Comment 2 for bug 1013466

Actually, it's not exactly the same problem. In question #199888, I was having a problem with EPD using dolfin from the Ubuntu repositories. Now, I compiled and installed all the fenics components in ~/.local and a similar problem is occuring.

This was how your machine solves the problem:
"For me, the H5Pset_dxpl_mpio symbol is defined in /usr/lib/libhdf5.so.6 and /usr/lib/libpetsc.so.3.1 is dynamically linked to it."

If I am required to make a link to solve the problem, then I would have thought it was a bug.

In addition, I completely removed EPD from my PATH environment variable, and with python and fenics from the Ubuntu repository, I get the following error:

In [1]: run d1_p2D.py
Reading DOLFIN parameters from file "dolfin_parameters.xml".
In instant.import_module_directly: Failed to import module 'fceecf1bb9e182af7207a4b16af02614b9d688fb' from '/home/chad/.instant/cache';
ImportError:/home/chad/.instant/cache/fceecf1bb9e182af7207a4b16af02614b9d688fb/_fceecf1bb9e182af7207a4b16af02614b9d688fb.so: undefined symbol: PyUnicodeUCS2_Decode;
Failed to import module found in cache. Modulename: 'fceecf1bb9e182af7207a4b16af02614b9d688fb';
Path: '/home/chad/.instant/cache';
ImportError:/home/chad/.instant/cache/fceecf1bb9e182af7207a4b16af02614b9d688fb/_fceecf1bb9e182af7207a4b16af02614b9d688fb.so: undefined symbol: PyUnicodeUCS2_Decode;
---------------------------------------------------------------------------
AssertionError Traceback (most recent call last)
/usr/lib/python2.7/dist-packages/IPython/utils/py3compat.pyc in execfile(fname, *where)
    173 else:
    174 filename = fname
--> 175 __builtin__.execfile(filename, *where)

/home/chad/Documents/dolfin-examples-1.0/stationary/poisson/d1_p2D.py in <module>()
     13 mesh = UnitSquare(6, 4)
     14 #mesh = UnitCube(6, 4, 5)

---> 15 V = FunctionSpace(mesh, 'Lagrange', 1)
     16
     17 # Define boundary conditions

/home/chad/.local/lib/python2.7/site-packages/dolfin/functions/functionspace.pyc in __init__(self, mesh, family, degree, form_degree, restriction)
    351
    352 # Initialize base class

--> 353 FunctionSpaceBase.__init__(self, mesh, element)
    354
    355 self.___degree = degree

/home/chad/.local/lib/python2.7/site-packages/dolfin/functions/functionspace.pyc in __init__(self, mesh, element)
     75
     76 # JIT-compile element to get ufc_element and ufc_dofmap

---> 77 ufc_element, ufc_dofmap = jit(self._ufl_element)
     78
     79 # Instantiate DOLFIN FiniteElement and DofMap

/home/chad/.local/lib/python2.7/site-packages/dolfin/compilemodules/jit.pyc in mpi_jit(*args, **kwargs)
     64 # Just call JIT compiler when running in serial

     65 if MPI.num_processes() == 1:
---> 66 return local_jit(*args, **kwargs)
     67
     68 # Compile first on process 0

/home/chad/.local/lib/python2.7/site-packages/dolfin/compilemodules/jit.pyc in jit(form, form_compiler_parameters, common_cell)
    152 raise RuntimeError, "Form compiler must implement the jit function."
    153
--> 154 return jit_compile(form, parameters=p, common_cell=common_cell)

/home/chad/.local/lib/python2.7/site-packages/ffc/jitcompiler.pyc in jit(ufl_object, parameters, common_cell)
     69 # Check if we get an element or a form

     70 if isinstance(ufl_object, FiniteElementBase):
---> 71 return jit_element(ufl_object, parameters)
     72 else:
     73 return jit_form(ufl_object, parameters, common_cell)

/home/chad/.local/lib/python2.7/site-packages/ffc/jitcompiler.pyc in jit_element(element, parameters)
    176
    177 # Compile form

--> 178 compiled_form, module, form_data, prefix = jit_form(form, parameters)
    179
    180 return _extract_element_and_dofmap(module, prefix, form_data)

/home/chad/.local/lib/python2.7/site-packages/ffc/jitcompiler.pyc in jit_form(form, parameters, common_cell)
    100 cache_dir = parameters["cache_dir"]
    101 if cache_dir == "": cache_dir = None
--> 102 module = instant.import_module(jit_object, cache_dir=cache_dir)
    103 if module:
    104

/home/chad/.local/lib/python2.7/site-packages/instant/cache.pyc in import_module(moduleid, cache_dir)
    154 # Look for module in disk cache

    155 modulename = moduleids[-1]
--> 156 return check_disk_cache(modulename, cache_dir, moduleids)
    157
    158

/home/chad/.local/lib/python2.7/site-packages/instant/cache.pyc in check_disk_cache(modulename, cache_dir, moduleids)
    120 if os.path.isdir(os.path.join(path, modulename)):
    121 # Found existing directory, try to import and place in memory cache

--> 122 module = import_and_cache_module(path, modulename, moduleids)
    123 if module:
    124 instant_debug("In instant.check_disk_cache: Imported module "\

/home/chad/.local/lib/python2.7/site-packages/instant/cache.pyc in import_and_cache_module(path, modulename, moduleids)
     66 def import_and_cache_module(path, modulename, moduleids):
     67 module, e = import_module_directly(path, modulename)
---> 68 instant_assert(module is not None, "Failed to import module found in cache. Modulename: '%s';\nPath: '%s';\n%s:%s;" % (modulename, path, type(e).__name__, e))
     69 for moduleid in moduleids:
     70 place_module_in_memory_cache(moduleid, module)

/home/chad/.local/lib/python2.7/site-packages/instant/output.pyc in instant_assert(condition, *message)
     53 _log.error(*message)
     54 text = message[0] % message[1:]
---> 55 raise AssertionError(text)
     56
     57 # Utility functions for file handling:

AssertionError: Failed to import module found in cache. Modulename: 'fceecf1bb9e182af7207a4b16af02614b9d688fb';
Path: '/home/chad/.instant/cache';
ImportError:/home/chad/.instant/cache/fceecf1bb9e182af7207a4b16af02614b9d688fb/_fceecf1bb9e182af7207a4b16af02614b9d688fb.so: undefined symbol: PyUnicodeUCS2_Decode;

In [2]: