SpikeInterface / SpikeInterface/spikeinterface

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

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#3,998 3 comments 0 reactions 1 assignee View on GitHub

@alejoe91 is already working on this.

Since Jun 19, 2025.

container sorters
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Description

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!

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