The code runs very slowly after this point “subprocess.run(f'{autodock} -M {protein_file} -s 0 -L ligands/0/ligand0.pdbqt -N outs/ligand0', shell=True, stdout=subprocess.DEVNULL, stderr=subprocess.DEVNULL)”

Rose-STL-Lab / LIMO

generative model for drug discovery

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The code runs very slowly after this point “subprocess.run(f'{autodock} -M {protein_file} -s 0 -L ligands/0/ligand0.pdbqt -N outs/ligand0', shell=True, stdout=subprocess.DEVNULL, stderr=subprocess.DEVNULL)” #4

Closed renyongqi529 closed 11 months ago

renyongqi529 commented 2 years ago

I see nvidia-smi is GPU-Util:0%,but Memory-Usage is used. I have AutoDock-GPU installed and it compiles fine.Please give me some pointers, thanks.

PeterEckmann1 commented 2 years ago

Hi, could you try removing stdout=subprocess.DEVNULL, stderr=subprocess.DEVNULL and paste what output you get? It's possible autodock is giving some errors that are being piped to DEVNULL.