INFO Extracting tiles from 34 slides (tile_px=256, tile_um=9.9x)
INFO Using 64 processes (pool=fork)
INFO No ROI for TCGA-86-6562-01Z-00-DX1.5dea3015-e606-4837-9f99-ac14f0aa091b, using whole slide.
Speed: ?
Extracting... ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 0% 0/34 ● -:--:--[ERROR:0@5.229] global parallel_impl.cpp:244 WorkerThread 50: Can't spawn new thread: res = 11
[ERROR:0@5.229] global parallel_impl.cpp:244 WorkerThread 51: Can't spawn new thread: res = 11
[ERROR:0@5.229] global parallel_impl.cpp:244 WorkerThread 51: Can't spawn new thread: res = 11
[ERROR:0@5.229] global parallel_impl.cpp:244 WorkerThread 52: Can't spawn new thread: res = 11
[ERROR:0@5.229] global parallel_impl.cpp:244 WorkerThread 52: Can't spawn new thread: res = 11
[ERROR:0@5.229] global parallel_impl.cpp:244 WorkerThread 53: Can't spawn new thread: res = 11
[ERROR:0@5.229] global parallel_impl.cpp:244 WorkerThread 53: Can't spawn new thread: res = 11
[ERROR:0@5.229] global parallel_impl.cpp:244 WorkerThread 54: Can't spawn new thread: res = 11
[ERROR:0@5.229] global parallel_impl.cpp:244 WorkerThread 54: Can't spawn new thread: res = 11
[ERROR:0@5.229] global parallel_impl.cpp:244 WorkerThread 55: Can't spawn new thread: res = 11
[ERROR:0@5.229] global parallel_impl.cpp:244 WorkerThread 55: Can't spawn new thread: res = 11
[ERROR:0@5.229] global parallel_impl.cpp:244 WorkerThread 56: Can't spawn new thread: res = 11
[ERROR:0@5.229] global parallel_impl.cpp:244 WorkerThread 56: Can't spawn new thread: res = 11
[ERROR:0@5.229] global parallel_impl.cpp:244 WorkerThread 57: Can't spawn new thread: res = 11
[ERROR:0@5.229] global parallel_impl.cpp:244 WorkerThread 57: Can't spawn new thread: res = 11
[ERROR:0@5.229] global parallel_impl.cpp:244 WorkerThread 58: Can't spawn new thread: res = 11
[ERROR:0@5.229] global parallel_impl.cpp:244 WorkerThread 58: Can't spawn new thread: res = 11
[ERROR:0@5.229] global parallel_impl.cpp:244 WorkerThread 59: Can't spawn new thread: res = 11
[ERROR:0@5.229] global parallel_impl.cpp:244 WorkerThread 59: Can't spawn new thread: res = 11
[ERROR:0@5.229] global parallel_impl.cpp:244 WorkerThread 60: Can't spawn new thread: res = 11
[ERROR:0@5.229] global parallel_impl.cpp:244 WorkerThread 60: Can't spawn new thread: res = 11
[ERROR:0@5.230] global parallel_impl.cpp:244 WorkerThread 61: Can't spawn new thread: res = 11
[ERROR:0@5.230] global parallel_impl.cpp:244 WorkerThread 61: Can't spawn new thread: res = 11
[ERROR:0@5.230] global parallel_impl.cpp:244 WorkerThread 62: Can't spawn new thread: res = 11
[07:31:39] INFO Finished tile extraction for TCGA-86-6562 (200 tiles of 2953 possible)
INFO No ROI for TCGA-86-7711-01Z-00-DX1.f64dd9d8-b9ca-4d1f-9783-d1042979132d, using whole slide.
