problem with libpetsc.so.3.1

[calbaker]

I am attempting to install FEniCS/dolfin within ~/.local using: http://fenicsproject.org/download/installation_from_source.html#installation-from-source

I am doing this because I use Enthought Python Distribution rather than the native python in Ubuntu 12.04. I can import ufc, ufl, and so forth, but importing dolfin gives me the following error:

In [5]: import dolfin
---------------------------------------------------------------------------
ImportError Traceback (most recent call last)
/home/chad/<ipython-input-5-7d9b2153bc0b> in <module>()
----> 1 import dolfin

/home/chad/.local/lib/python2.7/site-packages/dolfin/__init__.pyc in <module>()
     21
     22 # Import names from the compiled cpp module

---> 23 from dolfin.cppimports import *
     24 from dolfin.cppimports import __version__, __swigversion__
     25

/home/chad/.local/lib/python2.7/site-packages/dolfin/cppimports.py in <module>()
      2
      3 #--- Imports the SWIG-generated Python code (C++ interface) ---

----> 4 import dolfin.cpp as cpp
      5 __swigversion__ = cpp.__swigversion__
      6 __version__ = cpp.__dolfinversion__

/home/chad/.local/lib/python2.7/site-packages/dolfin/cpp.py in <module>()
     28 fp.close()
     29 return _mod
---> 30 _cpp = swig_import_helper()
     31 del swig_import_helper
     32 else:

/home/chad/.local/lib/python2.7/site-packages/dolfin/cpp.py in swig_import_helper()
     24 if fp is not None:
     25 try:
---> 26 _mod = imp.load_module('_cpp', fp, pathname, description)
     27 finally:
     28 fp.close()

ImportError: /usr/lib/petscdir/3.1/linux-gnu-c-opt/lib/libpetsc.so.3.1: undefined symbol: H5Pset_dxpl_mpio

Any ideas on how to fix this?

[Johannes Ring (johannr)]

Sorry, this is not a bug in DOLFIN. It is the same problem that you reported in question #199888.

[calbaker (calbaker)]

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(for...

[calbaker (calbaker)]

The bottom line is that I have tried three ways to run dolfin:

1. Compile and install in .local procduces this error:
ImportError: /usr/lib/petscdir/3.1/linux-gnu-c-opt/lib/libpetsc.so.3.1: undefined symbol: H5Pset_dxpl_mpio

2. Install from Ubuntu repositories and add to EPD path produces this error:
ImportError: /usr/lib/libpetsc.so.3.1: undefined symbol: H5Pset_dxpl_mpio

3. Remove EPD from path. Install fenics through Ubuntu. Run example examples-1.0/stationary/poisson/d1_p2D.py. Error:
ImportError:/home/chad/.instant/cache/fceecf1bb9e182af7207a4b16af02614b9d688fb/_fceecf1bb9e182af7207a4b16af02614b9d688fb.so: undefined symbol: PyUnicodeUCS2_Decode;

So no matter what, I cannot get dolfin running. I'm going to try make the libpetsc link to see if that works. I'll post the result.

[calbaker (calbaker)]

On creating that link, I get the following error:

/usr/lib/libslepc.so.3.1: undefined symbol: _PetscLogPHC

If this is not a bug, I'm certainly not planning to use FEniCS. Time to try FiPy I guess. At least I can get it to run.

[calbaker (calbaker)]

I completely reinstalled Ubuntu, and I am now able to run dolfin with EPD after having compiled and installed fenics to ~/.local. I have no idea why this worked.