Update ipk.py to avoid CPU oversubscription from raxml-ng side in bioconda recipe - Githubissues

phylo42 / IPK

Inference of phylo-k-mers

MIT License

4 stars 1 forks source link

Update ipk.py to avoid CPU oversubscription from raxml-ng side in bioconda recipe #26

Closed blinard-BIOINFO closed 4 months ago

blinard-BIOINFO commented 6 months ago

A fast fix to be bioconda recipe compatible.

makes ipk.py uses 1 thread by default
as a consequence raxml-ng command that is launched is assigned to 1 CPU
as a consequence, no crash related to raml-ng not allowing CPU oversubscription without specific debug options in the command-line.

Long term fix:

Option 1 (fast): add the option --force perf_threads to the raxml-ng command generated by ar::raxml_wrapper and keep same number of threads as defined by ipk-* command. See https://github.com/amkozlov/raxml-ng/wiki/Parallelization
Option 2 (harder): Make sure that ar::raxml_wrapper do not assign to raxml-ng more CPU than what the local environment allows.

nromashchenko commented 4 months ago

That was addressed in a1eeed8 a long ago actually... Sorry I close it too. It just turned out that certain things from develop never made it to main. That is also the source of the whole hassle with DB incompatibility for EPIK.

Some branch mismanagement from my part made the latest release and main actually broken, while our development branches are fine.

Again, main will catch up soon