterList(_object*, Teuchos::ParameterList const&, PyTrilinos::ResponseToIllegalParameters) in PyTrilinos_Teuchos_Util.cpp.o
  "_PyLong_FromVoidPtr", referenced from:
      _SwigPyObject_long in PyTrilinos_Teuchos_Util.cpp.o
      _SwigPyObject_format in PyTrilinos_Teuchos_Util.cpp.o
      _SwigPyObject_long in PyTrilinos_Epetra_Util.cpp.o
      _SwigPyObject_format in PyTrilinos_Epetra_Util.cpp.o
  "_PyObject_CallFunctionObjArgs", referenced from:
      _SwigPyObject_dealloc in PyTrilinos_Teuchos_Util.cpp.o
      _SwigPyObject_dealloc in PyTrilinos_Epetra_Util.cpp.o
  "_PyObject_Free", referenced from:
      _SwigPyObject_dealloc in PyTrilinos_Teuchos_Util.cpp.o
      _SwigPyObject_dealloc in PyTrilinos_Epetra_Util.cpp.o
  "_PyString_FromFormat", referenced from:
      _SwigPyObject_repr in PyTrilinos_Teuchos_Util.cpp.o
      _SwigPyObject_repr in PyTrilinos_Epetra_Util.cpp.o
  "_PyString_ConcatAndDel", referenced from:
      _SwigPyObject_repr in PyTrilinos_Teuchos_Util.cpp.o
      _SwigPyObject_repr in PyTrilinos_Epetra_Util.cpp.o
  "__Py_NotImplementedStruct", referenced from:
      _SwigPyObject_richcompare in PyTrilinos_Teuchos_Util.cpp.o
      _SwigPyObject_richcompare in PyTrilinos_Epetra_Util.cpp.o
  "_PyArg_UnpackTuple", referenced from:
      _SwigPyObject_own in PyTrilinos_Teuchos_Util.cpp.o
      _SwigPyObject_own in PyTrilinos_Epetra_Util.cpp.o
  "_PyObject_IsTrue", referenced from:
      _SwigPyObject_own in PyTrilinos_Teuchos_Util.cpp.o
      _SwigPyObject_own in PyTrilinos_Epetra_Util.cpp.o
  "_PyTuple_New", referenced from:
      _SwigPyObject_format in PyTrilinos_Teuchos_Util.cpp.o
      _SwigPyObject_format in PyTrilinos_Epetra_Util.cpp.o
      PyTrilinos::convertInArgsToPython(EpetraExt::ModelEvaluator::InArgs const&) in PyTrilinos_EpetraExt_Util.cpp.o
      PyTrilinos::convertArrayOfIntToPython(Teuchos::Array<int> const&) in PyTrilinos_EpetraExt_Util.cpp.o
      PyTrilinos::convertOutArgsToPython(EpetraExt::ModelEvaluator::OutArgs const&) in PyTrilinos_EpetraExt_Util.cpp.o
  "_PyTuple_SetItem", referenced from:
      _SwigPyObject_format in PyTrilinos_Teuchos_Util.cpp.o
      _SwigPyObject_format in PyTrilinos_Epetra_Util.cpp.o
      PyTrilinos::convertInArgsToPython(EpetraExt::ModelEvaluator::InArgs const&) in PyTrilinos_EpetraExt_Util.cpp.o
      PyTrilinos::convertArrayOfIntToPython(Teuchos::Array<int> const&) in PyTrilinos_EpetraExt_Util.cpp.o
      PyTrilinos::convertOutArgsToPython(EpetraExt::ModelEvaluator::OutArgs const&) in PyTrilinos_EpetraExt_Util.cpp.o
  "_PyString_Format", referenced from:
      _SwigPyObject_format in PyTrilinos_Teuchos_Util.cpp.o
      _SwigPyObject_format in PyTrilinos_Epetra_Util.cpp.o
  "_PyObject_GenericGetAttr", referenced from:
      _tmp in PyTrilinos_Teuchos_Util.cpp.o
      _tmp in PyTrilinos_Epetra_Util.cpp.o
  "_PyObject_IsInstance", referenced from:
      PyTrilinos::getEvaluationObjectAttr(_object*, char const*) in PyTrilinos_EpetraExt_Util.cpp.o
      PyTrilinos::getEvaluationItemObjectAttr(_object*, char const*, int) in PyTrilinos_EpetraExt_Util.cpp.o
      PyTrilinos::getDerivativeSupportObjectAttr(_object*, char const*) in PyTrilinos_EpetraExt_Util.cpp.o
      PyTrilinos::getDerivativeSupportItemObjectAttr(_object*, char const*, int) in PyTrilinos_EpetraExt_Util.cpp.o
      PyTrilinos::getDerivativePropertiesObjectAttr(_object*, char const*) in PyTrilinos_EpetraExt_Util.cpp.o
      PyTrilinos::getDerivativePropertiesItemObjectAttr(_object*, char const*, int) in PyTrilinos_EpetraExt_Util.cpp.o
      PyTrilinos::getDerivativeMultiVectorObjectAttr(_object*, char const*) in PyTrilinos_EpetraExt_Util.cpp.o
      ...
  "_PySequence_Size", referenced from:
      PyTrilinos::getDerivativeMultiVectorObjectAttr(_object*, char const*) in PyTrilinos_EpetraExt_Util.cpp.o
      EpetraExt::convertInArgsFromPython(_object*) in PyTrilinos_EpetraExt_Util.cpp.o
      EpetraExt::convertOutArgsFromPython(_object*) in PyTrilinos_EpetraExt_Util.cpp.o
  "_PySequence_GetItem", referenced from:
      PyTrilinos::getDerivativeMultiVectorObjectAttr(_object*, char const*) in PyTrilinos_EpetraExt_Util.cpp.o
  "_PyObject_CallObject", referenced from:
      PyTrilinos::convertInArgsToPython(EpetraExt::ModelEvaluator::InArgs const&) in PyTrilinos_EpetraExt_Util.cpp.o
      PyTrilinos::convertEvaluationToPython(EpetraExt::ModelEvaluator::Evaluation<Epetra_Vector>) in PyTrilinos_EpetraExt_Util.cpp.o
      PyTrilinos::convertDerivativePropertiesToPython(EpetraExt::ModelEvaluator::DerivativeProperties const&) in PyTrilinos_EpetraExt_Util.cpp.o
      PyTrilinos::convertDerivativeMultiVectorToPython(EpetraExt::ModelEvaluator::DerivativeMultiVector const&) in PyTrilinos_EpetraExt_Util.cpp.o
      PyTrilinos::convertArrayOfIntToPython(Teuchos::Array<int> const&) in PyTrilinos_EpetraExt_Util.cpp.o
      PyTrilinos::convertDerivativeToPython(EpetraExt::ModelEvaluator::Derivative const&) in PyTrilinos_EpetraExt_Util.cpp.o
      PyTrilinos::convertOutArgsToPython(EpetraExt::ModelEvaluator::OutArgs const&) in PyTrilinos_EpetraExt_Util.cpp.o
      ...
  "_PyObject_SetAttrString", referenced from:
      PyTrilinos::convertInArgsToPython(EpetraExt::ModelEvaluator::InArgs const&) in PyTrilinos_EpetraExt_Util.cpp.o
      PyTrilinos::convertEvaluationToPython(EpetraExt::ModelEvaluator::Evaluation<Epetra_Vector>) in PyTrilinos_EpetraExt_Util.cpp.o
      PyTrilinos::convertDerivativePropertiesToPython(EpetraExt::ModelEvaluator::DerivativeProperties const&) in PyTrilinos_EpetraExt_Util.cpp.o
      PyTrilinos::convertDerivativeMultiVectorToPython(EpetraExt::ModelEvaluator::DerivativeMultiVector const&) in PyTrilinos_EpetraExt_Util.cpp.o
      PyTrilinos::convertDerivativeToPython(EpetraExt::ModelEvaluator::Derivative const&) in PyTrilinos_EpetraExt_Util.cpp.o
      PyTrilinos::convertOutArgsToPython(EpetraExt::ModelEvaluator::OutArgs const&) in PyTrilinos_EpetraExt_Util.cpp.o
  "__Py_ZeroStruct", referenced from:
      PyTrilinos::convertDerivativePropertiesToPython(EpetraExt::ModelEvaluator::DerivativeProperties const&) in PyTrilinos_EpetraExt_Util.cpp.o
ld: symbol(s) not found for architecture x86_64
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make[2]: *** [packages/PyTrilinos/src/libpytrilinos.dylib] Error 1
make[1]: *** [packages/PyTrilinos/src/CMakeFiles/pytrilinos.dir/all] Error 2
make: *** [all] Error 2
Failure with exit status: 2
Exit message: There was a problem building trilinos-10.8.4-Source.

