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Segmentation violation on KS 2.5 #341

Closed
DradeAW opened this issue Feb 17, 2021 · 3 comments · Fixed by #595
Closed

Segmentation violation on KS 2.5 #341

DradeAW opened this issue Feb 17, 2021 · 3 comments · Fixed by #595

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@DradeAW
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DradeAW commented Feb 17, 2021

Hi,

I'm trying to run Kilosort 2.5 to compare it to Kilosort 3.0.
I've run it multiple times on the same dataset, and I always get a MathWorks crash at the same point.

Here is Kilosort's output:

>> main_kilosort
Looking for data inside /users/nsr/wyngaard/Documents/cells_tracking/0153/session_1/rec 
Time   0s. Computing whitening matrix.. 
Getting channel whitening matrix... 
Channel-whitening matrix computed. 
Time   3s. Loading raw data and applying filters... 
Time  42s. Finished preprocessing 882 batches. 
pitch is 1.250000e+01 um
0.16 sec, 1 batches, 3746 spikes 
10.10 sec, 101 batches, 326855 spikes 
19.94 sec, 201 batches, 631708 spikes 
29.81 sec, 301 batches, 966819 spikes 
39.47 sec, 401 batches, 1307872 spikes 
49.12 sec, 501 batches, 1640319 spikes 
58.76 sec, 601 batches, 1985039 spikes 
68.47 sec, 701 batches, 2349204 spikes 
78.11 sec, 801 batches, 2691355 spikes 
85.94 sec, 882 batches, 2978264 spikes 
time 125.81, Shifted up/down 882 batches. 
Time 128s. Optimizing templates ...
127.82 sec, 1 / 882 batches, 12 units, nspks: 1.4617, mu: 15.2345, nst0: 19, merges: 0.1000, 0.0000, 0.6000 
135.48 sec, 101 / 882 batches, 82 units, nspks: 1258.0793, mu: 16.4233, nst0: 1514, merges: 27.8284, 0.0000, 6.2809 
144.75 sec, 201 / 882 batches, 104 units, nspks: 1755.2932, mu: 15.5018, nst0: 1909, merges: 35.3697, 0.0206, 7.2095 
153.45 sec, 301 / 882 batches, 100 units, nspks: 1788.9709, mu: 13.9965, nst0: 1851, merges: 37.6225, 0.0698, 7.7475 
162.49 sec, 401 / 882 batches, 103 units, nspks: 1865.6586, mu: 13.9493, nst0: 1874, merges: 35.4091, 0.1482, 7.1276 
171.61 sec, 501 / 882 batches, 97 units, nspks: 1938.4247, mu: 13.3098, nst0: 1743, merges: 34.9356, 0.0409, 6.9028 
180.88 sec, 601 / 882 batches, 110 units, nspks: 2064.6244, mu: 14.0246, nst0: 1688, merges: 34.5311, 0.0050, 6.8794 
190.39 sec, 701 / 882 batches, 116 units, nspks: 2008.6936, mu: 13.7855, nst0: 1642, merges: 36.3633, 0.0006, 7.3005 
200.70 sec, 801 / 882 batches, 144 units, nspks: 2230.7116, mu: 15.4884, nst0: 1921, merges: 34.4691, 0.0001, 7.0181 
Elapsed time is 209.844289 seconds.
Finished learning templates 
Time 210s. Optimizing templates ...
210.33 sec, 1 / 882 batches, 144 units, nspks: 1802.0000, mu: 15.9700, nst0: 5613 
226.12 sec, 101 / 882 batches, 144 units, nspks: 145028.0000, mu: 15.9700, nst0: 4448 
241.37 sec, 201 / 882 batches, 144 units, nspks: 293595.0000, mu: 15.9700, nst0: 5235 
258.15 sec, 301 / 882 batches, 144 units, nspks: 470335.0000, mu: 15.9700, nst0: 5837 
275.21 sec, 401 / 882 batches, 144 units, nspks: 661092.0000, mu: 15.9700, nst0: 5058 
292.23 sec, 501 / 882 batches, 144 units, nspks: 854274.0000, mu: 15.9700, nst0: 5053 
309.97 sec, 601 / 882 batches, 144 units, nspks: 1070781.0000, mu: 15.9700, nst0: 6856 
328.51 sec, 701 / 882 batches, 144 units, nspks: 1310376.0000, mu: 15.9700, nst0: 4953 
346.16 sec, 801 / 882 batches, 144 units, nspks: 1532524.0000, mu: 15.9700, nst0: 5317 
Elapsed time is 360.917189 seconds.
Number of spikes before applying cutoff: 4664597
initialized spike counts
merged 76 into 74 
merged 82 into 84 
merged 80 into 84 
merged 83 into 81 
merged 84 into 81 
Found 0 splits, checked 1/144 clusters, nccg 0 
Found 1 splits, checked 1/145 clusters, nccg 0

And here is the crash report:

--------------------------------------------------------------------------------
       Segmentation violation detected at Wed Feb 17 14:08:37 2021 +0100
--------------------------------------------------------------------------------

