[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.

  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()]>)>
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
  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),

-- 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)
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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