[Debichem-devel] Bug#1108309: mdanalysis: FTBFS randomly: autobuilder hangs

[Santiago Vila]

Package: src:mdanalysis
Version: 2.9.0-8
Severity: serious
Tags: ftbfs trixie sid help

Dear maintainer:

During a rebuild of all packages in unstable, your package failed to build:

--------------------------------------------------------------------------------
[...]
testsuite/MDAnalysisTests/analysis/test_diffusionmap.py::test_long_traj PASSED [  1%]
testsuite/MDAnalysisTests/analysis/test_diffusionmap.py::test_updating_atomgroup PASSED [  1%]
testsuite/MDAnalysisTests/analysis/test_diffusionmap.py::test_not_universe_atomgroup_error PASSED [  1%]
testsuite/MDAnalysisTests/analysis/test_diffusionmap.py::test_DistanceMatrix_attr_warning PASSED [  1%]
testsuite/MDAnalysisTests/analysis/test_dihedrals.py::TestDihedral::test_dihedral[client_Dihedral0] PASSED [  1%]
testsuite/MDAnalysisTests/analysis/test_dihedrals.py::TestDihedral::test_dihedral_single_frame[client_Dihedral0] PASSED [  1%]
testsuite/MDAnalysisTests/analysis/test_dihedrals.py::TestDihedral::test_atomgroup_list[client_Dihedral0] PASSED [  1%]
testsuite/MDAnalysisTests/analysis/test_dihedrals.py::TestDihedral::test_enough_atoms[client_Dihedral0] PASSED [  1%]
testsuite/MDAnalysisTests/analysis/test_dihedrals.py::TestDihedral::test_dihedral_attr_warning[client_Dihedral0] 
E: Build killed with signal TERM after 30 minutes of inactivity
--------------------------------------------------------------------------------

Notes:

- The way it fails is not always the same. I've put a collection of different build logs here:

https://people.debian.org/~sanvila/build-logs/202506/

- The build does not always fail, but the failure rate here is around 90% (tested on systems
with 2 CPUs), which makes it not to be suitable for release. However, for some reason,
the failure rate is only 20% on single-cpu systems, maybe this difference means something.

- I believe, but I can't check anymore, that the failure rate raised a lot when I switched
my autobuilders to trixie (i.e. when I started to use the kernel of trixie).

- This failure where the autobuilder hangs also happens on the buildds. Please see:

https://buildd.debian.org/status/fetch.php?pkg=mdanalysis&arch=all&ver=2.9.0-3&stamp=1744942413&raw=0
https://buildd.debian.org/status/fetch.php?pkg=mdanalysis&arch=amd64&ver=2.9.0-7&stamp=1745409028&raw=0
https://buildd.debian.org/status/fetch.php?pkg=mdanalysis&arch=arm64&ver=2.9.0-6&stamp=1745371276&raw=0
https://buildd.debian.org/status/fetch.php?pkg=mdanalysis&arch=armel&ver=2.9.0-8&stamp=1747011477&raw=0
https://buildd.debian.org/status/fetch.php?pkg=mdanalysis&arch=i386&ver=2.9.0-2&stamp=1744893854&raw=0
https://buildd.debian.org/status/fetch.php?pkg=mdanalysis&arch=mips64el&ver=2.9.0-4&stamp=1745023633&raw=0

all of which end with a message like this:

E: Build killed with signal TERM after 150 minutes of inactivity

(In my build logs, I lowered the value to 30 minutes because I know that in normal
circumstances the package should take a lot less than that).

- There are also similar failures (autobuilder hang) in the reproducible-builds site:

https://tests.reproducible-builds.org/debian/rbuild/unstable/amd64/mdanalysis_2.9.0-8.rbuild.log.gz
https://tests.reproducible-builds.org/debian/logs/unstable/armhf/mdanalysis_2.8.0-4.build2.log.gz

- I have no idea of what's going on here, but as always, I can offer a VM to reproduce
(contact me privately for details).

Thanks.