[Debichem-devel] Bug#1032488: opendrop: arkode (sundials) error prevents interfacial tension analysis
Drew Parsons
dparsons at debian.org
Tue Mar 7 23:05:13 GMT 2023
Package: opendrop
Version: 3.3.1-4
Severity: grave
Tags: patch upstream
Justification: renders package unusable
debian patch sundials_nvector_API6.patch enabled opendrop to build
against sundials 6.
Nevertheless it still fails when attempting to analysis interfacial
tension measurements:
[ARKODE::ERKStep ERROR] erkStep_FullRHS
At t = inf, the right-hand side routine failed in an unrecoverable manner.
[ARKODE ERROR] ARKODE
At t = 0, the right-hand side routine failed in an unrecoverable manner.
Exception in callback PendantAnalysisJob._ylfit_done(<Future finis...e() failed.')>)
handle: <GLibSourceHandle PendantAnalysisJob._ylfit_done(<Future finis...ylfit_done()]>)>
concurrent.futures.process._RemoteTraceback:
"""
Traceback (most recent call last):
File "/usr/lib/python3.11/concurrent/futures/process.py", line 256, in _process_worker
r = call_item.fn(*call_item.args, **call_item.kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/python3/dist-packages/opendrop/fit/younglaplace/__init__.py", line 51, in young_laplace_fit
model.set_params(initial_params)
File "/usr/lib/python3/dist-packages/opendrop/fit/younglaplace/model.py", line 86, in set_params
dr_dBo, dz_dBo = radius * shape.DBo(s)
^^^^^^^^^^^^
File "opendrop/fit/younglaplace/shape.pyx", line 71, in opendrop.fit.younglaplace.shape.YoungLaplaceShape.DBo
File "opendrop/fit/younglaplace/shape.pyx", line 89, in opendrop.fit.younglaplace.shape.YoungLaplaceShape.DBo_array
RuntimeError: ERKStepEvolve() failed.
"""
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/usr/lib/python3/dist-packages/opendrop/vendor/aioglib/_loop.py", line 463, in __call__
self._context.run(self._callback, *self._args)
File "/usr/lib/python3/dist-packages/opendrop/app/ift/services/analysis.py", line 219, in _ylfit_done
raise e
File "/usr/lib/python3/dist-packages/opendrop/app/ift/services/analysis.py", line 217, in _ylfit_done
result = fut.result()
^^^^^^^^^^^^
RuntimeError: ERKStepEvolve() failed.
Upstream has prepared a patch to update properly for sundials 6 in
commit cf9d5aa (development branch),
https://github.com/jdber1/opendrop/commit/cf9d5aa2f06d625f306114d001a99934cb913ff0
-- System Information:
Debian Release: 12.0
APT prefers unstable
APT policy: (500, 'unstable'), (1, 'experimental')
merged-usr: no
Architecture: amd64 (x86_64)
Foreign Architectures: i386
Kernel: Linux 6.1.0-5-amd64 (SMP w/8 CPU threads; PREEMPT)
Kernel taint flags: TAINT_PROPRIETARY_MODULE, TAINT_OOT_MODULE
Locale: LANG=en_AU.UTF-8, LC_CTYPE=en_AU.UTF-8 (charmap=UTF-8), LANGUAGE=en_AU:en
Shell: /bin/sh linked to /bin/dash
Init: systemd (via /run/systemd/system)
LSM: AppArmor: enabled
Versions of packages opendrop depends on:
ii gir1.2-gdkpixbuf-2.0 2.42.10+dfsg-1+b1
ii gir1.2-gtk-3.0 3.24.36-4
ii libc6 2.36-8
ii libgcc-s1 12.2.0-14
ii libpython3.11 3.11.2-5
ii libstdc++6 12.2.0-14
ii libsundials-arkode5 6.4.1+dfsg1-3
ii python3 3.11.2-1
ii python3-cairo 1.20.1-5+b1
ii python3-gi 3.42.2-3+b1
ii python3-injector 0.20.1-1
ii python3-matplotlib 3.6.3-1+b1
ii python3-numpy 1:1.24.2-1
ii python3-opencv 4.6.0+dfsg-11
ii python3-scipy 1.10.1-2
opendrop recommends no packages.
Versions of packages opendrop suggests:
ii opendrop-doc 3.3.1-4.1
-- no debconf information
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