marker icon indicating copy to clipboard operation
marker copied to clipboard
verified publisher icon datalab-to

Seg-fault running marker_single, likely caused by unstable Torch version

Open SidSethi opened this issue 7 months ago • 8 comments

Env

  • macOS 15, M-series Mac
  • Python 3.13.3 (Homebrew)
  • marker-pdf 1.7.2 (pipx install marker-pdf[full])
  • torch 2.7.0

Repro

> GOOGLE_API_KEY=... marker_single 'filename.pdf' --output_format markdown --use_llm --format_lines

Recognizing layout: 100%|██████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 8/8 [00:09<00:00,  1.18s/it]
LLM layout relabelling: 3it [00:01,  2.14it/s]
Running OCR Error Detection: 100%|███████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 12/12 [00:00<00:00, 17.09it/s]
Detecting bboxes: 100%|██████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 12/12 [00:05<00:00,  2.35it/s]
Recognizing Text:   3%|████▉                                                                                                                                                                                       | 53/2032 [00:10<05:06,  6.45it/s]
zsh: segmentation fault  GOOGLE_API_KEY=... marker_single
/opt/homebrew/Cellar/[email protected]/3.13.3_1/Frameworks/Python.framework/Versions/3.13/lib/python3.13/multiprocessing/resource_tracker.py:301: UserWarning: resource_tracker: There appear to be 1 leaked semaphore objects to clean up at shutdown: {'/loky-16920-_odxfu43'}
  warnings.warn(

Work-arounds

  1. TORCH_DEVICE=cpu marker_single … → works (no GPU).
  2. Reinstall on Python 3.12: pipx reinstall marker-pdf --python python3.12 → works with MPS.

Likely Cause Torch 2.3 MPS backend is still unstable on Python 3.13; Marker’s multi-process OCR hits a semaphore bug.

Suggestion

  • Warn or auto-set TORCH_DEVICE=cpu when running on py 3.13 + macOS, or
  • Pin requires-python to < 3.13 until Torch fixes MPS.

SidSethi avatar May 21 '25 22:05 SidSethi

I am still getting segfaults on apple silicon using python 3.11.11, with device=cpu, only happens with --force_ocr flag set

malibrated avatar May 24 '25 03:05 malibrated

I get the same error - unless I omit "--format_lines". Without that, it works. Tried with device=cpu and device=mps

dirk-fr avatar May 30 '25 20:05 dirk-fr

@dirk-fr @SidSethi @malibrated

Can you try with a newer version of marker? We fixed a bug in surya (which is packaged with marker) to bring down the VRAM in non flash-attention environments, which is probably the source of the error for y'all.

tarun-menta avatar Jun 25 '25 20:06 tarun-menta

still breaks on certain PDFs for me, no idea why, see tests below, m3 macbook pro, works on CPU

(base) xxxxx@Xxxxxs-MacBook-Pro ~ % marker_single "/Users/xxxxx/Documents/pdf/06_Annual Reports/1996 Annual Report.pdf"
--processors marker.processors.large_page_to_image.LargePageToImageProcessor \ --output_format markdown --paginate_output --strip_existing_ocr --output_dir "/Users/xxxxx/Documents/pdf/06_Annual Reports" Recognizing layout: 100%|███████████████████████████| 1/1 [00:01<00:00, 1.44s/it] Running OCR Error Detection: 100%|██████████████████| 2/2 [00:00<00:00, 18.68it/s] Detecting bboxes: 100%|█████████████████████████████| 2/2 [00:00<00:00, 2.73it/s] Recognizing Text: 0%| | 0/897 [00:00<?, ?it/s]zsh: segmentation fault marker_single --processors --output_format markdown --paginate_output
(base) xxxxx@Xxxxxs-MacBook-Pro ~ % /opt/anaconda3/lib/python3.12/multiprocessing/resource_tracker.py:254: UserWarning: resource_tracker: There appear to be 1 leaked semaphore objects to clean up at shutdown warnings.warn('resource_tracker: There appear to be %d '

