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superphy / prairiedog

next-gen pangenome graphs for predictive genomics
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Running prairiedog for diffpool #48

Closed kevinkle closed 5 years ago

kevinkle commented 5 years ago

This seems to be max parallelism for 62.4G ram

snakemake -j 12
kevinkle commented 5 years ago

It's looking like it takes about all 62GB of ram + 118GB of swap to load 110 genomes

kevinkle commented 5 years ago

find . -maxdepth 1 -type f |head -1000|xargs cp -t "$destdir"

kevinkle commented 5 years ago

rule 'offset' found max_num_nodes to be 2344649

kevinkle commented 5 years ago

wontfix. will likely switch to pytorch geomtric's implementation of diffpool instead of using diffpool directly