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.moll...@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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