Configuration:
  Crash Decoding           : Disabled - No sandbox or build area path
  Crash Mode               : continue (default)
  Default Encoding         : UTF-8
  Deployed                 : false
  Desktop Environment      : ubuntu:GNOME
  GNU C Library            : 2.31 stable
  Graphics Driver          : NVIDIA Corporation Quadro K620/PCIe/SSE2 Version 4.6.0 NVIDIA 460.32.03
  Graphics card 1          : 0x10de ( 0x10de ) 0x1e82 Version 460.32.3.0 (0-0-0)
  Graphics card 2          : 0x10de ( 0x10de ) 0x13bb Version 460.32.3.0 (0-0-0)
  Java Version             : Java 1.8.0_202-b08 with Oracle Corporation Java HotSpot(TM) 64-Bit Server VM mixed mode
  MATLAB Architecture      : glnxa64
  MATLAB Entitlement ID    : 1263502
  MATLAB Root              : /usr/local/matlab/R2019b
  MATLAB Version           : 9.7.0.1247435 (R2019b) Update 2
  OpenGL                   : hardware
  Operating System         : Ubuntu 20.04.2 LTS
  Process ID               : 494867
  Processor ID             : x86 Family 6 Model 85 Stepping 4, GenuineIntel
  Session Key              : ab088b61-6a35-47a0-87b1-5572d388d56b
  Static TLS mitigation    : Enabled: Full
  Window System            : The X.Org Foundation (12009000), display :0

Fault Count: 1


Abnormal termination:
Segmentation violation

Register State (from fault):
  RAX = 00007f5413bdab24  RBX = 00007f52acb4afc4
  RCX = 0000000000000004  RDX = 0000000000000000
  RSP = 00007f5994836390  RBP = 0000000000000002
  RSI = 00007f5413bda824  RDI = 00007f52acb4b144

   R8 = 00007f5413bda9a4   R9 = 0000000000000060
  R10 = 0000000000000000  R11 = 00007f52acb4ae44
  R12 = 00007f5413bda6a4  R13 = 00007f52acb4b2c4
  R14 = 00000000000ffe24  R15 = 000000007fffffff