Speed: 571 img/s
Extracting... ━╺━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 3% 1/34 ● -:--:--
Traceback (most recent call last):
File "/lus/eagle/clone/g2/projects/GeomicVar/tarak/multimodal_learning_T1/preprocessing/slideflow_preprocessing.py", line 45, in <module>
dataset.extract_tiles(qc='blur', # ‘otsu’, ‘blur’, ‘both’, or None # qc.GaussianV2()
File "/lus/eagle/clone/g2/projects/GeomicVar/tarak/multimodal_learning_T1/slideflow/slideflow/slideflow_scratch_env/lib/python3.9/site-packages/slideflow/dataset.py", line 1762, in extract_tiles
wsi = _prepare_slide(
File "/lus/eagle/clone/g2/projects/GeomicVar/tarak/multimodal_learning_T1/slideflow/slideflow/slideflow_scratch_env/lib/python3.9/site-packages/slideflow/dataset.py", line 140, in _prepare_slide
slide.qc(method=qc, **qc_kwargs)
File "/lus/eagle/clone/g2/projects/GeomicVar/tarak/multimodal_learning_T1/slideflow/slideflow/slideflow_scratch_env/lib/python3.9/site-packages/slideflow/slide/wsi.py", line 2552, in qc
mask = qc(self)
File "/lus/eagle/clone/g2/projects/GeomicVar/tarak/multimodal_learning_T1/slideflow/slideflow/slideflow_scratch_env/lib/python3.9/site-packages/slideflow/slide/qc/gaussian_v2.py", line 125, in __call__
blur_mask = super().__call__(wsi)
File "/lus/eagle/clone/g2/projects/GeomicVar/tarak/multimodal_learning_T1/slideflow/slideflow/slideflow_scratch_env/lib/python3.9/site-packages/slideflow/slide/qc/strided_qc.py", line 379, in __call__
if self.filter_pool is not None:
File "/lus/eagle/clone/g2/projects/GeomicVar/tarak/multimodal_learning_T1/slideflow/slideflow/slideflow_scratch_env/lib/python3.9/site-packages/slideflow/slide/qc/strided_qc.py", line 255, in filter_pool
self._filter_pool = mp.dummy.Pool(self.filter_threads)
File "/lus/eagle/clone/g2/projects/GeomicVar/tarak/multimodal_learning_T1/slideflow/slideflow/slideflow_scratch_env/lib/python3.9/multiprocessing/dummy/__init__.py", line 124, in Pool
return ThreadPool(processes, initializer, initargs)
File "/lus/eagle/clone/g2/projects/GeomicVar/tarak/multimodal_learning_T1/slideflow/slideflow/slideflow_scratch_env/lib/python3.9/multiprocessing/pool.py", line 927, in __init__
Pool.__init__(self, processes, initializer, initargs)
File "/lus/eagle/clone/g2/projects/GeomicVar/tarak/multimodal_learning_T1/slideflow/slideflow/slideflow_scratch_env/lib/python3.9/multiprocessing/pool.py", line 250, in __init__
self._result_handler.start()
File "/lus/eagle/clone/g2/projects/GeomicVar/tarak/multimodal_learning_T1/slideflow/slideflow/slideflow_scratch_env/lib/python3.9/threading.py", line 899, in start
_start_new_thread(self._bootstrap, ())
RuntimeError: can't start new thread
Exception in thread Thread-1:
Traceback (most recent call last):
File "/lus/eagle/clone/g2/projects/GeomicVar/tarak/multimodal_learning_T1/slideflow/slideflow/slideflow_scratch_env/lib/python3.9/threading.py", line 980, in _bootstrap_inner
self.run()
File "/lus/eagle/clone/g2/projects/GeomicVar/tarak/multimodal_learning_T1/slideflow/slideflow/slideflow_scratch_env/lib/python3.9/threading.py", line 917, in run
self._target(*self._args, **self._kwargs)
File "/lus/eagle/clone/g2/projects/GeomicVar/tarak/multimodal_learning_T1/slideflow/slideflow/slideflow_scratch_env/lib/python3.9/multiprocessing/managers.py", line 194, in accepter
t.start()
File "/lus/eagle/clone/g2/projects/GeomicVar/tarak/multimodal_learning_T1/slideflow/slideflow/slideflow_scratch_env/lib/python3.9/threading.py", line 899, in start
_start_new_thread(self._bootstrap, ())
RuntimeError: can't start new thread
Expected behavior
Environment:
Slideflow Version (e.g., 1.0): 2.3.1
OS (e.g., Ubuntu):
How you installed Slideflow (pip, source): Tried using both 'pip install' and install from source
Python version: 3.9
CUDA/cuDNN version: 12.1
GPU models and configuration: A100
Any other relevant information:
Additional context
The issue doesn't arise when 'blur' isn't used (e.g., qc='otsu')
Description
To Reproduce
Steps to reproduce the behavior:
Expected behavior
Environment:
pip, source): Tried using both 'pip install' and install from sourceAdditional context
The issue doesn't arise when 'blur' isn't used (e.g., qc='otsu')