Bug#1009079: mdtraj: autopkgtest timeout on arm64 (downloading pdb file?)
Control: severity -1 serious Control: user debian...@lists.debian.org Control: usertag -1 flaky needs-internet Hi, On Thu, 07 Apr 2022 10:46:43 +1000 Stuart Prescott wrote: The autopkgtest tets for mdtraj attempts to download a pdb file and then use that in calculations. This is failing (either all the time or intermittently) with a timeout: I looked at the results of the autopkgtest of you package because it was showing up as a regression for the upload of gcc-12. Because the unstable-to-testing migration software now blocks on regressions in testing, flaky tests, i.e. tests that flip between passing and failing without changes to the list of installed packages, are causing people unrelated to your package to spend time on these tests. Don't hesitate to reach out if you need help and some more information from our infrastructure. Our arm64 workers are located in China, I wouldn't be surprised if the required connection isn't optimal, so I suspect increasing the timeout sufficiently is going to solve the issue, although making it more robust against connection issues would be smart too (e.g. retrying a small number of times in case of failure). Also, as the autopkgtest spec says [1], please mark your test with the "needs-internet" restriction. Paul [1] https://salsa.debian.org/ci-team/autopkgtest/-/blob/master/doc/README.package-tests.rst OpenPGP_signature Description: OpenPGP digital signature
Bug#1009079: mdtraj: autopkgtest timeout on arm64 (downloading pdb file?)
Source: mdtraj
Version: 1.9.7-2
Severity: important
X-Debbugs-Cc: stu...@debian.org
Dear Maintainer,
The autopkgtest tets for mdtraj attempts to download a pdb file and then use
that in calculations. This is failing (either all the time or intermittently)
with a timeout:
https://ci.debian.net/data/autopkgtest/unstable/arm64/m/mdtraj/20581005/log.gz
except Empty:
> raise Exception(
'Timeout (%.1f) when executing the following %s cell: "%s"'
%
(TIMEOUT, cell.cell_type, cell.source.strip()))
E Exception: Timeout (60.0) when executing the following code
cell: "# pull a random protein from the PDB
E # (The unitcell info happens to be wrong)
E traj = md.load_pdb('http://www.rcsb.org/pdb/files/2MI7.pdb')
E
E # just for example, use the first frame as the 'native'
conformation
E q = best_hummer_q(traj, traj[0])"
rscb.org is not fast to serve up the pdb files, but I'm not sure if that is
the cause, whether the download is failing entirely, or whether the computation
that follows is just slow.
If this is an isolated use of a single pdb file in the tests, perhaps the
Debian package could carry that pdb file as some test data and patch the test
to use the local file instead.
An internest using test should also be marked as "needs-internet".
regards
Stuart
