mem-error while running contacts analysis for CHOL #43
Description
I encountered a MemoryError while running contacts analysis in basicrta. It completes the progress bar for all frames, but fails while saving the pickle files. The error is below;
python -m basicrta.contacts --top chol_protein3.pdb --traj chol_protein3.xtc --sel1 "chainID A" --sel2 "resname CHOL" --cutoff 7.0 --nproc 12
~/miniconda3/envs/basicrta1.1/lib/python3.12/site-packages/MDAnalysis/topology/PDBParser.py:350: UserWarning: Element information is missing, elements attribute will not be populated. If needed these can be guessed using universe.guess_TopologyAttrs(context='default', to_guess=['elements']).
warnings.warn("Element information is missing, elements attribute "
running MapContacts to generate contacts_max10.0.pkl
overall progress: 100%|█████████████████████████████████████████████████████████████████| 100/100 [4:46:07<00:00, 171.68s/it]
Traceback (most recent call last):
File "<frozen runpy>", line 198, in _run_module_as_main
File "<frozen runpy>", line 88, in _run_code
File "/nfs/homes3/rjoshi44/Projects/basicrta1.1/basicrta/basicrta/contacts.py", line 393, in <module>
mc.run()
File "~/basicrta1.1/basicrta/basicrta/contacts.py", line 94, in run
contact_map.dump(self.contacts_filename, protocol=5)
File "~/miniconda3/envs/basicrta1.1/lib/python3.12/site-packages/numpy/_core/_methods.py", line 247, in _dump
pickle.dump(self, f, protocol=protocol)
MemoryError