  RIP = 00007f5455ffb25c  EFL = 0000000000010202

   CS = 0033   FS = 0000   GS = 0000

Stack Trace (from fault):
[  0] 0x00007f5455ffb25c        /usr/local/matlab/R2019b/bin/glnxa64/mkl.so+20177500 mkl_blas_avx512_xsswap+00001068
[  1] 0x00007f54556f8711        /usr/local/matlab/R2019b/bin/glnxa64/mkl.so+10729233 mkl_lapack_sgetf2+00000353
[  2] 0x00007f5455a6769b        /usr/local/matlab/R2019b/bin/glnxa64/mkl.so+14329499 mkl_lapack_sgetrf_local+00001563
[  3] 0x00007f5455a67389        /usr/local/matlab/R2019b/bin/glnxa64/mkl.so+14328713 mkl_lapack_sgetrf_local+00000777
[  4] 0x00007f5455a67389        /usr/local/matlab/R2019b/bin/glnxa64/mkl.so+14328713 mkl_lapack_sgetrf_local+00000777
[  5] 0x00007f54551f1d69        /usr/local/matlab/R2019b/bin/glnxa64/mkl.so+05459305 mkl_lapack_sgetrf_int+00008217
[  6] 0x00007f5455127eae        /usr/local/matlab/R2019b/bin/glnxa64/mkl.so+04632238 mkl_lapack_sgetrf+00000718
[  7] 0x00007f54550c99ca        /usr/local/matlab/R2019b/bin/glnxa64/mkl.so+04245962 sgetrf+00000154
[  8] 0x00007f546ab6d90d /usr/local/matlab/R2019b/bin/glnxa64/libmwmagma.so+01628429 magma_sgetrf_gpu+00002877
[  9] 0x00007f5494586599   /usr/local/matlab/R2019b/bin/glnxa64/libmwgpu.so+08418713
[ 10] 0x00007f54943c47f2   /usr/local/matlab/R2019b/bin/glnxa64/libmwgpu.so+06576114
[ 11] 0x00007f54943c5abc   /usr/local/matlab/R2019b/bin/glnxa64/libmwgpu.so+06580924
[ 12] 0x00007f54945751a0   /usr/local/matlab/R2019b/bin/glnxa64/libmwgpu.so+08348064
[ 13] 0x00007f54943ceff8   /usr/local/matlab/R2019b/bin/glnxa64/libmwgpu.so+06619128
[ 14] 0x00007f54943cf652   /usr/local/matlab/R2019b/bin/glnxa64/libmwgpu.so+06620754
[ 15] 0x00007f54943d0a7a   /usr/local/matlab/R2019b/bin/glnxa64/libmwgpu.so+06625914
[ 16] 0x00007f549466d9d7   /usr/local/matlab/R2019b/bin/glnxa64/libmwgpu.so+09365975
[ 17] 0x00007f549466dee7   /usr/local/matlab/R2019b/bin/glnxa64/libmwgpu.so+09367271
[ 18] 0x00007f54941afc0c   /usr/local/matlab/R2019b/bin/glnxa64/libmwgpu.so+04393996
[ 19] 0x00007f549409109d   /usr/local/matlab/R2019b/bin/glnxa64/libmwgpu.so+03219613
[ 20] 0x00007f598f4525b8 /usr/local/matlab/R2019b/bin/glnxa64/libmwmcos_impl.so+04040120
[ 21] 0x00007f598f455938 /usr/local/matlab/R2019b/bin/glnxa64/libmwmcos_impl.so+04053304
[ 22] 0x00007f598f45d932 /usr/local/matlab/R2019b/bin/glnxa64/libmwmcos_impl.so+04086066
[ 23] 0x00007f598f4517c1 /usr/local/matlab/R2019b/bin/glnxa64/libmwmcos_impl.so+04036545
[ 24] 0x00007f598f5de5cf /usr/local/matlab/R2019b/bin/glnxa64/libmwmcos_impl.so+05662159
[ 25] 0x00007f598f5d7a27 /usr/local/matlab/R2019b/bin/glnxa64/libmwmcos_impl.so+05634599
[ 26] 0x00007f599d773f86 /usr/local/matlab/R2019b/bin/glnxa64/libmwm_dispatcher.so+00561030
[ 27] 0x00007f599d7742d1 /usr/local/matlab/R2019b/bin/glnxa64/libmwm_dispatcher.so+00561873 _ZN18Mfh_MATLAB_fn_impl8dispatchEiPSt10unique_ptrI11mxArray_tagN6matrix6detail17mxDestroy_deleterEEiPPS1_+00000033
[ 28] 0x00007f599ae21323 /usr/local/matlab/R2019b/bin/glnxa64/libmwm_lxe.so+14025507
[ 29] 0x00007f599ae260d6 /usr/local/matlab/R2019b/bin/glnxa64/libmwm_lxe.so+14045398
[ 30] 0x00007f599af2cebe /usr/local/matlab/R2019b/bin/glnxa64/libmwm_lxe.so+15122110
[ 31] 0x00007f599af20211 /usr/local/matlab/R2019b/bin/glnxa64/libmwm_lxe.so+15069713
[ 32] 0x00007f599af202c8 /usr/local/matlab/R2019b/bin/glnxa64/libmwm_lxe.so+15069896
[ 33] 0x00007f599ae8ce34 /usr/local/matlab/R2019b/bin/glnxa64/libmwm_lxe.so+14466612
[ 34] 0x00007f599aeb41cd /usr/local/matlab/R2019b/bin/glnxa64/libmwm_lxe.so+14627277
[ 35] 0x00007f599a781890 /usr/local/matlab/R2019b/bin/glnxa64/libmwm_lxe.so+07080080
[ 36] 0x00007f599a769ea2 /usr/local/matlab/R2019b/bin/glnxa64/libmwm_lxe.so+06983330
[ 37] 0x00007f599a76e383 /usr/local/matlab/R2019b/bin/glnxa64/libmwm_lxe.so+07000963
[ 38] 0x00007f599acdd0f1 /usr/local/matlab/R2019b/bin/glnxa64/libmwm_lxe.so+12697841
[ 39] 0x00007f599ae0e8a1 /usr/local/matlab/R2019b/bin/glnxa64/libmwm_lxe.so+13949089
[ 40] 0x00007f599ae0f99d /usr/local/matlab/R2019b/bin/glnxa64/libmwm_lxe.so+13953437
[ 41] 0x00007f599d7f115f /usr/local/matlab/R2019b/bin/glnxa64/libmwm_dispatcher.so+01073503 _ZN8Mfh_file20dispatch_file_commonEMS_FviPP11mxArray_tagiS2_EiS2_iS2_+00000207
