Hi all,
I am currently attempting to use the cbcbeat project for simulation of monodomain and bidomain equations in cardiac electrophysiology - see https://cbcbeat.readthedocs.io/en/latest/ . I am using Docker with fenics 2017.2.0. I have installed libajoint and dolfin-adjoint using the ppa:
sudo apt-add-repository ppa:libadjoint/ppa
sudo apt-get update
sudo apt-get install python-dolfin-adjoint
sudo apt-add-repository ppa:libadjoint/ppa
sudo apt-get update
sudo apt-get install libadjoint libadjoint-dev python-libadjoint
basic tests run fine, as does the monodomain demo. However, when we move to the bidomain demo, errors begin to appear:
fenics@xxxxx:~/local/cbcbeat/demo/bidomain-biventricular$ python demo_biventricular.py
Traceback (most recent call last):
File “demo_biventricular.py”, line 231, in
main()
File “demo_biventricular.py”, line 156, in main
set_log_level(LogLevel.INFO)
NameError: global name ‘LogLevel’ is not defined
Aborted (core dumped)
… and if the above line is commented,
enics@xxxxx:~/local/cbcbeat/demo/bidomain-biventricular$ python demo_biventricular.py
Setting up application parameters
<Parameter set “Application” containing 6 parameter(s) and parameter set(s)>
Application | type value range access change
T | double 10.000000 Not set 0 0
cell_model | string FitzHughNagumo Not set 0 0
directory | string results_2019_22Nov_23h_09m Not set 0 0
healthy | bool 1 Not set 0 0
stimulus_amplitude | double 30.000000 Not set 0 0
timestep | double 0.100000 Not set 0 0
Setting up cardiac model
Traceback (most recent call last):
File “demo_biventricular.py”, line 231, in
main()
File “demo_biventricular.py”, line 164, in main
(heart, gs) = setup_cardiac_model(application_parameters)
File “demo_biventricular.py”, line 145, in setup_cardiac_model
pulse = CompiledExpression(compile_cpp_code(cpp_stimulus).Stimulus(),
NameError: global name ‘CompiledExpression’ is not defined
Aborted (core dumped)
- so it looks like some modules are not being loaded correctly. It looks like LogLevel is part of dolfin, so this suggests that either dolfin isn’t being loaded properly or the wrong version of dolfin is being used for this code ( https://fenicsproject.org/docs/dolfin/1.4.0/cpp/programmers-reference/log/LogLevel.html ).
Does anyone have any ideas as to where the problem may lie?
Thanks in advance
John Walmsley