Issue using docker container with Kilosort 2 and 2.5 : error while loading shared libraries

[jmcdaniel2]

Hi all,
When I am trying to use kilosort 2 or 2.5 through the use of a docker container I get the following error

"ks2_5_compiled: error while loading shared libraries: /opt/matlabruntime/R2022b/sys/os/glnxa64/libstdc++.so.6: file too short"

The code I am using to run the sorter is

import spikeinterface.full as si

basepath = Path(r"D:\Ephys\20250611_LY_TS232F\Record Node 101\experiment1")
rec3 = si.read_openephys(basepath / 'recording3',stream_name='Record Node 101#OneBox-100.ProbeA-AP') 

params = si.get_default_sorter_params('kilosort2_5')
sorting_KS2 = si.run_sorter('kilosort2_5',rec3, folder = basepath / 'rec3kilosort2_5', verbose = True, docker_image = True,installation_mode = 'pypi',**params)

Any help figuring this out would be greatly appreciated!

[samuelgarcia]

Oups. This looks like a deep and painfull bug in the built container.
@alejoe91 : do you still have residual of power to handle this docker ks2 stuff ?

[alejoe91]

Can you share the full trace?

@samuelgarcia I plan to rebuild the matlab containers with a newer Python version sometimes next week

[jmcdaniel2]

I attached the spike interface log file and this is the trace but I deleted the lines where it was writing the binary recording

SpikeSortingError                         Traceback (most recent call last)
Cell In[15], [line 1](vscode-notebook-cell:?execution_count=15&line=1)
----> [1](vscode-notebook-cell:?execution_count=15&line=1) sorting_KS2 = si.run_sorter('kilosort2',rec3, folder = basepath / 'rec3kilosort2', verbose = True, docker_image=True,**params)

File c:\Users\Lab\.conda\envs\kilosort\lib\site-packages\spikeinterface\sorters\runsorter.py:192, in run_sorter(sorter_name, recording, folder, remove_existing_folder, delete_output_folder, verbose, raise_error, docker_image, singularity_image, delete_container_files, with_output, output_folder, **sorter_params)
    186         if not has_spython():
    187             raise RuntimeError(
    188                 "The python `spython` package must be installed to "
    189                 "run singularity. Install with `pip install spython`"
    190             )
--> [192](file:///C:/Users/Lab/.conda/envs/kilosort/lib/site-packages/spikeinterface/sorters/runsorter.py:192)     return run_sorter_container(
    193         container_image=container_image,
    194         mode=mode,
    195         **common_kwargs,
    196     )
    198 return run_sorter_local(**common_kwargs)

File c:\Users\Lab\.conda\envs\kilosort\lib\site-packages\spikeinterface\sorters\runsorter.py:647, in run_sorter_container(sorter_name, recording, mode, container_image, folder, remove_existing_folder, delete_output_folder, verbose, raise_error, with_output, delete_container_files, extra_requirements, installation_mode, spikeinterface_version, spikeinterface_folder_source, output_folder, **sorter_params)
    645 if run_error:
    646     if raise_error:
--> [647](file:///C:/Users/Lab/.conda/envs/kilosort/lib/site-packages/spikeinterface/sorters/runsorter.py:647)         raise SpikeSortingError(f"Spike sorting in {mode} failed with the following error:\n{run_sorter_output}")
    648 else:
    649     if with_output:

SpikeSortingError: Spike sorting in docker failed with the following error:
/Ephys/20250611_LY_TS232F/Record Node 101/experiment1/in_container_sorter_script.py:23: DeprecationWarning: `output_folder` is deprecated and will be removed in version 0.103.0 Please use folder instead
  sorting = run_sorter_local(

Traceback (most recent call last):
  File "/Ephys/20250611_LY_TS232F/Record Node 101/experiment1/in_container_sorter_script.py", line 23, in <module>
RUNNING SHELL SCRIPT: /Ephys/20250611_LY_TS232F/Record Node 101/experiment1/rec3kilosort2/sorter_output/run_kilosort2.sh
ks2_compiled: error while loading shared libraries: /opt/matlabruntime/R2022b/sys/os/glnxa64/libstdc++.so.6: file too short

Error running kilosort2
    sorting = run_sorter_local(
  File "/root/.local/lib/python3.9/site-packages/spikeinterface/sorters/runsorter.py", line 260, in run_sorter_local
    SorterClass.run_from_folder(folder, raise_error, verbose)
  File "/root/.local/lib/python3.9/site-packages/spikeinterface/sorters/basesorter.py", line 310, in run_from_folder
    raise SpikeSortingError(
spikeinterface.sorters.utils.misc.SpikeSortingError: Spike sorting error trace:
Traceback (most recent call last):
  File "/root/.local/lib/python3.9/site-packages/spikeinterface/sorters/basesorter.py", line 270, in run_from_folder
    SorterClass._run_from_folder(sorter_output_folder, sorter_params, verbose)
  File "/root/.local/lib/python3.9/site-packages/spikeinterface/sorters/external/kilosortbase.py", line 217, in _run_from_folder
    raise Exception(f"{cls.sorter_name} returned a non-zero exit code")
Exception: kilosort2 returned a non-zero exit code

Spike sorting failed. You can inspect the runtime trace in /Ephys/20250611_LY_TS232F/Record Node 101/experiment1/rec3kilosort2/spikeinterface_log.json.

spikeinterface_log.json