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Advanced Multilanguage Interface to CVODES and IDAS
https://amici.readthedocs.io/
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Occassional segfaults in ExampleSplinesSwameye2003.ipynb #2579

Closed dweindl closed 2 weeks ago

dweindl commented 2 weeks ago

Occassional segfaults when executing ExampleSplinesSwameye2003.ipynb. Happened twice within the last 3 weeks.

https://github.com/AMICI-dev/AMICI/actions/runs/11763765371/job/32768158595:

[NbConvertApp] Executing cell:
# Plot ML fit for pEpoR (all regularization strengths)
fig, ax = plt.subplots(figsize=(6.5, 3.5))
for regstrength in sorted(regproblems.keys()):
    t, pEpoR = simulate_pEpoR(
        problem=regproblems[regstrength], result=regresults[regstrength]
    )
    if regstrength == chosen_regstrength:
        kwargs = dict(
            color="black",
            label=f"$\\mathbf{{\\lambda = {regstrength}}}$",
            zorder=2,
        )
    else:
        kwargs = dict(label=f"$\\lambda = {regstrength}$", alpha=0.5)
    ax.plot(t, pEpoR, **kwargs)
ax.plot(
    df_pEpoR["time"],
    df_pEpoR["measurement"],
    "o",
    color="black",
    markerfacecolor="none",
    label="experimental data",
)
ylim1 = ax.get_ylim()[0]
ax.plot(
    nodes,
    len(nodes) * [ylim1],
    "x",
    color="black",
    label="spline nodes",
    zorder=10,
    clip_on=False,
)
ax.set_ylim(ylim1, ax.get_ylim()[1])
ax.set_xlabel("time")
ax.set_ylabel("pEpoR")
ax.set_xlim(-3.0, 63.0)
ax.set_ylim(-0.05299052022388704, 1.126290214024833)
ax.legend()
ax.figure.tight_layout()
# ax.set_ylabel("input function")
# print(f"xlim = {ax.get_xlim()}, ylim = {ax.get_ylim()}")
# ax.figure.savefig('fit_15nodes_lambdas.pdf')
[NbConvertApp] msg_type: status
    output, resources = self.export_single_notebook(
                        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/runner/work/AMICI/AMICI/venv/lib/python3.11/site-packages/nbconvert/nbconvertapp.py", line 487, in export_single_notebook
    output, resources = self.exporter.from_filename(
                        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/runner/work/AMICI/AMICI/venv/lib/python3.11/site-packages/nbconvert/exporters/templateexporter.py", line 386, in from_filename
    return super().from_filename(filename, resources, **kw)  # type:ignore[return-value]
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/runner/work/AMICI/AMICI/venv/lib/python3.11/site-packages/nbconvert/exporters/exporter.py", line 201, in from_filename
    return self.from_file(f, resources=resources, **kw)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/runner/work/AMICI/AMICI/venv/lib/python3.11/site-packages/nbconvert/exporters/templateexporter.py", line 392, in from_file
    return super().from_file(file_stream, resources, **kw)  # type:ignore[return-value]
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/runner/work/AMICI/AMICI/venv/lib/python3.11/site-packages/nbconvert/exporters/exporter.py", line 220, in from_file
    return self.from_notebook_node(
           ^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/runner/work/AMICI/AMICI/venv/lib/python3.11/site-packages/nbconvert/exporters/templateexporter.py", line 408, in from_notebook_node
    nb_copy, resources = super().from_notebook_node(nb, resources, **kw)
                         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/runner/work/AMICI/AMICI/venv/lib/python3.11/site-packages/nbconvert/exporters/exporter.py", line 154, in from_notebook_node
    nb_copy, resources = self._preprocess(nb_copy, resources)
                         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/runner/work/AMICI/AMICI/venv/lib/python3.11/site-packages/nbconvert/exporters/exporter.py", line 353, in _preprocess
    nbc, resc = preprocessor(nbc, resc)
                ^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/runner/work/AMICI/AMICI/venv/lib/python3.11/site-packages/nbconvert/preprocessors/base.py", line 48, in __call__
    return self.preprocess(nb, resources)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/runner/work/AMICI/AMICI/venv/lib/python3.11/site-packages/nbconvert/preprocessors/execute.py", line 103, in preprocess
    self.preprocess_cell(cell, resources, index)
  File "/home/runner/work/AMICI/AMICI/venv/lib/python3.11/site-packages/nbconvert/preprocessors/execute.py", line 124, in preprocess_cell
    cell = self.execute_cell(cell, index, store_history=True)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/runner/work/AMICI/AMICI/venv/lib/python3.11/site-packages/jupyter_core/utils/__init__.py", line 165, in wrapped
    return loop.run_until_complete(inner)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/hostedtoolcache/Python/3.11.10/x64/lib/python3.11/asyncio/base_events.py", line 654, in run_until_complete
    return future.result()
           ^^^^^^^^^^^^^^^
  File "/home/runner/work/AMICI/AMICI/venv/lib/python3.11/site-packages/nbclient/client.py", line 1009, in async_execute_cell
    raise DeadKernelError("Kernel died") from None
nbclient.exceptions.DeadKernelError: Kernel died

Previously this happened here: https://github.com/AMICI-dev/AMICI/actions/runs/11495925466/job/31996499560?pr=2563 (Oct 24)

dweindl commented 2 weeks ago

Also

dweindl commented 2 weeks ago

The issue is probaly in Model.clone:

Current thread 0x00007fb917717b80 (most recent call first):
  File "/home/runner/work/AMICI/AMICI/python/sdist/amici/amici.py", line 5226 in clone
  File "/home/runner/work/AMICI/AMICI/venv/lib/python3.11/site-packages/pypesto/objective/amici/amici.py", line 298 in __deepcopy__
  File "/opt/hostedtoolcache/Python/3.11.10/x64/lib/python3.11/copy.py", line 153 in deepcopy
  File "/home/runner/work/AMICI/AMICI/venv/lib/python3.11/site-packages/pypesto/objective/amici/amici.py", line 615 in set_custom_timepoints
  File "/tmp/ipykernel_21629/2584272737.py", line 12 in _simulate