[ 42] 0x00007f599d7f2c5e /usr/local/matlab/R2019b/bin/glnxa64/libmwm_dispatcher.so+01080414
[ 43] 0x00007f599d7f31a1 /usr/local/matlab/R2019b/bin/glnxa64/libmwm_dispatcher.so+01081761 _ZN8Mfh_file8dispatchEiPSt10unique_ptrI11mxArray_tagN6matrix6detail17mxDestroy_deleterEEiPPS1_+00000033
[ 44] 0x00007f599ae21323 /usr/local/matlab/R2019b/bin/glnxa64/libmwm_lxe.so+14025507
[ 45] 0x00007f599ae260d6 /usr/local/matlab/R2019b/bin/glnxa64/libmwm_lxe.so+14045398
[ 46] 0x00007f599af2cebe /usr/local/matlab/R2019b/bin/glnxa64/libmwm_lxe.so+15122110
[ 47] 0x00007f599af2036c /usr/local/matlab/R2019b/bin/glnxa64/libmwm_lxe.so+15070060
[ 48] 0x00007f599ae8ce34 /usr/local/matlab/R2019b/bin/glnxa64/libmwm_lxe.so+14466612
[ 49] 0x00007f599aeb347d /usr/local/matlab/R2019b/bin/glnxa64/libmwm_lxe.so+14623869
[ 50] 0x00007f599a63283b /usr/local/matlab/R2019b/bin/glnxa64/libmwm_lxe.so+05707835
[ 51] 0x00007f599a634a74 /usr/local/matlab/R2019b/bin/glnxa64/libmwm_lxe.so+05716596
[ 52] 0x00007f599a63181d /usr/local/matlab/R2019b/bin/glnxa64/libmwm_lxe.so+05703709
[ 53] 0x00007f599a61ecf1 /usr/local/matlab/R2019b/bin/glnxa64/libmwm_lxe.so+05627121
[ 54] 0x00007f599a61ef29 /usr/local/matlab/R2019b/bin/glnxa64/libmwm_lxe.so+05627689
[ 55] 0x00007f599a631026 /usr/local/matlab/R2019b/bin/glnxa64/libmwm_lxe.so+05701670
[ 56] 0x00007f599a631126 /usr/local/matlab/R2019b/bin/glnxa64/libmwm_lxe.so+05701926
[ 57] 0x00007f599a76ac49 /usr/local/matlab/R2019b/bin/glnxa64/libmwm_lxe.so+06986825
[ 58] 0x00007f599a76e383 /usr/local/matlab/R2019b/bin/glnxa64/libmwm_lxe.so+07000963
[ 59] 0x00007f599acdd0f1 /usr/local/matlab/R2019b/bin/glnxa64/libmwm_lxe.so+12697841
[ 60] 0x00007f599ac87693 /usr/local/matlab/R2019b/bin/glnxa64/libmwm_lxe.so+12347027
[ 61] 0x00007f599ac8bd2f /usr/local/matlab/R2019b/bin/glnxa64/libmwm_lxe.so+12365103
[ 62] 0x00007f599ac8f0e2 /usr/local/matlab/R2019b/bin/glnxa64/libmwm_lxe.so+12378338
[ 63] 0x00007f599ad2bf8f /usr/local/matlab/R2019b/bin/glnxa64/libmwm_lxe.so+13021071
[ 64] 0x00007f599ad2c279 /usr/local/matlab/R2019b/bin/glnxa64/libmwm_lxe.so+13021817
[ 65] 0x00007f59a40594c4 /usr/local/matlab/R2019b/bin/glnxa64/libmwbridge.so+00341188 _Z8mnParserv+00000596
[ 66] 0x00007f599d93c5b5   /usr/local/matlab/R2019b/bin/glnxa64/libmwmcr.so+01017269
[ 67] 0x00007f59b059d42b   /usr/local/matlab/R2019b/bin/glnxa64/libmwmvm.so+03097643 _ZN14cmddistributor15PackagedTaskIIP10invokeFuncIN7mwboost8functionIFvvEEEEENS2_10shared_ptrINS2_13unique_futureIDTclfp_EEEEEERKT_+00000059
[ 68] 0x00007f59b059d518   /usr/local/matlab/R2019b/bin/glnxa64/libmwmvm.so+03097880 _ZNSt17_Function_handlerIFN7mwboost3anyEvEZN14cmddistributor15PackagedTaskIIP10createFuncINS0_8functionIFvvEEEEESt8functionIS2_ET_EUlvE_E9_M_invokeERKSt9_Any_data+00000024
[ 69] 0x00007f599da8c89c   /usr/local/matlab/R2019b/bin/glnxa64/libmwiqm.so+00751772 _ZN7mwboost6detail8function21function_obj_invoker0ISt8functionIFNS_3anyEvEES4_E6invokeERNS1_15function_bufferE+00000028
[ 70] 0x00007f599da8c557   /usr/local/matlab/R2019b/bin/glnxa64/libmwiqm.so+00750935 _ZN3iqm18PackagedTaskPlugin7executeEP15inWorkSpace_tag+00000439
[ 71] 0x00007f599d92b015   /usr/local/matlab/R2019b/bin/glnxa64/libmwmcr.so+00946197
[ 72] 0x00007f599da716a0   /usr/local/matlab/R2019b/bin/glnxa64/libmwiqm.so+00640672
[ 73] 0x00007f599da55e01   /usr/local/matlab/R2019b/bin/glnxa64/libmwiqm.so+00527873
[ 74] 0x00007f599da56a7f   /usr/local/matlab/R2019b/bin/glnxa64/libmwiqm.so+00531071
[ 75] 0x00007f599d912575   /usr/local/matlab/R2019b/bin/glnxa64/libmwmcr.so+00845173
[ 76] 0x00007f599d912b93   /usr/local/matlab/R2019b/bin/glnxa64/libmwmcr.so+00846739
[ 77] 0x00007f599d913404   /usr/local/matlab/R2019b/bin/glnxa64/libmwmcr.so+00848900
[ 78] 0x00007f59aee28bdd /usr/local/matlab/R2019b/bin/glnxa64/libmwboost_thread.so.1.65.1+00080861
[ 79] 0x00007f59af9f8609              /lib/x86_64-linux-gnu/libpthread.so.0+00038409
[ 80] 0x00007f59af387293                    /lib/x86_64-linux-gnu/libc.so.6+01188499 clone+00000067
[ 81] 0x0000000000000000                                   <unknown-module>+00000000
@DradeAW
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DradeAW commented Feb 17, 2021

