Dijitso failed to load existing file

installation
1

Dear community, I recently reinstalled the lagacy version of fenics on my cluster with conda as I messed up my conda environment with some other installations last week.

I used conda install -c conda-forge fenics for the installation. (Before doing so, I deleted my miniconda folder and reinstalled conda).

After that, I found that my fenics code no longer runs with an “dijitso failed to load existing file” error. I tried to run the demo code from fenics tutorial and got the same error:

Calling FFC just-in-time (JIT) compiler, this may take some time.
dijitso failed to load existing file:
        /home/spshu/.cache/dijitso/lib/libdijitso-dolfin_expression_c49ebd8fd6c25a3c31b612f2a1752a2c.so
error is:
        /home/spshu/.cache/dijitso/lib/libdijitso-dolfin_expression_c49ebd8fd6c25a3c31b612f2a1752a2c.so: undefined symbol: _ZNK6dolfin8Variable3strEb
Traceback (most recent call last):
  File "/home/spshu/miniconda3/lib/python3.9/site-packages/dolfin/jit/jit.py", line 168, in compile_class
    submodule = dijitso.extract_factory_function(module, "create_" + module_name)()
  File "/home/spshu/miniconda3/lib/python3.9/site-packages/dijitso/jit.py", line 47, in extract_factory_function
    function = getattr(lib, name)
AttributeError: 'NoneType' object has no attribute 'create_dolfin_expression_c49ebd8fd6c25a3c31b612f2a1752a2c'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/spshu/tmp_scratch/demo.py", line 18, in <module>
    u_D = Expression('1 + x[0]*x[0] + 2*x[1]*x[1]', degree=2)
  File "/home/spshu/miniconda3/lib/python3.9/site-packages/dolfin/function/expression.py", line 400, in __init__
    self._cpp_object = jit.compile_expression(cpp_code, params)
  File "/home/spshu/miniconda3/lib/python3.9/site-packages/dolfin/function/jit.py", line 158, in compile_expression
    expression = compile_class(cpp_data, mpi_comm=mpi_comm)
  File "/home/spshu/miniconda3/lib/python3.9/site-packages/dolfin/jit/jit.py", line 170, in compile_class
    raise RuntimeError("Unable to compile C++ code with dijitso")
RuntimeError: Unable to compile C++ code with dijitso

Do you have any insights on this error? How can I fix it? Thanks!

2

dijitso uses a cache to speed up processing when the same weak form is used. The cache might be stale due a version upgrade. Try clearing it with dijitso clean.

3

Unfortunately this does not solve the problem.

After running the dijitso clean command, when running the demo code, "Calling FFC just-in-time (JIT) compiler, this may take some time." appears as expected, but the same “dijitso failed to load existing file” error follows.

4

Hi Milankovich007, we are also encountering this issue when installing FEniCS. Did you find the cause?

5

Dear @milankovich007 and @Daniel_Korchinski.

I was wondering if you have made any progress in resolving this issue?
I have experienced the same issue when installing the development version of FEniCS (2019.2.0.dev0) using the spack package manager .

Notably, I too get the exact same message: undefined symbol: _ZNK6dolfin8Variable3strEb

I don’t know if it helps, but I was able to trace the error originally being thrown in dijitso/cache.py in the following call to LoadLibrary.

        try:
            lib = ctypes.cdll.LoadLibrary(lib_filename)
        except os.error as e:
            lib = None
            emsg = analyse_load_error(e, lib_filename, cache_params)
            warning(emsg)