Hi, while using the inference PanNuke checkpoint, I have been encountering the following problems. Do you have a potential solution for that?
here's my code:
py run_infer.py --gpu="0,1" --nr_types=6 --type_info_path="C:\Users\Downloads\hover_net-master\hover_net-master\type_info.json" --batch_size=32 --model_mode=fast --model_path="C:\Users\Downloads\hovernet_fast_pannuke_type_tf2pytorch.tar" --nr_inference_workers=1 --nr_post_proc_workers=8 wsi --input_dir="C:\Users\Downloads\Dataset\sample_wsis" --output_dir="C:\Users\Downloads\Dataset\output" --proc_mag=40 --save_mask --save_thumb
here's the error message:
|2022-12-01|06:21:27.509| [INFO] .... Detect #GPUS: 1
|2022-12-01|06:21:29.509| [INFO] ................ Process: 74833
|2022-12-01|06:21:56.497| [INFO] ............ WARNING: No mask found, generating mask via thresholding at 1.25x!
|2022-12-01|06:21:57.468| [INFO] ........ Preparing Input Output Placement: 27.9592747
Process Chunk 0/16: 100%|#########################| 1/1 [00:32<00:00, 32.05s/it]
Process Chunk 1/16: 100%|#####################| 73/73 [1:19:30<00:00, 65.35s/it]
Process Chunk 4/16: 100%|#########################| 1/1 [00:29<00:00, 29.68s/it]
Process Chunk 5/16: 100%|#######################| 10/10 [10:32<00:00, 63.29s/it]
Process Chunk 6/16: 100%|#######################| 32/32 [34:29<00:00, 64.67s/it]
Process Chunk 7/16: 100%|#########################| 5/5 [04:43<00:00, 56.68s/it]
Process Chunk 8/16: 100%|#######################| 34/34 [36:08<00:00, 63.77s/it]
Process Chunk 9/16: 100%|#######################| 17/17 [17:33<00:00, 61.97s/it]
Process Chunk 10/16: 100%|######################| 16/16 [17:21<00:00, 65.08s/it]
Process Chunk 11/16: 100%|########################| 1/1 [01:04<00:00, 64.91s/it]
|2022-12-01|09:45:00.969| [INFO] ........ Inference Time: 12183.417727600001
Post Proc Phase 1: 100%|########################| 70/70 [00:57<00:00, 1.21it/s]
Post Proc Phase 2: 0%| | 0/106 [00:00<?, ?it/s]Traceback (most recent call last):
File "", line 1, in
Traceback (most recent call last):
Traceback (most recent call last):
File "C:\Users\AppData\Local\Programs\Python\Python39\lib\multiprocessing\spawn.py", line 116, in spawn_main
Traceback (most recent call last):
File "", line 1, in
File "", line 1, in
exitcode = _main(fd, parent_sentinel)
File "", line 1, in
File "C:\Users\AppData\Local\Programs\Python\Python39\lib\multiprocessing\spawn.py", line 116, in spawn_main
Traceback (most recent call last):
File "", line 1, in
File "C:\Users\AppData\Local\Programs\Python\Python39\lib\multiprocessing\spawn.py", line 116, in spawn_main
exitcode = _main(fd, parent_sentinel)
exitcode = _main(fd, parent_sentinel)
File "C:\Users\AppData\Local\Programs\Python\Python39\lib\multiprocessing\spawn.py", line 116, in spawn_main
File "C:\Users\AppData\Local\Programs\Python\Python39\lib\multiprocessing\spawn.py", line 125, in _main
File "C:\Users\AppData\Local\Programs\Python\Python39\lib\multiprocessing\spawn.py", line 116, in spawn_main
File "C:\Users\AppData\Local\Programs\Python\Python39\lib\multiprocessing\spawn.py", line 125, in _main
File "C:\Users\AppData\Local\Programs\Python\Python39\lib\multiprocessing\spawn.py", line 125, in _main
exitcode = _main(fd, parent_sentinel)
File "C:\Users\AppData\Local\Programs\Python\Python39\lib\multiprocessing\spawn.py", line 125, in _main
