error while running the inference example

velocirraptor23 commented 4 months ago

Hi, I am running this as the example: python -m inference --config default_inference_args.yaml --protein_ligand_csv data/protein_ligand_example.csv --out_dir results/ Before I was able to run it completely but I reinstalled the things becuase I messed up the enviroment and now I am getting this error. Not sure what that means. File "/cluster/ddu/cmmartinez001/miniconda3/envs/diffdock/lib/python3.9/runpy.py", line 197, in _run_module_as_main return _run_code(code, main_globals, None, File "/cluster/ddu/cmmartinez001/miniconda3/envs/diffdock/lib/python3.9/runpy.py", line 87, in _run_code exec(code, run_globals) File "/cluster/ddu/cmmartinez001/DiffDock/inference.py", line 41, in resource.setrlimit(resource.RLIMIT_NOFILE, (64000, rlimit[1])) ValueError: current limit exceeds maximum limit

Any help would be highly appreciated.

BW,

Cesar

velocirraptor23 commented 4 months ago

I change the number to 4000, it did the emebedings with ESM but the I got another error: Generating ESM language model embeddings Processing 1 of 1 batches (4 sequences) 0it [00:00, ?it/s]Segmentation fault

Not sure at this poinr what happened. Also wondering what that number means and why decreasing it allowed me to run the code.

BW,

Cesar

jsilter commented 4 months ago

Generally a segmentation fault means the computer ran out of memory. So you may need better hardware. We also have a huggingface space available: https://huggingface.co/spaces/reginabarzilaygroup/DiffDock-Web

velocirraptor23 commented 4 months ago

but it was working first. dont understand what has changed. Is that cache memory? Or a new update has made something more heavy in terms of memory?

gcorso / DiffDock

error while running the inference example #223