[Debian-med-packaging] Bug#986256: Bug#986256: simka: flaky amd64 autopkgtest: regularly times out after 2:47 h

[Étienne Mollier]

Hi Graham,

Graham Inggs, on 2021-04-06 20:15:30 +0200:
> This is still occurring with simka 1.5.3-3, see:
> https://ci.debian.net/packages/s/simka/testing/amd64/

Thanks for having noticed it.  It looks like I got caught by the
Python script not taking the -nb-cores argument, contrary to the
shell script.  While I couldn't reproduce the hang on emulator,
it seems I can just reproduce the problem by enforcing the cores
count to 48 within the Python script.  The test is precisely
hanging at this location:

	[...]
	Command for visualizing results with metadata annotations:
		python ../scripts/visualization/run-visualization.py -in ./simka_results/ -out ./simka_results/ -pca -heatmap -tree -metadata-in ../example/dataset_metadata.csv -metadata-variable VARIABLE_1
	TESTING k=31 t=0
	simka -in simka_input.txt -out ./__results__/results_k31_t0 -out-tmp ./temp_output -simple-dist -complex-dist -kmer-size 31 -abundance-min 0 -verbose 0 -nb-cores 48
		OK
	TESTING k=21 t=0
	simka -in simka_input.txt -out ./__results__/results_k21_t0 -out-tmp ./temp_output -simple-dist -complex-dist -kmer-size 21 -abundance-min 0 -verbose 0 -nb-cores 48
		OK
	TESTING k=31 t=2
	simka -in simka_input.txt -out ./__results__/results_k31_t2 -out-tmp ./temp_output -simple-dist -complex-dist -kmer-size 31 -abundance-min 2 -verbose 0 -nb-cores 48
	_

The output on CI infrastructure is a bit misleading, because the
standard output is not flushed on each output line by default.
I enforced flushed output manually in the Python script to have
a cleared view.  But I /believe/ I could reproduce precisely the
deadlock this time.  Hopefully a further upload with controlled
cores count at this level should do the trick.

Have a nice day,  :)
-- 
Étienne Mollier <etienne.mollier at mailoo.org>
Fingerprint:  8f91 b227 c7d6 f2b1 948c  8236 793c f67e 8f0d 11da
Sent from /dev/pts/2, please excuse my verbosity.
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