prepare(preparation_data)
File "C:\Users\AppData\Local\Programs\Python\Python39\lib\multiprocessing\spawn.py", line 236, in prepare
_fixup_main_from_path(data['init_main_from_path'])
File "C:\Users\AppData\Local\Programs\Python\Python39\lib\multiprocessing\spawn.py", line 287, in _fixup_main_from_path
main_content = runpy.run_path(main_path,
File "C:\Users\AppData\Local\Programs\Python\Python39\lib\runpy.py", line 268, in run_path
return _run_module_code(code, init_globals, run_name,
prepare(preparation_data)
File "C:\Users\AppData\Local\Programs\Python\Python39\lib\multiprocessing\spawn.py", line 236, in prepare
prepare(preparation_data)
File "C:\Users\AppData\Local\Programs\Python\Python39\lib\multiprocessing\spawn.py", line 236, in prepare
prepare(preparation_data)
_fixup_main_from_path(data['init_main_from_path'])
File "C:\Users\AppData\Local\Programs\Python\Python39\lib\runpy.py", line 97, in _run_module_code
_fixup_main_from_path(data['init_main_from_path'])
File "C:\Users\AppData\Local\Programs\Python\Python39\lib\multiprocessing\spawn.py", line 236, in prepare
exitcode = _main(fd, parent_sentinel)
File "C:\Users\AppData\Local\Programs\Python\Python39\lib\multiprocessing\spawn.py", line 125, in _main
_run_code(code, mod_globals, init_globals,
File "C:\Users\AppData\Local\Programs\Python\Python39\lib\runpy.py", line 87, in _run_code
prepare(preparation_data)
File "C:\Users\AppData\Local\Programs\Python\Python39\lib\multiprocessing\spawn.py", line 236, in prepare
_fixup_main_from_path(data['init_main_from_path'])
exec(code, run_globals)
File "C:\Users\Downloads\hover_net-master\hover_net-master\run_infer.py", line 74, in
_fixup_main_from_path(data['init_main_from_path'])
File "C:\Users\AppData\Local\Programs\Python\Python39\lib\multiprocessing\spawn.py", line 287, in _fixup_main_from_path
File "C:\Users\AppData\Local\Programs\Python\Python39\lib\multiprocessing\spawn.py", line 287, in _fixup_main_from_path
File "C:\Users\AppData\Local\Programs\Python\Python39\lib\multiprocessing\spawn.py", line 287, in fixup_main_from_path
import torch
main_content = runpy.run_path(main_path,
File "C:\Users\AppData\Local\Programs\Python\Python39\lib\runpy.py", line 268, in run_path
main_content = runpy.run_path(main_path,
File "C:\Users\AppData\Local\Programs\Python\Python39\lib\runpy.py", line 268, in run_path
File "C:\Users\AppData\Local\Programs\Python\Python39\lib\site-packages\torch_init.py", line 129, in
main_content = runpy.run_path(main_path,
File "C:\Users\AppData\Local\Programs\Python\Python39\lib\runpy.py", line 268, in run_path
return _run_module_code(code, init_globals, run_name,
return _run_module_code(code, init_globals, run_name,
File "C:\Users\AppData\Local\Programs\Python\Python39\lib\multiprocessing\spawn.py", line 287, in _fixup_main_from_path
raise err
File "C:\Users\AppData\Local\Programs\Python\Python39\lib\runpy.py", line 97, in _run_module_code
return _run_module_code(code, init_globals, run_name,
File "C:\Users\AppData\Local\Programs\Python\Python39\lib\runpy.py", line 97, in _run_module_code
main_content = runpy.run_path(main_path,
OSError: [WinError 1455] The paging file is too small for this operation to complete. Error loading "C:\Users\AppData\Local\Programs\Python\Python39\lib\site-packages\torch\lib\cufft64_10.dll" or one of its dependencies.