Same thing with KS 2.0

Kilosort output:

>> main_kilosort
Looking for data inside /users/nsr/wyngaard/Documents/cells_tracking/0153/session_1/rec 
Time   0s. Determining good channels.. 
found 42533 threshold crossings in 216.48 seconds of data 
found 5 bad channels 
Time   8s. Computing whitening matrix.. 
Getting channel whitening matrix... 
Channel-whitening matrix computed. 
Time   9s. Loading raw data and applying filters... 
Time  43s. Finished preprocessing 883 batches. 
random seed for clusterSingleBatches: 1
Obtained 7 PC waveforms in 0.56 seconds 
time 0.37, pre clustered 1 / 883 batches 
time 21.91, pre clustered 501 / 883 batches 
time 0.23, compared 1 / 883 batches 
time 4.08, compared 501 / 883 batches 
time 14.19, Re-ordered 883 batches. 
Time  16s. Optimizing templates ...
16.43 sec, 1 / 884 batches, 11 units, nspks: 1.0201, mu: 10.0000, nst0: 11, merges: 0.1000, 0.0000 
22.50 sec, 101 / 884 batches, 91 units, nspks: 1574.3259, mu: 16.7999, nst0: 1585, merges: 26.1476, 0.0000 
30.04 sec, 201 / 884 batches, 84 units, nspks: 1807.1248, mu: 13.9422, nst0: 1826, merges: 33.4932, 0.0523 
38.15 sec, 301 / 884 batches, 96 units, nspks: 2131.1644, mu: 14.4977, nst0: 2100, merges: 33.1611, 0.0064 
47.73 sec, 401 / 884 batches, 126 units, nspks: 2676.0427, mu: 15.8288, nst0: 3353, merges: 31.9637, 0.0438 
60.51 sec, 501 / 884 batches, 166 units, nspks: 2799.8441, mu: 18.6288, nst0: 2232, merges: 33.3871, 0.0573 
71.25 sec, 601 / 884 batches, 121 units, nspks: 2315.7751, mu: 14.6334, nst0: 2469, merges: 35.6178, 0.1113 
80.24 sec, 701 / 884 batches, 113 units, nspks: 2226.3205, mu: 13.8008, nst0: 2205, merges: 34.4147, 0.0135 
89.37 sec, 801 / 884 batches, 118 units, nspks: 2339.3804, mu: 13.9152, nst0: 3192, merges: 33.4793, 0.0245 
Elapsed time is 96.862483 seconds.
Finished learning templates 
Time  97s. Optimizing templates ...
97.26 sec, 1 / 442 batches, 113 units, nspks: 111.5000, mu: 14.0128, nst0: 6082 
112.54 sec, 101 / 442 batches, 113 units, nspks: 2303.6729, mu: 13.7678, nst0: 5331 
128.11 sec, 201 / 442 batches, 113 units, nspks: 2347.0150, mu: 13.5916, nst0: 6055 
144.16 sec, 301 / 442 batches, 113 units, nspks: 2441.7808, mu: 13.3921, nst0: 6253 
161.84 sec, 401 / 442 batches, 113 units, nspks: 2986.6930, mu: 13.8521, nst0: 9068 
Elapsed time is 169.755360 seconds.
Time 171s. Optimizing templates ...
171.60 sec, 1 / 441 batches, 113 units, nspks: 98.8500, mu: 14.0128, nst0: 5178 
186.73 sec, 101 / 441 batches, 113 units, nspks: 2230.6135, mu: 14.0607, nst0: 7170 
203.04 sec, 201 / 441 batches, 113 units, nspks: 2244.5088, mu: 13.6953, nst0: 6138 
218.10 sec, 301 / 441 batches, 113 units, nspks: 2031.5353, mu: 13.1647, nst0: 5063 
233.79 sec, 401 / 441 batches, 113 units, nspks: 2086.2446, mu: 13.1743, nst0: 5985 
Elapsed time is 240.638243 seconds.
Number of spikes before applying cutoff: 5311359
Finished compressing time-varying templates 
initialized spike counts
merged 96 into 95 
merged 36 into 37 
merged 68 into 69 
Found 0 splits, checked 1/113 clusters, nccg 0

MathWorks crash report:

--------------------------------------------------------------------------------
       Segmentation violation detected at Wed Feb 17 14:31:17 2021 +0100
--------------------------------------------------------------------------------

Configuration:
  Crash Decoding           : Disabled - No sandbox or build area path
  Crash Mode               : continue (default)
  Default Encoding         : UTF-8
  Deployed                 : false
  Desktop Environment      : ubuntu:GNOME
  GNU C Library            : 2.31 stable
  Graphics Driver          : NVIDIA Corporation Quadro K620/PCIe/SSE2 Version 4.6.0 NVIDIA 460.32.03
  Graphics card 1          : 0x10de ( 0x10de ) 0x1e82 Version 460.32.3.0 (0-0-0)
  Graphics card 2          : 0x10de ( 0x10de ) 0x13bb Version 460.32.3.0 (0-0-0)
  Java Version             : Java 1.8.0_202-b08 with Oracle Corporation Java HotSpot(TM) 64-Bit Server VM mixed mode
  MATLAB Architecture      : glnxa64
  MATLAB Entitlement ID    : 1263502
  MATLAB Root              : /usr/local/matlab/R2019b
  MATLAB Version           : 9.7.0.1247435 (R2019b) Update 2
  OpenGL                   : hardware
  Operating System         : Ubuntu 20.04.2 LTS
  Process ID               : 499048
  Processor ID             : x86 Family 6 Model 85 Stepping 4, GenuineIntel
  Session Key              : 33dffafd-c712-4363-a2af-db208b0475a9
  Static TLS mitigation    : Enabled: Full
  Window System            : The X.Org Foundation (12009000), display :0

