Reentry Protocol (example 21) not working once model is changed

Question

Hi,

I am changing the model from COURTEMANCHE to GPB, the example throws me the following error:

Traceback (most recent call last):
  File "/home/silvalab/.local/lib/python3.8/site-packages/bin/tuneCV", line 157, in <module>
    run()
  File "/home/silvalab/.local/lib/python3.8/site-packages/carputils/tools.py", line 528, in wrapped
    ret = run(args, job)
  File "/home/silvalab/.local/lib/python3.8/site-packages/bin/tuneCV", line 140, in run
    to.iterateCV(job)
  File "/home/silvalab/.local/lib/python3.8/site-packages/carputils/tuning.py", line 561, in iterateCV
    self.vel_ = self.measureCV(os.path.join(ItJobID, 'init_acts_lats-thresh.dat'))
  File "/home/silvalab/.local/lib/python3.8/site-packages/carputils/tuning.py", line 477, in measureCV
    lats = loadtxt(actsFile)
  File "/home/silvalab/.local/lib/python3.8/site-packages/numpy/lib/npyio.py", line 961, in loadtxt
    fh = np.lib._datasource.open(fname, 'rt', encoding=encoding)
  File "/home/silvalab/.local/lib/python3.8/site-packages/numpy/lib/_datasource.py", line 195, in open
    return ds.open(path, mode, encoding=encoding, newline=newline)
  File "/home/silvalab/.local/lib/python3.8/site-packages/numpy/lib/_datasource.py", line 535, in open
    raise IOError("%s not found." % path)
OSError: imp_GPB_vel_0.3_dx_400.0_It_0/init_acts_lats-thresh.dat not found.
Traceback (most recent call last):
  File "./run.py", line 730, in <module>
    run()
  File "/home/silvalab/.local/lib/python3.8/site-packages/carputils/tools.py", line 528, in wrapped
    ret = run(args, job)
  File "./run.py", line 456, in run
    converge_CV(args,job)
  File "./run.py", line 657, in converge_CV
    job.bash(cmd)
  File "/home/silvalab/.local/lib/python3.8/site-packages/carputils/job/job.py", line 242, in bash
    self.register(ShellCommand(cmd, message), *args, **kwargs)
  File "/home/silvalab/.local/lib/python3.8/site-packages/carputils/job/job.py", line 119, in register
    self._queue.pop(0).execute()
  File "/home/silvalab/.local/lib/python3.8/site-packages/carputils/job/command.py", line 163, in execute
    divertoutput.call(self._cmd, stdout=self._stdout, stderr=self._stderr)
  File "/home/silvalab/.local/lib/python3.8/site-packages/carputils/divertoutput.py", line 43, in wrapped
    return func(cmd, *args, **kwargs)
  File "/home/silvalab/.local/lib/python3.8/site-packages/carputils/divertoutput.py", line 147, in call
    raise subprocess.CalledProcessError(proc.returncode, cmd[0])
subprocess.CalledProcessError: Command '/home/silvalab/.local/lib/python3.8/site-packages/bin/tuneCV' returned non-zero exit status 1.

I have been trying to debug the issue for a couple days now, but I have not found any solution. Please let me know if the simulation works on your end with GPB. This error is outputted after running the following command:

python3 ./run.py --np 2 --protocol PSD --visualize --model GPB

When I try to prepace as well, I get the same error.

Best,

Sushruth

Answer 1

Hi Sushruth,

from what I can see the error comes from tuneCV and not from the protocol itself. The tutorial is using tuneCV to output the conductivities to match the prescribed conduction velocity. Then, it is running a single cell experiment to initialize each element of the model with a prescribed state. I assume that the model GPB does not have the same ionic currents as the Courtemanche one. If you want to use a different model you have not only to change the model but also to change the ionic current and conductance modifications ("modelpar" in the convergeCV function https://git.opencarp.org/openCARP/experiments/-/blob/master/tutorials/02_EP_tissue/21_reentry_induction/run.py#L663) and in the single cell initialization procedure (https://git.opencarp.org/openCARP/experiments/-/blob/master/tutorials/02_EP_tissue/21_reentry_induction/run.py#L709). Try to accordingly modify these.

Best,

Luca