The process gets stuck while running "gimble gridsearch" and has taken a long time without moving forward.

[kuangzhuoran]

My command is :"gimble gridsearch -z analysis/Chr1.z -g makegrid/Chr1.BA -d tally/windows_kmax2 -p 5 -f".
My gimble version is v1.0.3.

I see:
[+] Running 'gimble gridsearch' ...
[+] Gathering data for gridsearch ...
[+] Searching with grid 'Chr1.AB' along tally 'windows_kmax2' ...
[%] Gridsearch: 100%|█████████████████████████████████████████| 54432/54432 [15:35<00:00, 58.21it/s]

But it's been 12 hours, and it's still stuck here with no changes

[kuangzhuoran]

I ran the analysis separately for each chromosome. This chromosome is 209 Mb long, and I also tried the shortest chromosome (37 Mb), but encountered the same issue.

[kuangzhuoran]

CPU usage is not very high.
It seems that the whole process has become a zombie process.

[kuangzhuoran]

If I add -w parameter, like:
"gimble gridsearch -z analysis/Chr29.z -g makegrid/Chr29.BA -d tally/windows_kmax2 -p 5 -f -w"

I can see the ouput file was generated:
Chr29.gridsearch_windows_kmax2.windowsum_makegrid_0.best.bed
Chr29.gridsearch_windows_kmax2.windowsum_makegrid_0.sliced_param.me.bed

[kuangzhuoran]

It was probably due to server resource issues.
I re-ran the command while the server was idle and it completed quickly, but now I've encountered a new issue.
Will these error messages affect the output? (ChatGPT told me they won't affect any output.)

Here is:
[%] Gridsearch: 100%|████████████████████████████████████████| 54432/54432 [05:40<00:00, 159.89it/s]

[+] Gridsearch can be accessed with 'gridsearch/windows_kmax2/Chr1.BA'
[*] Total runtime was 00h:25m:50.395s
Traceback (most recent call last):
File "/home/106public/.conda/envs/gimble/lib/python3.8/multiprocessing/process.py", line 315, in _bootstrap
self.run()
File "/home/106public/.conda/envs/gimble/lib/python3.8/multiprocessing/process.py", line 108, in run
self._target(*self._args, **self._kwargs)
File "/home/106public/.conda/envs/gimble/lib/python3.8/multiprocessing/managers.py", line 616, in _run_server
server.serve_forever()
File "/home/106public/.conda/envs/gimble/lib/python3.8/multiprocessing/managers.py", line 182, in serve_forever
sys.exit(0)
SystemExit: 0

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "/home/106public/.conda/envs/gimble/lib/python3.8/multiprocessing/util.py", line 300, in _run_finalizers
finalizer()
File "/home/106public/.conda/envs/gimble/lib/python3.8/multiprocessing/util.py", line 224, in call
res = self._callback(*self._args, **self._kwargs)
File "/home/106public/.conda/envs/gimble/lib/python3.8/multiprocessing/util.py", line 133, in _remove_temp_dir
rmtree(tempdir)
File "/home/106public/.conda/envs/gimble/lib/python3.8/shutil.py", line 718, in rmtree
_rmtree_safe_fd(fd, path, onerror)
File "/home/106public/.conda/envs/gimble/lib/python3.8/shutil.py", line 675, in _rmtree_safe_fd
onerror(os.unlink, fullname, sys.exc_info())
File "/home/106public/.conda/envs/gimble/lib/python3.8/shutil.py", line 673, in _rmtree_safe_fd
os.unlink(entry.name, dir_fd=topfd)
OSError: [Errno 16] Device or resource busy: '.nfs000000003cbe9d5200000006'