Fault Count: 1


Abnormal termination:
Segmentation violation

Register State (from fault):
  RAX = 0000000054c2df6b  RBX = 0000000000000300
  RCX = 00007f08a7ce5b6c  RDX = 000000000000000e
  RSP = 00007f0dcfc923c0  RBP = 0000000000000003
  RSI = 0000000000000038  RDI = 0000000054c2df69

   R8 = 0000000000003fff   R9 = 00007f0754c2e148
  R10 = 00007f0754cb2780  R11 = 0000000054c2df48
  R12 = 0000000000000008  R13 = 0000000000000002
  R14 = fffffffffffffffe  R15 = 00007f0754c2ddc0

  RIP = 00007f082a45a6c7  EFL = 0000000000010202

   CS = 0033   FS = 0000   GS = 0000

Stack Trace (from fault):
[  0] 0x00007f082a45a6c7        /usr/local/matlab/R2019b/bin/glnxa64/mkl.so+10729159 mkl_lapack_sgetf2+00000279
[  1] 0x00007f082a7c969b        /usr/local/matlab/R2019b/bin/glnxa64/mkl.so+14329499 mkl_lapack_sgetrf_local+00001563
[  2] 0x00007f082a7c9389        /usr/local/matlab/R2019b/bin/glnxa64/mkl.so+14328713 mkl_lapack_sgetrf_local+00000777
[  3] 0x00007f082a7c9389        /usr/local/matlab/R2019b/bin/glnxa64/mkl.so+14328713 mkl_lapack_sgetrf_local+00000777
[  4] 0x00007f0829f53d69        /usr/local/matlab/R2019b/bin/glnxa64/mkl.so+05459305 mkl_lapack_sgetrf_int+00008217
[  5] 0x00007f0829e89eae        /usr/local/matlab/R2019b/bin/glnxa64/mkl.so+04632238 mkl_lapack_sgetrf+00000718
[  6] 0x00007f0829e2b9ca        /usr/local/matlab/R2019b/bin/glnxa64/mkl.so+04245962 sgetrf+00000154
[  7] 0x00007f083f8cf90d /usr/local/matlab/R2019b/bin/glnxa64/libmwmagma.so+01628429 magma_sgetrf_gpu+00002877
[  8] 0x00007f0998970599   /usr/local/matlab/R2019b/bin/glnxa64/libmwgpu.so+08418713
[  9] 0x00007f09987ae7f2   /usr/local/matlab/R2019b/bin/glnxa64/libmwgpu.so+06576114
[ 10] 0x00007f09987afabc   /usr/local/matlab/R2019b/bin/glnxa64/libmwgpu.so+06580924
[ 11] 0x00007f099895f1a0   /usr/local/matlab/R2019b/bin/glnxa64/libmwgpu.so+08348064
[ 12] 0x00007f09987b8ff8   /usr/local/matlab/R2019b/bin/glnxa64/libmwgpu.so+06619128
[ 13] 0x00007f09987b9652   /usr/local/matlab/R2019b/bin/glnxa64/libmwgpu.so+06620754
[ 14] 0x00007f09987baa7a   /usr/local/matlab/R2019b/bin/glnxa64/libmwgpu.so+06625914
[ 15] 0x00007f0998a579d7   /usr/local/matlab/R2019b/bin/glnxa64/libmwgpu.so+09365975
[ 16] 0x00007f0998a57ee7   /usr/local/matlab/R2019b/bin/glnxa64/libmwgpu.so+09367271
[ 17] 0x00007f0998599c0c   /usr/local/matlab/R2019b/bin/glnxa64/libmwgpu.so+04393996
[ 18] 0x00007f099847b09d   /usr/local/matlab/R2019b/bin/glnxa64/libmwgpu.so+03219613
[ 19] 0x00007f0dce9fd5b8 /usr/local/matlab/R2019b/bin/glnxa64/libmwmcos_impl.so+04040120
[ 20] 0x00007f0dcea00938 /usr/local/matlab/R2019b/bin/glnxa64/libmwmcos_impl.so+04053304
[ 21] 0x00007f0dcea08932 /usr/local/matlab/R2019b/bin/glnxa64/libmwmcos_impl.so+04086066
[ 22] 0x00007f0dce9fc7c1 /usr/local/matlab/R2019b/bin/glnxa64/libmwmcos_impl.so+04036545
[ 23] 0x00007f0dceb895cf /usr/local/matlab/R2019b/bin/glnxa64/libmwmcos_impl.so+05662159
[ 24] 0x00007f0dceb82a27 /usr/local/matlab/R2019b/bin/glnxa64/libmwmcos_impl.so+05634599
[ 25] 0x00007f0ddcdd0f86 /usr/local/matlab/R2019b/bin/glnxa64/libmwm_dispatcher.so+00561030
[ 26] 0x00007f0ddcdd12d1 /usr/local/matlab/R2019b/bin/glnxa64/libmwm_dispatcher.so+00561873 _ZN18Mfh_MATLAB_fn_impl8dispatchEiPSt10unique_ptrI11mxArray_tagN6matrix6detail17mxDestroy_deleterEEiPPS1_+00000033
