[BUG] dolfinx MPI_ABORT due to tqdm progress bar

[RemDelaporteMathurin]

Describe the bug
We recently realised kaelyndunnell/hisp#18 that using the tqdm progress bar could cause crashes when it isn't closed after calling run

To Reproduce

with dolfinx>=0.8 run:

import festim as F

my_model = F.HydrogenTransportProblem()

my_model.mesh = F.Mesh1D([0, 0.1, 0.2, 0.3, 0.5, 1])

tungsten = F.Material(D_0=1, E_D=0)

w_subdomain = F.VolumeSubdomain1D(id=1, borders=[0, 1], material=tungsten)

my_model.subdomains = [w_subdomain]

my_model.species = [F.Species("H")]

my_model.temperature = 500

my_model.boundary_conditions = []


my_model.settings = F.Settings(atol=1e-10, rtol=1e-10, final_time=1)

my_model.settings.stepsize = F.Stepsize(initial_value=0.1)

my_model.initialise()
my_model.run()


class RandomClass:  # this triggers the crash
    def __init__(self):
        pass

** Fix **

The progress bar needs to be closed. All we need to do is add self.progress_bar.close() at the end of

FESTIM/festim/problem.py

Lines 105 to 119 in 77c97b3

	def run(self):
	"""Runs the model"""
	if self.settings.transient:
	# Solve transient
	if self.show_progress_bar:
	self.progress_bar = tqdm.autonotebook.tqdm(
	desc=f"Solving {self.__class__.__name__}",
	total=self.settings.final_time,
	unit_scale=True,
	)
	while self.t.value < self.settings.final_time:
	self.iterate()
	if self.show_progress_bar:
	self.progress_bar.refresh() # refresh progress bar to show 100%

It can also be closed manually after calling run.

[RemDelaporteMathurin]

@kaelyndunnell I think you can fix this