(base) xxxxx@Xxxxxs-MacBook-Pro ~ % marker_single "/Users/xxxxx/Documents/pdf/06_Annual Reports/1996 Annual Report.pdf" --output_format markdown --paginate_output --strip_existing_ocr --output_dir "/Users/xxxxx/Documents/pdf/06_Annual Reports" Recognizing layout: 100%|███████████████████████████| 1/1 [00:01<00:00, 1.45s/it] Running OCR Error Detection: 100%|██████████████████| 2/2 [00:00<00:00, 18.60it/s] Detecting bboxes: 100%|█████████████████████████████| 2/2 [00:00<00:00, 2.72it/s] Recognizing Text: 0%| | 0/897 [00:00<?, ?it/s]zsh: segmentation fault marker_single --output_format markdown --paginate_output --strip_existing_oc (base) xxxxx@Xxxxxs-MacBook-Pro ~ % /opt/anaconda3/lib/python3.12/multiprocessing/resource_tracker.py:254: UserWarning: resource_tracker: There appear to be 1 leaked semaphore objects to clean up at shutdown warnings.warn('resource_tracker: There appear to be %d '

(base) xxxxx@Xxxxxs-MacBook-Pro ~ % TORCH_DEVICE=cpu OMP_NUM_THREADS=1 MKL_NUM_THREADS=1
marker_single "/Users/xxxxx/Documents/pdf/06_Annual Reports/1996 Annual Report.pdf"
--output_format markdown
--paginate_output
--strip_existing_ocr
--output_dir "/Users/xxxxx/Documents/pdf/06_Annual Reports" Recognizing layout: 100%|███████████████████████████| 1/1 [00:05<00:00, 5.83s/it] Running OCR Error Detection: 100%|██████████████████| 2/2 [00:00<00:00, 72.70it/s] Detecting bboxes: 100%|█████████████████████████████| 2/2 [00:08<00:00, 4.05s/it] Recognizing Text: 100%|█████████████████████████| 896/896 [04:11<00:00, 3.56it/s] Detecting bboxes: 100%|█████████████████████████████| 1/1 [00:03<00:00, 3.02s/it] Recognizing Text: 100%|███████████████████████████| 96/96 [00:18<00:00, 5.14it/s] Recognizing tables: 100%|███████████████████████████| 1/1 [00:02<00:00, 2.68s/it] 2025-06-26 11:17:49,099 [INFO] marker: Saved markdown to /Users/xxxxx/Documents/pdf/06_Annual Reports/1996 Annual Report 2025-06-26 11:17:49,099 [INFO] marker: Total time: 292.76327896118164

(base) xxxxx@Xxxxxs-MacBook-Pro ~ % python -m pip show marker-pdf
Name: marker-pdf Version: 1.7.5 Summary: Convert documents to markdown with high speed and accuracy. Home-page: Author: Vik Paruchuri Author-email: [email protected] License: GPL-3.0-or-later Location: /opt/anaconda3/lib/python3.12/site-packages Requires: anthropic, click, filetype, ftfy, google-genai, markdown2, markdownify, openai, pdftext, Pillow, pre-commit, pydantic, pydantic-settings, python-dotenv, rapidfuzz, regex, scikit-learn, surya-ocr, torch, tqdm, transformers Required-by:

kllgjc avatar Jun 26 '25 15:06 kllgjc

still breaks on certain PDFs for me, no idea why, see tests below, m3 macbook pro, works on CPU

(base) xxxxx@Xxxxxs-MacBook-Pro ~ % marker_single "/Users/xxxxx/Documents/pdf/06_Annual Reports/1996 Annual Report.pdf" --processors marker.processors.large_page_to_image.LargePageToImageProcessor \ --output_format markdown --paginate_output --strip_existing_ocr --output_dir "/Users/xxxxx/Documents/pdf/06_Annual Reports" Recognizing layout: 100%|███████████████████████████| 1/1 [00:01<00:00, 1.44s/it] Running OCR Error Detection: 100%|██████████████████| 2/2 [00:00<00:00, 18.68it/s] Detecting bboxes: 100%|█████████████████████████████| 2/2 [00:00<00:00, 2.73it/s] Recognizing Text: 0%| | 0/897 [00:00<?, ?it/s]zsh: segmentation fault marker_single --processors --output_format markdown --paginate_output (base) xxxxx@Xxxxxs-MacBook-Pro ~ % /opt/anaconda3/lib/python3.12/multiprocessing/resource_tracker.py:254: UserWarning: resource_tracker: There appear to be 1 leaked semaphore objects to clean up at shutdown warnings.warn('resource_tracker: There appear to be %d '