[ 27] 0x00007f0dda3fc323 /usr/local/matlab/R2019b/bin/glnxa64/libmwm_lxe.so+14025507
[ 28] 0x00007f0dda4010d6 /usr/local/matlab/R2019b/bin/glnxa64/libmwm_lxe.so+14045398
[ 29] 0x00007f0dda507ebe /usr/local/matlab/R2019b/bin/glnxa64/libmwm_lxe.so+15122110
[ 30] 0x00007f0dda4fb211 /usr/local/matlab/R2019b/bin/glnxa64/libmwm_lxe.so+15069713
[ 31] 0x00007f0dda4fb2c8 /usr/local/matlab/R2019b/bin/glnxa64/libmwm_lxe.so+15069896
[ 32] 0x00007f0dda467e34 /usr/local/matlab/R2019b/bin/glnxa64/libmwm_lxe.so+14466612
[ 33] 0x00007f0dda48f1cd /usr/local/matlab/R2019b/bin/glnxa64/libmwm_lxe.so+14627277
[ 34] 0x00007f0dd9d5c890 /usr/local/matlab/R2019b/bin/glnxa64/libmwm_lxe.so+07080080
[ 35] 0x00007f0dd9d44ea2 /usr/local/matlab/R2019b/bin/glnxa64/libmwm_lxe.so+06983330
[ 36] 0x00007f0dd9d49383 /usr/local/matlab/R2019b/bin/glnxa64/libmwm_lxe.so+07000963
[ 37] 0x00007f0dda2b80f1 /usr/local/matlab/R2019b/bin/glnxa64/libmwm_lxe.so+12697841
[ 38] 0x00007f0dda3e98a1 /usr/local/matlab/R2019b/bin/glnxa64/libmwm_lxe.so+13949089
[ 39] 0x00007f0dda3ea99d /usr/local/matlab/R2019b/bin/glnxa64/libmwm_lxe.so+13953437
[ 40] 0x00007f0ddce4e15f /usr/local/matlab/R2019b/bin/glnxa64/libmwm_dispatcher.so+01073503 _ZN8Mfh_file20dispatch_file_commonEMS_FviPP11mxArray_tagiS2_EiS2_iS2_+00000207
[ 41] 0x00007f0ddce4fc5e /usr/local/matlab/R2019b/bin/glnxa64/libmwm_dispatcher.so+01080414
[ 42] 0x00007f0ddce501a1 /usr/local/matlab/R2019b/bin/glnxa64/libmwm_dispatcher.so+01081761 _ZN8Mfh_file8dispatchEiPSt10unique_ptrI11mxArray_tagN6matrix6detail17mxDestroy_deleterEEiPPS1_+00000033
[ 43] 0x00007f0dda3fc323 /usr/local/matlab/R2019b/bin/glnxa64/libmwm_lxe.so+14025507
[ 44] 0x00007f0dda4010d6 /usr/local/matlab/R2019b/bin/glnxa64/libmwm_lxe.so+14045398
[ 45] 0x00007f0dda507ebe /usr/local/matlab/R2019b/bin/glnxa64/libmwm_lxe.so+15122110
[ 46] 0x00007f0dda4fb36c /usr/local/matlab/R2019b/bin/glnxa64/libmwm_lxe.so+15070060
[ 47] 0x00007f0dda467e34 /usr/local/matlab/R2019b/bin/glnxa64/libmwm_lxe.so+14466612
[ 48] 0x00007f0dda48e47d /usr/local/matlab/R2019b/bin/glnxa64/libmwm_lxe.so+14623869
[ 49] 0x00007f0dd9c0d83b /usr/local/matlab/R2019b/bin/glnxa64/libmwm_lxe.so+05707835
[ 50] 0x00007f0dd9c0fa74 /usr/local/matlab/R2019b/bin/glnxa64/libmwm_lxe.so+05716596
[ 51] 0x00007f0dd9c0c81d /usr/local/matlab/R2019b/bin/glnxa64/libmwm_lxe.so+05703709
[ 52] 0x00007f0dd9bf9cf1 /usr/local/matlab/R2019b/bin/glnxa64/libmwm_lxe.so+05627121
[ 53] 0x00007f0dd9bf9f29 /usr/local/matlab/R2019b/bin/glnxa64/libmwm_lxe.so+05627689
[ 54] 0x00007f0dd9c0c026 /usr/local/matlab/R2019b/bin/glnxa64/libmwm_lxe.so+05701670
[ 55] 0x00007f0dd9c0c126 /usr/local/matlab/R2019b/bin/glnxa64/libmwm_lxe.so+05701926
[ 56] 0x00007f0dd9d45c49 /usr/local/matlab/R2019b/bin/glnxa64/libmwm_lxe.so+06986825
[ 57] 0x00007f0dd9d49383 /usr/local/matlab/R2019b/bin/glnxa64/libmwm_lxe.so+07000963
[ 58] 0x00007f0dda2b80f1 /usr/local/matlab/R2019b/bin/glnxa64/libmwm_lxe.so+12697841
[ 59] 0x00007f0dda262693 /usr/local/matlab/R2019b/bin/glnxa64/libmwm_lxe.so+12347027
[ 60] 0x00007f0dda266d2f /usr/local/matlab/R2019b/bin/glnxa64/libmwm_lxe.so+12365103
[ 61] 0x00007f0dda26a0e2 /usr/local/matlab/R2019b/bin/glnxa64/libmwm_lxe.so+12378338
[ 62] 0x00007f0dda306f8f /usr/local/matlab/R2019b/bin/glnxa64/libmwm_lxe.so+13021071
[ 63] 0x00007f0dda307279 /usr/local/matlab/R2019b/bin/glnxa64/libmwm_lxe.so+13021817
