Linux process status is D

[bj600800]

After running the fold.py script for 3 hours, the process is in sleeping status with status D reported by shell command Top. I am not sure the really cause of the bug, but here is an assumption.

In fold.py script, may be due to the implementation of data_reader is an iterater rather than the DataLoader of Pytorch. The heavy I/O operations make the process stucked. While the extract.py used the DataLoader of Pytorch for loading the sequences at once.

[bj600800]

Here is an example code for resumable prediction if anyone need it. Put this code block after 134 line in scripts/fold.py.

    if os.path.exists(args.pdb):
        predicted_proteins = set()
        for filename in os.listdir(args.pdb):
            if filename.endswith(".pdb"):
                protein_name = filename[:-4]
                predicted_proteins.add(protein_name)
        all_sequences = [(name, sequence) for (name, sequence) in all_sequences if name not in predicted_proteins]