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drorlab / combind

Integrated physics-based and ligand-based modeling.
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Execution killed during Featurization #8

Closed matany58 closed 2 years ago

matany58 commented 2 years ago

Execution killed while executing the command;

Featurization combind featurize features docking//_pv.maegz

The following message was received; Extracting glide scores. Extracting names. Computing RMSDs to native poses Computing interaction fingerprints. Killed I ran the command again and received the error below Fatal Python error: Bus error

Then the execution stops, any assistance will be appreciated

jpaggi commented 2 years ago

I haven't seen "Fatal Python error: Bus error" before. Is it possible that you are running out of memory? At least on the cluster I normally use, jobs ending with "Killed" is generally due to running out of memory.

matany58 commented 2 years ago

Thank you

Also how long does it take to execute combind featurize features docking//_pv.maegz

jpaggi commented 2 years ago

It depends on the number of ligands and number of poses per ligand. For around 10 ligands with 100 poses each, featurize should take a few hours.