[ 64] 0x00007f0ddc0094c4 /usr/local/matlab/R2019b/bin/glnxa64/libmwbridge.so+00341188 _Z8mnParserv+00000596
[ 65] 0x00007f0ddcf995b5   /usr/local/matlab/R2019b/bin/glnxa64/libmwmcr.so+01017269
[ 66] 0x00007f0defb7a42b   /usr/local/matlab/R2019b/bin/glnxa64/libmwmvm.so+03097643 _ZN14cmddistributor15PackagedTaskIIP10invokeFuncIN7mwboost8functionIFvvEEEEENS2_10shared_ptrINS2_13unique_futureIDTclfp_EEEEEERKT_+00000059
[ 67] 0x00007f0defb7a518   /usr/local/matlab/R2019b/bin/glnxa64/libmwmvm.so+03097880 _ZNSt17_Function_handlerIFN7mwboost3anyEvEZN14cmddistributor15PackagedTaskIIP10createFuncINS0_8functionIFvvEEEEESt8functionIS2_ET_EUlvE_E9_M_invokeERKSt9_Any_data+00000024
[ 68] 0x00007f0ddd0e989c   /usr/local/matlab/R2019b/bin/glnxa64/libmwiqm.so+00751772 _ZN7mwboost6detail8function21function_obj_invoker0ISt8functionIFNS_3anyEvEES4_E6invokeERNS1_15function_bufferE+00000028
[ 69] 0x00007f0ddd0e9557   /usr/local/matlab/R2019b/bin/glnxa64/libmwiqm.so+00750935 _ZN3iqm18PackagedTaskPlugin7executeEP15inWorkSpace_tag+00000439
[ 70] 0x00007f0ddcf88015   /usr/local/matlab/R2019b/bin/glnxa64/libmwmcr.so+00946197
[ 71] 0x00007f0ddd0ce6a0   /usr/local/matlab/R2019b/bin/glnxa64/libmwiqm.so+00640672
[ 72] 0x00007f0ddd0b2e01   /usr/local/matlab/R2019b/bin/glnxa64/libmwiqm.so+00527873
[ 73] 0x00007f0ddd0b3a7f   /usr/local/matlab/R2019b/bin/glnxa64/libmwiqm.so+00531071
[ 74] 0x00007f0ddcf6f575   /usr/local/matlab/R2019b/bin/glnxa64/libmwmcr.so+00845173
[ 75] 0x00007f0ddcf6fb93   /usr/local/matlab/R2019b/bin/glnxa64/libmwmcr.so+00846739
[ 76] 0x00007f0ddcf70404   /usr/local/matlab/R2019b/bin/glnxa64/libmwmcr.so+00848900
[ 77] 0x00007f0dee405bdd /usr/local/matlab/R2019b/bin/glnxa64/libmwboost_thread.so.1.65.1+00080861
[ 78] 0x00007f0deefd5609              /lib/x86_64-linux-gnu/libpthread.so.0+00038409
[ 79] 0x00007f0dee964293                    /lib/x86_64-linux-gnu/libc.so.6+01188499 clone+00000067
[ 80] 0x0000000000000000                                   <unknown-module>+00000000

@LauraGwilliams
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Hi, I am having the same issue with Kilosort 2.5. Weirdly enough it runs fine when I provide the incorrect channel map (neuropixPhase3B1_kilosortChanMap.mat) but gives a segmentation issue when I provide the correct one (neuropixPhase3B2_kilosortChanMap.mat).

Any help with this would be greatly appreciated!!

@DradeAW
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DradeAW commented May 18, 2021 •
edited
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I managed to solve this issue thanks to #199.

The issue seems to happen only on Linux, and I solved this issue by installing the latest version of Intel MKL sudo apt install intel-mkl, and by adding these 2 lines to my .bashrc file:

export BLAS_VERSION=/usr/lib/x86_64-linux-gnu/mkl/libblas.so
export LAPACK_VERSION=/usr/lib/x86_64-linux-gnu/mkl/liblapack.so

@DradeAW DradeAW closed this as completed May 18, 2021
@alejoe91 alejoe91 mentioned this issue Oct 6, 2022
Closed
@carsen-stringer carsen-stringer mentioned this issue Feb 29, 2024
Merged
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adding rtd and badges MouseLand/Kilosort
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@DradeAW @LauraGwilliams