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ctb
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@ctb ctb commented Nov 4, 2024

add debug symbols, force specific python version for wheel building.

To run flamegraph

create environment, build wheel, etc.

then (for Mac OS X, which requires sudo):

sudo flamegraph -o fastmultigather.svg -- python -m sourmash scripts fastmultig\
ather SRR606249.abundtrim.sig gtdb-rs207.genomic-reps.dna.k31.zip -c 1
sudo flamegraph -o fastgather.svg -- python -m sourmash scripts SRR606249.abund\
trim.sig gtdb-rs207.genomic-reps.dna.k31.zip -o xxx.csv -c 1

@luizirber
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Have you tried py-spy? It also generates flamegraphs, and can resolve Python call stacks + native extensions properly:
https://github.com/benfred/py-spy?tab=readme-ov-file#record
https://github.com/benfred/py-spy?tab=readme-ov-file#can-py-spy-profile-native-extensions

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2 participants