Errors using cbcbeat and Docker

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)

Does anyone have any ideas as to where the problem may lie?

Thanks in advance
John Walmsley

Hi, latest version of cbcbeat supports dolfin 2019.1.0.
You Need to roll back your cbcbeat version to the 2017.2.0 TAG:
https://bitbucket.org/meg/cbcbeat/src/2017.2.0/

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Thanks Jorgen, will try this out.

Now i am trying to install the cbcbeat but access denied error occur.
SS Attached

As far as Im aware, there is no docker-image of cbcbeat on dockerhub: Docker Hub
For information about how to install cbcbeat see: cbcbeat/INSTALL at py3 · minrk/cbcbeat · GitHub

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