Comments (7)
Accompany0313
commented on September 21, 2024
Hi,
Have you solved your problem? I had the same problem.
Thanks！
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GMFranceschini
commented on September 21, 2024
Unfortunately, it has not been solved so far.
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ruochiz
commented on September 21, 2024
For debugging purpose, if you set, OMP_NUM_THREADS=1 in environment, would that change the observed behavior? I agree that this multiprocessing + global variable function is probably the stuck point.
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GMFranceschini
commented on September 21, 2024
So, in the environment, I do:
export OMP_NUM_THREADS=1
Then, I run the script, but it gets stuck as before with no additional info.
Also, I tried to do:
train_pool = ProcessPoolExecutor(max_workers=1)
But I have the same problem.
I know that some iterations run until the end of one_threads_generate_neg() because I added a print right before the return. In the case of a single process, a couple of iterations are complete, and then it hangs.
I am currently trying to use pdb to get a more precise idea of where the problem is.
This is what I get when I do a keyboard interrupt with CTRL+C (I don't know if this is useful):
^CTraceback (most recent call last):
File "/work/FAC/FBM/DBC/gciriell/default/gianmarco/schic/Higashi/scripts/WGD_FH.py", line 37, in <module>
higashi_model.train_for_imputation_nbr_0()
File "/work/FAC/FBM/DBC/gciriell/default/gianmarco/tools/mamba_root/envs/higashi_local/lib/python3.9/site-packages/higashi/Higashi_wrapper.py", line 1336, in train_for_imputation_nbr_0
self.train_for_imputation_no_nbr()
File "/work/FAC/FBM/DBC/gciriell/default/gianmarco/tools/mamba_root/envs/higashi_local/lib/python3.9/site-packages/higashi/Higashi_wrapper.py", line 1394, in train_for_imputation_no_nbr
self.train(
File "/work/FAC/FBM/DBC/gciriell/default/gianmarco/tools/mamba_root/envs/higashi_local/lib/python3.9/site-packages/higashi/Higashi_wrapper.py", line 1099, in train
bce_loss, mse_loss, train_accu, auc1, auc2, str1, str2, train_pool, train_p_list = self.train_epoch(
File "/work/FAC/FBM/DBC/gciriell/default/gianmarco/tools/mamba_root/envs/higashi_local/lib/python3.9/site-packages/higashi/Higashi_wrapper.py", line 897, in train_epoch
for p in as_completed(train_p_list):
File "/work/FAC/FBM/DBC/gciriell/default/gianmarco/tools/mamba_root/envs/higashi_local/lib/python3.9/concurrent/futures/_base.py", line 245, in as_completed
waiter.event.wait(wait_timeout)
File "/work/FAC/FBM/DBC/gciriell/default/gianmarco/tools/mamba_root/envs/higashi_local/lib/python3.9/threading.py", line 581, in wait
signaled = self._cond.wait(timeout)
File "/work/FAC/FBM/DBC/gciriell/default/gianmarco/tools/mamba_root/envs/higashi_local/lib/python3.9/threading.py", line 312, in wait
waiter.acquire()
KeyboardInterrupt
^CException ignored in: <module 'threading' from '/work/FAC/FBM/DBC/gciriell/default/gianmarco/tools/mamba_root/envs/higashi_local/lib/python3.9/threading.py'>
Traceback (most recent call last):
File "/work/FAC/FBM/DBC/gciriell/default/gianmarco/tools/mamba_root/envs/higashi_local/lib/python3.9/threading.py", line 1447, in _shutdown
atexit_call()
File "/work/FAC/FBM/DBC/gciriell/default/gianmarco/tools/mamba_root/envs/higashi_local/lib/python3.9/concurrent/futures/process.py", line 95, in _python_exit
t.join()
File "/work/FAC/FBM/DBC/gciriell/default/gianmarco/tools/mamba_root/envs/higashi_local/lib/python3.9/threading.py", line 1060, in join
self._wait_for_tstate_lock()
File "/work/FAC/FBM/DBC/gciriell/default/gianmarco/tools/mamba_root/envs/higashi_local/lib/python3.9/threading.py", line 1080, in _wait_for_tstate_lock
if lock.acquire(block, timeout):
KeyboardInterrupt:
^CError in atexit._run_exitfuncs:
Traceback (most recent call last):
File "/work/FAC/FBM/DBC/gciriell/default/gianmarco/tools/mamba_root/envs/higashi_local/lib/python3.9/multiprocessing/popen_fork.py", line 27, in poll
pid, sts = os.waitpid(self.pid, flag)
KeyboardInterrupt
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ruochiz
commented on September 21, 2024
That's very strange.... Cuz these 3 parameters would have default values anyway...
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Accompany0313
commented on September 21, 2024
There's a problem. I can't run it now without setting those three parameters. I feel like there's something wrong with my environment.
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GMFranceschini
commented on September 21, 2024
If I can help you identify the problem somehow, please let me know. I'm happy to put some time into it.
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