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/.local/lib/python2.7/site-packages/dolfin/functions/functionspace.pyc in __init__(self, mesh, family, degree, form_degree, restriction)
351
352 # Initialize base class
/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
/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
/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
/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;
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: libhdf5. so.6 and /usr/lib/ libpetsc. so.3.1 is dynamically linked to it."
"For me, the H5Pset_dxpl_mpio symbol is defined in /usr/lib/
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 parameters. xml". import_ module_ directly: Failed to import module 'fceecf1bb9e182 af7207a4b16af02 614b9d688fb' from '/home/ chad/.instant/ cache'; /home/chad/ .instant/ cache/fceecf1bb 9e182af7207a4b1 6af02614b9d688f b/_fceecf1bb9e1 82af7207a4b16af 02614b9d688fb. so: undefined symbol: PyUnicodeUCS2_ Decode; af7207a4b16af02 614b9d688fb' ; chad/.instant/ cache'; /home/chad/ .instant/ cache/fceecf1bb 9e182af7207a4b1 6af02614b9d688f b/_fceecf1bb9e1 82af7207a4b16af 02614b9d688fb. so: undefined symbol: PyUnicodeUCS2_ Decode; ------- ------- ------- ------- ------- ------- ------- ------- ------- ----- python2. 7/dist- packages/ IPython/ utils/py3compat .pyc in execfile(fname, *where) _.execfile( filename, *where)
Reading DOLFIN parameters from file "dolfin_
In instant.
ImportError:
Failed to import module found in cache. Modulename: 'fceecf1bb9e182
Path: '/home/
ImportError:
-------
AssertionError Traceback (most recent call last)
/usr/lib/
173 else:
174 filename = fname
--> 175 __builtin_
/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 FunctionSpaceBa se.__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) cell=common_ cell)
152 raise RuntimeError, "Form compiler must implement the jit function."
153
--> 154 return jit_compile(form, parameters=p, common_
/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): ufl_object, parameters) ufl_object, parameters, common_cell)
---> 71 return jit_element(
72 else:
73 return jit_form(
/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) element_ and_dofmap( module, prefix, form_data)
179
180 return _extract_
/home/chad/ .local/ lib/python2. 7/site- packages/ ffc/jitcompiler .pyc in jit_form(form, parameters, common_cell) "cache_ dir"] import_ module( jit_object, cache_dir= cache_dir)
100 cache_dir = parameters[
101 if cache_dir == "": cache_dir = None
--> 102 module = instant.
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] cache(modulenam e, cache_dir, moduleids)
--> 156 return check_disk_
157
158
/home/chad/ .local/ lib/python2. 7/site- packages/ instant/ cache.pyc in check_disk_ cache(modulenam e, cache_dir, moduleids) isdir(os. path.join( path, modulename)):
120 if os.path.
121 # Found existing directory, try to import and place in memory cache
--> 122 module = import_ and_cache_ module( path, modulename, moduleids) check_disk_ cache: Imported module "\
123 if module:
124 instant_debug("In instant.
/home/chad/ .local/ lib/python2. 7/site- packages/ instant/ cache.pyc in import_ and_cache_ module( path, modulename, moduleids) and_cache_ module( path, modulename, moduleids): module_ directly( path, modulename) 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)) in_memory_ cache(moduleid, module)
66 def import_
67 module, e = import_
---> 68 instant_
69 for moduleid in moduleids:
70 place_module_
/home/chad/ .local/ lib/python2. 7/site- packages/ instant/ output. pyc in instant_ assert( condition, *message) *message) text)
53 _log.error(
54 text = message[0] % message[1:]
---> 55 raise AssertionError(
56
57 # Utility functions for file handling:
AssertionError: Failed to import module found in cache. Modulename: 'fceecf1bb9e182 af7207a4b16af02 614b9d688fb' ; chad/.instant/ cache'; /home/chad/ .instant/ cache/fceecf1bb 9e182af7207a4b1 6af02614b9d688f b/_fceecf1bb9e1 82af7207a4b16af 02614b9d688fb. so: undefined symbol: PyUnicodeUCS2_ Decode;
Path: '/home/
ImportError:
In [2]: