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Error using gpuArray/subsasgn #178

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dervinism opened this issue Jan 15, 2020 · 15 comments · Fixed by #595
Closed

Error using gpuArray/subsasgn #178

dervinism opened this issue Jan 15, 2020 · 15 comments · Fixed by #595

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@dervinism
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The following error comes up when trying to spike sort:

Error using gpuArray/subsasgn
An unexpected error occurred trying to launch a kernel. The CUDA error was:
invalid argument

Error in triageTemplates2 (line 13)
W(:,idrop,:) = []; % remove those templates everywhere

Error in learnTemplates (line 173)
triageTemplates2(ops, iW, C2C, W, U, dWU, mu, nsp, ndrop);

Error in learnAndSolve8b (line 12)
rez = learnTemplates(rez, iorder0);

The error would not occur with an earlier version of kilosort 2.
@marius10p
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How many channels are you spike sorting and how large is your ops.NT? You might want to increase that.

@dervinism
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384 channels and ops.NT = 65600. What is a more appropriate size of ops.NT?

@marius10p
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This should be fine. Does the data look ok in the Matlab GUI? Is the configuration loading ok?

At what point in spike sorting does this occur? Please copy paste the entire command line output.

@dervinism
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The full output is below. I have inspected the data in Neuroscope and it looks fine.

Time 0s. Determining good channels..
found 466760 threshold crossings in 216.48 seconds of data
found 1 bad channels
Time 135s. Computing whitening matrix..
Getting channel whitening matrix...
Channel-whitening matrix computed.
Time 320s. Loading raw data and applying filters...
Time 5519s. Finished preprocessing 5641 batches.
Time 5544s. Optimizing templates ...
5545.54 sec, 1 / 5642 batches, 73 units, nspks: 10.5094, mu: 15.4873, nst0: 148, merges: 0.0000, 0.0000
5650.22 sec, 101 / 5642 batches, 644 units, nspks: 2977.1750, mu: 18.0233, nst0: 2116, merges: 161.0984, 0.8422
5763.19 sec, 201 / 5642 batches, 619 units, nspks: 2605.5461, mu: 16.0886, nst0: 3175, merges: 191.7767, 0.3088
5888.27 sec, 301 / 5642 batches, 709 units, nspks: 7335.9526, mu: 17.0413, nst0: 21916, merges: 181.7466, 0.0375
6325.21 sec, 401 / 5642 batches, 943 units, nspks: 18447.2108, mu: 18.3517, nst0: 17200, merges: 181.5536, 0.6145
6813.57 sec, 501 / 5642 batches, 949 units, nspks: 19390.8017, mu: 17.3007, nst0: 19142, merges: 191.8793, 0.9471
7347.50 sec, 601 / 5642 batches, 990 units, nspks: 22840.3854, mu: 17.7964, nst0: 24606, merges: 189.9499, 1.1294
7839.86 sec, 701 / 5642 batches, 943 units, nspks: 18537.4612, mu: 16.1950, nst0: 2395, merges: 192.7472, 1.4088
8369.98 sec, 801 / 5642 batches, 929 units, nspks: 21237.7122, mu: 16.4087, nst0: 24493, merges: 196.6207, 1.5093
8870.91 sec, 901 / 5642 batches, 933 units, nspks: 20239.3667, mu: 15.8552, nst0: 20696, merges: 198.8503, 0.8396
9406.39 sec, 1001 / 5642 batches, 980 units, nspks: 20660.9258, mu: 16.7722, nst0: 17581, merges: 192.6847, 1.0744
9932.23 sec, 1101 / 5642 batches, 990 units, nspks: 20860.3573, mu: 16.3507, nst0: 22802, merges: 192.7324, 0.9377
10451.44 sec, 1201 / 5642 batches, 977 units, nspks: 20121.9869, mu: 15.8568, nst0: 20031, merges: 189.2927, 0.7484
10967.25 sec, 1301 / 5642 batches, 971 units, nspks: 19968.8203, mu: 15.7011, nst0: 19520, merges: 196.7373, 0.7241
11474.12 sec, 1401 / 5642 batches, 968 units, nspks: 20556.5244, mu: 15.1839, nst0: 19869, merges: 200.2376, 0.6578
12010.41 sec, 1501 / 5642 batches, 953 units, nspks: 20078.1549, mu: 15.2764, nst0: 19475, merges: 200.4092, 1.0238
12531.12 sec, 1601 / 5642 batches, 953 units, nspks: 20763.7382, mu: 15.3400, nst0: 24758, merges: 197.2555, 0.7744
13031.27 sec, 1701 / 5642 batches, 958 units, nspks: 20075.2219, mu: 15.1028, nst0: 22702, merges: 196.7768, 0.8559
13553.13 sec, 1801 / 5642 batches, 946 units, nspks: 19941.0031, mu: 14.9568, nst0: 18682, merges: 200.5547, 0.5993
14062.60 sec, 1901 / 5642 batches, 970 units, nspks: 20002.2660, mu: 14.9212, nst0: 17685, merges: 197.8236, 0.4033
14583.65 sec, 2001 / 5642 batches, 989 units, nspks: 20359.3396, mu: 14.6510, nst0: 18905, merges: 195.2433, 0.2824
Error using gpuArray/subsasgn
An unexpected error occurred trying to launch a kernel. The CUDA error was:
invalid argument