_run_code(code, mod_globals, init_globals,
File "C:\Users\AppData\Local\Programs\Python\Python39\lib\runpy.py", line 97, in _run_module_code
_run_code(code, mod_globals, init_globals,
File "C:\Users\AppData\Local\Programs\Python\Python39\lib\runpy.py", line 268, in run_path
File "C:\Users\AppData\Local\Programs\Python\Python39\lib\runpy.py", line 87, in _run_code
File "C:\Users\AppData\Local\Programs\Python\Python39\lib\runpy.py", line 87, in _run_code
_run_code(code, mod_globals, init_globals,
return _run_module_code(code, init_globals, run_name,
exec(code, run_globals)
File "C:\Users\AppData\Local\Programs\Python\Python39\lib\runpy.py", line 87, in run_code
exec(code, run_globals)
File "C:\Users\AppData\Local\Programs\Python\Python39\lib\runpy.py", line 97, in run_module_code
File "C:\Users\Downloads\hover_net-master\hover_net-master\run_infer.py", line 74, in
exec(code, run_globals)
File "C:\Users\Downloads\hover_net-master\hover_net-master\run_infer.py", line 74, in
run_code(code, mod_globals, init_globals,
import torch
File "C:\Users\Downloads\hover_net-master\hover_net-master\run_infer.py", line 74, in
import torch
File "C:\Users\AppData\Local\Programs\Python\Python39\lib\runpy.py", line 87, in run_code
File "C:\Users\AppData\Local\Programs\Python\Python39\lib\site-packages\torch_init.py", line 129, in
import torch
File "C:\Users\AppData\Local\Programs\Python\Python39\lib\site-packages\torch_init.py", line 129, in
exec(code, run_globals)
File "C:\Users\Downloads\hover_net-master\hover_net-master\run_infer.py", line 74, in
File "C:\Users\AppData\Local\Programs\Python\Python39\lib\site-packages\torch_init.py", line 129, in
raise err
raise err
import torch
raise err
OSError: [WinError 1455] The paging file is too small for this operation to complete. Error loading "C:\Users\AppData\Local\Programs\Python\Python39\lib\site-packages\torch\lib\cufft64_10.dll" or one of its dependencies.
OSError: [WinError 1455] The paging file is too small for this operation to complete. Error loading "C:\Users\AppData\Local\Programs\Python\Python39\lib\site-packages\torch\lib\cufft64_10.dll" or one of its dependencies.
File "C:\Users\AppData\Local\Programs\Python\Python39\lib\site-packages\torch_init.py", line 129, in
OSError: [WinError 1455] The paging file is too small for this operation to complete. Error loading "C:\Users\AppData\Local\Programs\Python\Python39\lib\site-packages\torch\lib\cudnn_cnn_infer64_8.dll" or one of its dependencies.
raise err
OSError: [WinError 1455] The paging file is too small for this operation to complete. Error loading "C:\Users\AppData\Local\Programs\Python\Python39\lib\site-packages\torch\lib\cusolver64_11.dll" or one of its dependencies.
|2022-12-01|09:45:59.795| [ERROR] Crash
Traceback (most recent call last):
File "C:\Users\Downloads\hover_net-master\hover_net-master\infer\wsi.py", line 746, in process_wsi_list
self.process_single_file(wsi_path, msk_path, self.output_dir)
File "C:\Users\Downloads\hover_net-master\hover_net-master\infer\wsi.py", line 689, in process_single_file
self.__dispatch_post_processing(
File "C:\Users\Downloads\hover_net-master\hover_net-master\infer\wsi.py", line 435, in __dispatch_post_processing
assert not silent_crash
AssertionError
Post Proc Phase 2: 0%| | 0/106 [00:00<?, ?it/s]
Traceback (most recent call last):
File "C:\Users\Downloads\hover_net-master\hover_net-master\run_infer.py", line 186, in
infer.process_wsi_list(run_args)
File "C:\Users\Downloads\hover_net-master\hover_net-master\infer\wsi.py", line 750, in process_wsi_list
rm_n_mkdir(self.cache_path) # clean up all cache
File "C:\Users\Downloads\hover_net-master\hover_net-master\misc\utils.py", line 59, in rm_n_mkdir
shutil.rmtree(dir_path)
File "C:\Users\AppData\Local\Programs\Python\Python39\lib\shutil.py", line 740, in rmtree
return _rmtree_unsafe(path, onerror)
File "C:\Users\AppData\Local\Programs\Python\Python39\lib\shutil.py", line 618, in _rmtree_unsafe
onerror(os.unlink, fullname, sys.exc_info())
File "C:\Users\AppData\Local\Programs\Python\Python39\lib\shutil.py", line 616, in _rmtree_unsafe
os.unlink(fullname)
PermissionError: [WinError 32] The process cannot access the file because it is being used by another process: 'cache\pred_inst.npy'`
vqdang
