Refine stuck in get_cubes_list when preprocessing_ncpus > 1

[mpm896]

Hello,

I'm running into an issue during refine where it's getting stuck in the prepare.py phase in the function get_cubes_list. I felt this problem was similar to #31 so I tried running with --preprocessing_ncpus 1 and it made it through the subtomogram preparation. I'm wondering if there's any way to overcome this issue?

Our computational setup is via a Docker image on an AWS instance, where all my processing is run within a NFS directory. I'm not sure if this is similar to a mounted SMB volume like in #31. This image is running Ubuntu 18.04. Let me know if you have any advice with this. The error I receive after ctrl+c is pasted below:

12-04 15:50:14, INFO     Noise Level:0.0

^CTraceback (most recent call last):
  File "/common/workdir/IsoNet/bin/isonet.py", line 497, in <module>
    fire.Fire(ISONET)
  File "/cloud-home/X/.magellan/conda/envs/isonet/lib/python3.10/site-packages/fire/core.py", line 135, in Fire
    component_trace = _Fire(component, args, parsed_flag_args, context, name)
  File "/cloud-home/X/.magellan/conda/envs/isonet/lib/python3.10/site-packages/fire/core.py", line 468, in _Fire
    component, remaining_args = _CallAndUpdateTrace(
  File "/cloud-home/X/.magellan/conda/envs/isonet/lib/python3.10/site-packages/fire/core.py", line 684, in _CallAndUpdateTrace
    component = fn(*varargs, **kwargs)
  File "/common/workdir/IsoNet/bin/isonet.py", line 391, in refine
    run(d_args)
  File "/common/workdir/IsoNet/bin/refine.py", line 115, in run
    get_cubes_list(args)
  File "/common/workdir/IsoNet/preprocessing/prepare.py", line 184, in get_cubes_list
    p.map(func,inp)
  File "/cloud-home/X/.magellan/conda/envs/isonet/lib/python3.10/multiprocessing/pool.py", line 367, in map
    return self._map_async(func, iterable, mapstar, chunksize).get()
  File "/cloud-home/X/.magellan/conda/envs/isonet/lib/python3.10/multiprocessing/pool.py", line 768, in get
    self.wait(timeout)
  File "/cloud-home/X/.magellan/conda/envs/isonet/lib/python3.10/multiprocessing/pool.py", line 765, in wait
    self._event.wait(timeout)
  File "/cloud-home/X/.magellan/conda/envs/isonet/lib/python3.10/threading.py", line 607, in wait
    signaled = self._cond.wait(timeout)
  File "/cloud-home/X/.magellan/conda/envs/isonet/lib/python3.10/threading.py", line 320, in wait
    waiter.acquire()
KeyboardInterrupt