Created attachment 1702738 [details] Patch to fix the crash Description of problem: Pymol crashes when loading a structure or session, which renders pymol basically unusable. This crash is caused by a combination of a bug in pymol 2.4.0 and being compiled with "-D_GLIBCXX_ASSERTIONS". For details please see the upstream issue I filed about this: https://github.com/schrodinger/pymol-open-source/issues/119 Version-Release number of selected component (if applicable): pymol-2.4.0-1.fc32 How reproducible: Reliably Steps to Reproduce: 1. start pymol 2. run "fetch 1fcn" Actual results: pymol process aborts with the following error message: /usr/include/c++/10/bits/stl_vector.h:1045: std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](std::vector<_Tp, _Alloc>::size_type) [with _Tp = ObjectMolecule*; _Alloc = std::allocator<ObjectMolecule*>; std::vector<_Tp, _Alloc>::reference = ObjectMolecule*&; std::vector<_Tp, _Alloc>::size_type = long unsigned int]: Assertion '__builtin_expect(__n < this->size(), true)' failed. Expected results: A protein structure to be shown Additional info: I've attached a simple patch that fixes the issue for me. Alternatively a backport of the upstream commit that fixed the bug as a side effect of a larger refactor could be used: https://github.com/schrodinger/pymol-open-source/commit/09413be126569173129928de2ab67d38df4f8e1f
Thank you very much Sebastian. I'll add the patch within next 12 h.
FEDORA-2020-de575db525 has been submitted as an update to Fedora 31. https://bodhi.fedoraproject.org/updates/FEDORA-2020-de575db525
FEDORA-2020-f0019484ef has been submitted as an update to Fedora 32. https://bodhi.fedoraproject.org/updates/FEDORA-2020-f0019484ef
FEDORA-2020-de575db525 has been pushed to the Fedora 31 testing repository. In short time you'll be able to install the update with the following command: `sudo dnf upgrade --enablerepo=updates-testing --advisory=FEDORA-2020-de575db525` You can provide feedback for this update here: https://bodhi.fedoraproject.org/updates/FEDORA-2020-de575db525 See also https://fedoraproject.org/wiki/QA:Updates_Testing for more information on how to test updates.
FEDORA-2020-f0019484ef has been pushed to the Fedora 32 testing repository. In short time you'll be able to install the update with the following command: `sudo dnf upgrade --enablerepo=updates-testing --advisory=FEDORA-2020-f0019484ef` You can provide feedback for this update here: https://bodhi.fedoraproject.org/updates/FEDORA-2020-f0019484ef See also https://fedoraproject.org/wiki/QA:Updates_Testing for more information on how to test updates.
FEDORA-2020-de575db525 has been pushed to the Fedora 31 stable repository. If problem still persists, please make note of it in this bug report.
FEDORA-2020-f0019484ef has been pushed to the Fedora 32 stable repository. If problem still persists, please make note of it in this bug report.