spikeinterface: ArrayMemoryError when using tridesclous

Hi Sam - no worries, I know you’re super busy. Great idea though about using docker. Unfortunately, I get the error pasted below. @Can, thank you for all your ideas! I’ll try them if I can’t get docker to work. But to answer your first question, the raw file is 20.6GB.

Starting container
Installing spikeinterface==0.95.1 in spikeinterface/tridesclous-base
Installing extra requirements: ['neo']
Running tridesclous sorter inside spikeinterface/tridesclous-base
Stopping container
---------------------------------------------------------------------------
SpikeSortingError                         Traceback (most recent call last)
Input In [9], in <cell line: 17>()
      1 #####################################################
      2 ### Option 1: Run local sorter (recommended) ###########
      3 #####################################################
   (...)
     14 ### Option 2: run sorter directly from docker ###
     15 #####################################################
     16 start_time = time.time()
---> 17 sorting_TDC = ss.run_sorter(
     18     'tridesclous',
     19     recording_saved,
     20     output_folder= '_output_TDC',
     21     remove_existing_folder=True,
     22     detect_threshold=threshold,
     23     docker_image="spikeinterface/tridesclous-base", 
     24     verbose=True,
     25 )
     26 print("--- _output_TDC took %s seconds ---" % (time.time() - start_time))
     27 print(f'Tridesclous found {len(sorting_TDC.get_unit_ids())} units')

File ~\Anaconda3\envs\sienv\lib\site-packages\spikeinterface\sorters\runsorter.py:136, in run_sorter(sorter_name, recording, output_folder, remove_existing_folder, delete_output_folder, verbose, raise_error, docker_image, singularity_image, with_output, **sorter_params)
    134         else:
    135             container_image = singularity_image
--> 136     return run_sorter_container(
    137         container_image=container_image,
    138         mode=mode,
    139         **common_kwargs,
    140     )
    142 return run_sorter_local(**common_kwargs)

File ~\Anaconda3\envs\sienv\lib\site-packages\spikeinterface\sorters\runsorter.py:548, in run_sorter_container(sorter_name, recording, mode, container_image, output_folder, remove_existing_folder, delete_output_folder, verbose, raise_error, with_output, extra_requirements, **sorter_params)
    546 if run_error:
    547     if raise_error:
--> 548         raise SpikeSortingError(
    549             f"Spike sorting in {mode} failed with the following error:\n{run_sorter_output}")
    550 else:
    551     if with_output:

SpikeSortingError: Spike sorting in docker failed with the following error:
b'Traceback (most recent call last):\n  File "/Users/huynh/spike_epsztein/Phan/proj_nexus_v2/in_container_sorter_script.py", line 17, in <module>\n    sorting = run_sorter_local(\n  File "/usr/local/lib/python3.8/site-packages/spikeinterface/sorters/runsorter.py", line 157, in run_sorter_local\n    output_folder = SorterClass.initialize_folder(\n  File "/usr/local/lib/python3.8/site-packages/spikeinterface/sorters/basesorter.py", line 123, in initialize_folder\n    shutil.rmtree(str(output_folder))\n  File "/usr/local/lib/python3.8/shutil.py", line 718, in rmtree\n    _rmtree_safe_fd(fd, path, onerror)\n  File "/usr/local/lib/python3.8/shutil.py", line 655, in _rmtree_safe_fd\n    _rmtree_safe_fd(dirfd, fullname, onerror)\n  File "/usr/local/lib/python3.8/shutil.py", line 655, in _rmtree_safe_fd\n    _rmtree_safe_fd(dirfd, fullname, onerror)\n  File "/usr/local/lib/python3.8/shutil.py", line 675, in _rmtree_safe_fd\n    onerror(os.unlink, fullname, sys.exc_info())\n  File "/usr/local/lib/python3.8/shutil.py", line 673, in _rmtree_safe_fd\n    os.unlink(entry.name, dir_fd=topfd)\nPermissionError: [Errno 13] Permission denied: \'all_peaks.raw\'\n'

Hi Can, thank you for the quick response. Yes, this same data set worked with Kilosort3, Spyking Circus, and Iron Cluster.
I’ll check if the ram is maxed out when I run it. I’ll also loked into Swap. Thanks!

The array is very large, I am not sure if that is normal.

You are out of memory (OOM), how much RAM do you have? You can increase your swap memory, but this will impact performance.

Unless there is a setting for PCs with low RAM on tridesclous, and there is no mistake in your configuration, the best way forward is to get a PC with more RAM.