(base) xxxxx@Xxxxxs-MacBook-Pro ~ % marker_single "/Users/xxxxx/Documents/pdf/06_Annual Reports/1996 Annual Report.pdf" --output_format markdown --paginate_output --strip_existing_ocr --output_dir "/Users/xxxxx/Documents/pdf/06_Annual Reports" Recognizing layout: 100%|███████████████████████████| 1/1 [00:01<00:00, 1.45s/it] Running OCR Error Detection: 100%|██████████████████| 2/2 [00:00<00:00, 18.60it/s] Detecting bboxes: 100%|█████████████████████████████| 2/2 [00:00<00:00, 2.72it/s] Recognizing Text: 0%| | 0/897 [00:00<?, ?it/s]zsh: segmentation fault marker_single --output_format markdown --paginate_output --strip_existing_oc (base) xxxxx@Xxxxxs-MacBook-Pro ~ % /opt/anaconda3/lib/python3.12/multiprocessing/resource_tracker.py:254: UserWarning: resource_tracker: There appear to be 1 leaked semaphore objects to clean up at shutdown warnings.warn('resource_tracker: There appear to be %d '

(base) xxxxx@Xxxxxs-MacBook-Pro ~ % TORCH_DEVICE=cpu OMP_NUM_THREADS=1 MKL_NUM_THREADS=1 marker_single "/Users/xxxxx/Documents/pdf/06_Annual Reports/1996 Annual Report.pdf" --output_format markdown --paginate_output --strip_existing_ocr --output_dir "/Users/xxxxx/Documents/pdf/06_Annual Reports" Recognizing layout: 100%|███████████████████████████| 1/1 [00:05<00:00, 5.83s/it] Running OCR Error Detection: 100%|██████████████████| 2/2 [00:00<00:00, 72.70it/s] Detecting bboxes: 100%|█████████████████████████████| 2/2 [00:08<00:00, 4.05s/it] Recognizing Text: 100%|█████████████████████████| 896/896 [04:11<00:00, 3.56it/s] Detecting bboxes: 100%|█████████████████████████████| 1/1 [00:03<00:00, 3.02s/it] Recognizing Text: 100%|███████████████████████████| 96/96 [00:18<00:00, 5.14it/s] Recognizing tables: 100%|███████████████████████████| 1/1 [00:02<00:00, 2.68s/it] 2025-06-26 11:17:49,099 [INFO] marker: Saved markdown to /Users/xxxxx/Documents/pdf/06_Annual Reports/1996 Annual Report 2025-06-26 11:17:49,099 [INFO] marker: Total time: 292.76327896118164

(base) xxxxx@Xxxxxs-MacBook-Pro ~ % python -m pip show marker-pdf Name: marker-pdf Version: 1.7.5 Summary: Convert documents to markdown with high speed and accuracy. Home-page: Author: Vik Paruchuri Author-email: [email protected] License: GPL-3.0-or-later Location: /opt/anaconda3/lib/python3.12/site-packages Requires: anthropic, click, filetype, ftfy, google-genai, markdown2, markdownify, openai, pdftext, Pillow, pre-commit, pydantic, pydantic-settings, python-dotenv, rapidfuzz, regex, scikit-learn, surya-ocr, torch, tqdm, transformers Required-by:

same +1. works only for certain PDFs.

Radar-Lei avatar Jul 08 '25 12:07 Radar-Lei

I got the same errors with python 3.13 & 3.12 while process a 800 pages pdf, with or without --recognition_batch_size. My macbook is M1 64GB. Reduce the batch_size only make it crash earlier.

However when I reduce the pages with --page_range "0-300", it no longer crash with segmentation fault. But then I have to use export TORCH_DEVICE=cpu to fix the RuntimeError: stack expects a non-empty TensorList error.

tl;dr: use export TORCH_DEVICE=cpu and --page_range to reduce the pages works for me.

taiansu avatar Aug 13 '25 22:08 taiansu

got the same error with python 3.13 & 3.12 while processing a 100 pages pdf. export TORCH_DEVICE=cpu solved the problem

Omarov3000 avatar Aug 20 '25 17:08 Omarov3000

Same error with most files

ma-r-s avatar Aug 28 '25 05:08 ma-r-s