Related branches

lp:~fenics-core/dorsal/main
Revision history for this message
Johannes Ring (johannr) wrote :

I don't know, I didn't have to do anything special to build Trilinos on Lion.

I can look into it again when the new Mac buildbot is in place.

Revision history for this message
Johannes Ring (johannr) wrote :

I ran into the same problem on the new Mac buildbot, but I fixed it by linking PyTrilinos with the Python library.

Changed in dorsal:
status: New → Confirmed
assignee: nobody → Johannes Ring (johannr)
importance: Undecided → Low
status: Confirmed → Fix Committed
matse (m-anselmann)
Changed in dorsal:
status: Fix Committed → Fix Released
Johannes Ring (johannr)
Changed in dorsal:
status: Fix Released → Fix Committed
Revision history for this message
Jack Hale (jack-hale) wrote :

Hi Johannes,

Here are a few things that I had trouble with compiling on Mountain Lion with dorsal and macports.

1) Making sure linking is against the python framework installed by MacPorts. It is necessary to use pass the PYTHON_LIBRARY to option, otherwise it will link against the system python and the module will crash on import.
2) Enabling HDF5 and having HDF5 from macports breaks. I had to disable HDF5 in Dolfin.
3) DYLD_LIBRARY_PATH is not set in fenics.conf only LD_LIBRARY_PATH which doesn't work on Mac.

Otherwise everything seems to work, MPI, OpenMP, Trilinos and PyTrilinos, PETSc and SLEPc are all in there.

Revision history for this message
Jack Hale (jack-hale) wrote :

So here are the changes I made to get it to work in the attachment.

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