Error in triageTemplates2 (line 13)
W(:,idrop,:) = []; % remove those templates everywhere

Error in learnTemplates (line 173)
triageTemplates2(ops, iW, C2C, W, U, dWU, mu, nsp, ndrop);

Error in learnAndSolve8b (line 12)
rez = learnTemplates(rez, iorder0);

Error in ks_master_file2 (line 33)
rez = learnAndSolve8b(rez);

Error in spikeSortingPipeline (line 389)
ks_master_file2;

Error in init (line 27)
spikeSortingPipeline(inp);

@dervinism
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I cannot launch the kilosort gui. I get the following error:

kilosort
No constructor 'handle.listener' with matching signature found.

Error in uiextras.Container (line 95)
obj.Listeners{end+1,1} = handle.listener( containerObj, findprop( containerObj, 'PixelBounds' ), 'PropertyPostSet',
@obj.onResized );

Error in uiextras.Box (line 38)
obj@uiextras.Container( varargin{:} );

Error in uiextras.VBox (line 44)
obj@uiextras.Box( varargin{:} );

Error in ksGUI/build (line 100)
obj.H.root = uiextras.VBox('Parent', f,...

Error in ksGUI (line 47)
obj.build(parent);

Error in kilosort (line 17)
h = ksGUI(f);

@nsteinme
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nsteinme commented Feb 8, 2020 via email

@dervinism
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I have looked at the data using kilosort gui but I don't see any issues with the data.

@dervinism
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Any progress on this issue recently?

@marius10p
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Can you post screenshots from the GUI please, after scrolling to different sections of the data? It looks to me like it's finding way too many spikes, which usually indicates a configuration problem or artifacts that dominate the variance of the data.

@dervinism
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There might be more than usual of low amplitude high frequency noise in the data. Is there an amplitude threshold parameter that can be adjusted to reduce detectability of such unwanted events?

@marius10p
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If you can post pictures, I can give a more informed opinion. There is a threshold parameter in the GUI, same one that you can set in the configuration script (ops.Th).

@dervinism
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The kilosort gui no longer works...

@dervinism
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There was an old toolbox version on the path. Here is the screenshot with the GUI. What is the meaning of the threshold parameter values. Default values appear to be 10 and 4.
trace_example

@marius10p
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readme
Kilosort1 paper (the threshold works the same way)

@TRuikes
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TRuikes commented Oct 2, 2020

@dervinism did you manage to solve this?

@carsen-stringer carsen-stringer mentioned this issue Feb 29, 2024
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adding rtd and badges MouseLand/Kilosort
4 participants
@marius10p @nsteinme @TRuikes @dervinism