Kilosort3 container issue

[ghost]

Hi,

I'm trying to get kilosort3 to run inside a singularity container. I'm running it on a cluster gpu node with a rtx2080ti gpu. I can get pykilosort to work in a container just fine, but would like to run kilosort3 as this is the latest version. I've tried installing a number of different versions of spikeinterface locally and inside the container, from 0.97.1 up to the latest version, but all of them give the following index error:

"Warning: X does not support locale C.UTF-8", "Time 0s. Computing whitening matrix..", "Getting channel whitening matrix...", "Channel-whitening matrix computed.", "Time 6s. Loading raw data and applying filters...", "Time 8s. Finished preprocessing 220 batches.", "Drift correction ENABLED", "vertical pitch size is 1.000000e+01", "horizontal pitch size is 5", "Columns 1 through 7", "", "-10.0000 -7.5000 -5.0000 -2.5000 0 2.5000 5.0000", "", "Columns 8 through 9", "", "7.5000 10.0000", "", "6", "", "----------------------------------------Index in position 1 exceeds array bounds. Index must not exceed 4."

Does anyone have any idea why this is happening and what I could do to fix it?

Thanks!

[alejoe91]

HI @rbedfordwork

Unfortunately it seems to be related to KS3 specifically.
Can you try to upgrade SpikeInterface to 0.98.2?
Also, are you abel to run KS2.5?

Cheers
Alessio

[ghost]

Yes I've tried both KS3 and KS2.5 with SpikeInterface 0.98.2, and both return the exact same index error.

[alejoe91]

On all datasets? It could be that something specific to that dataset is making the fail...

[samuelgarcia]

Hi. The error is a matlab error and not a spikeinterface error. SO it will be hard to fix this in our side.
As Alessio mention this error is data driven for a situtaion not handled so other dataset should be OK.

[zm711]

@samuelgarcia, seems like the user deleted their account. You want this issue to be open for others or okay to close?

[alejoe91]

I would say OK to close! Thanks for checking @zm711