Matlab crashes with segmentation fault on some datasets

[juli-p]

Hello,

I run into problems using potpourri in matlab on some datasets. I do not get any error message from the script itself but instead matlab just crashes. Below is the crash report.

Unfortunately I cannot upload the actual datasets because I am not allowed to publish them but I hope that still someone can help me with this issue. As I also have some datasets that work thus I assume that it is not a device-dependent problem.

MATLAB crash file:/home/julian/matlab_crash_dump.4180-1:


--------------------------------------------------------------------------------
          Segmentation violation detected at 2021-06-28 16:40:36 +0200
--------------------------------------------------------------------------------

Configuration:
  Crash Decoding           : Disabled - No sandbox or build area path
  Crash Mode               : continue (default)
  Default Encoding         : UTF-8
  Deployed                 : false
  Desktop Environment      : X-Cinnamon
  GNU C Library            : 2.29 stable
  Graphics Driver          : Unknown hardware 
  Graphics card 1          : 0x8086 ( 0x8086 ) 0x3e92 Version 0.0.0.0 (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    : 1354367
  MATLAB Root              : /home/julian/Software/matlab
  MATLAB Version           : 9.9.0.1538559 (R2020b) Update 3
  OpenGL                   : hardware
  Operating System         : "Fedora release 30 (Thirty)"
  Process ID               : 4180
  Processor ID             : x86 Family 6 Model 158 Stepping 10, GenuineIntel
  Session Key              : 8777ef34-fd3e-4c24-a712-acb23f25ca59
  Static TLS mitigation    : Enabled: Full
  Window System            : Fedora Project (12006000), display :0

Fault Count: 1


Abnormal termination:
Segmentation violation

Current Thread: 'MCR 0 interpret' id 140293788190464

Register State (from fault):
  RAX = 006d002e006f0066  RBX = 00007f98b1685f20
  RCX = 0000000000000090  RDX = 0000000000000009
  RSP = 00007f98b1685d40  RBP = 00007f98b1687e90
  RSI = 0000000000000019  RDI = 00007f98ab44f290

   R8 = 00007f98ab44ee10   R9 = 0000000000000000
  R10 = 0000000000000000  R11 = 00007f98a8000080
  R12 = 00007f98b16864c0  R13 = 00007f98b16864c0
  R14 = 00007f97816c9478  R15 = 00007f98d8166d60

  RIP = 00007f977c4f3d35  EFL = 0000000000010206

   CS = 0033   FS = 0000   GS = 0000

Stack Trace (from fault):
[  0] 0x00007f977c4f3d35 /home/julian/Dokumente/Potpourri/epistasis_test_mex.mexa64+00073013 mexFunction+00004405
[  1] 0x00007f98b7e2179f /home/julian/Software/matlab/bin/glnxa64/libmex.so+00837535
[  2] 0x00007f98b7e218a5 /home/julian/Software/matlab/bin/glnxa64/libmex.so+00837797
[  3] 0x00007f98b7e21c77 /home/julian/Software/matlab/bin/glnxa64/libmex.so+00838775
[  4] 0x00007f98b7e22804 /home/julian/Software/matlab/bin/glnxa64/libmex.so+00841732
[  5] 0x00007f98b7e10bdc /home/julian/Software/matlab/bin/glnxa64/libmex.so+00768988
[  6] 0x00007f98bb567720 /home/julian/Software/matlab/bin/glnxa64/libmwm_dispatcher.so+01160992 _ZN8Mfh_file20dispatch_file_commonEMS_FviPP11mxArray_tagiS2_EiS2_iS2_+00000208
[  7] 0x00007f98bb568e4c /home/julian/Software/matlab/bin/glnxa64/libmwm_dispatcher.so+01166924
[  8] 0x00007f98bb569311 /home/julian/Software/matlab/bin/glnxa64/libmwm_dispatcher.so+01168145 _ZN8Mfh_file8dispatchEiPSt10unique_ptrI11mxArray_tagN6matrix6detail17mxDestroy_deleterEEiPPS1_+00000033
[  9] 0x00007f98b8b37964 /home/julian/Software/matlab/bin/glnxa64/libmwm_lxe.so+10959204
[ 10] 0x00007f98b8b3b712 /home/julian/Software/matlab/bin/glnxa64/libmwm_lxe.so+10974994
[ 11] 0x00007f98b8c5dabd /home/julian/Software/matlab/bin/glnxa64/libmwm_lxe.so+12163773
[ 12] 0x00007f98b8c5156a /home/julian/Software/matlab/bin/glnxa64/libmwm_lxe.so+12113258
[ 13] 0x00007f98b8be4e8d /home/julian/Software/matlab/bin/glnxa64/libmwm_lxe.so+11669133
[ 14] 0x00007f98b8be4f60 /home/julian/Software/matlab/bin/glnxa64/libmwm_lxe.so+11669344
[ 15] 0x00007f98b8716274 /home/julian/Software/matlab/bin/glnxa64/libmwm_lxe.so+06627956
[ 16] 0x00007f98b87182b4 /home/julian/Software/matlab/bin/glnxa64/libmwm_lxe.so+06636212
[ 17] 0x00007f98b8715391 /home/julian/Software/matlab/bin/glnxa64/libmwm_lxe.so+06624145
[ 18] 0x00007f98b870d3a5 /home/julian/Software/matlab/bin/glnxa64/libmwm_lxe.so+06591397
[ 19] 0x00007f98b870d891 /home/julian/Software/matlab/bin/glnxa64/libmwm_lxe.so+06592657
[ 20] 0x00007f98b8714c0a /home/julian/Software/matlab/bin/glnxa64/libmwm_lxe.so+06622218
[ 21] 0x00007f98b8714d06 /home/julian/Software/matlab/bin/glnxa64/libmwm_lxe.so+06622470
[ 22] 0x00007f98b883c566 /home/julian/Software/matlab/bin/glnxa64/libmwm_lxe.so+07832934
[ 23] 0x00007f98b883eea5 /home/julian/Software/matlab/bin/glnxa64/libmwm_lxe.so+07843493
[ 24] 0x00007f98b8a53f21 /home/julian/Software/matlab/bin/glnxa64/libmwm_lxe.so+10026785
[ 25] 0x00007f98b8a05013 /home/julian/Software/matlab/bin/glnxa64/libmwm_lxe.so+09703443
[ 26] 0x00007f98b8a0864f /home/julian/Software/matlab/bin/glnxa64/libmwm_lxe.so+09717327
[ 27] 0x00007f98b8a0ac92 /home/julian/Software/matlab/bin/glnxa64/libmwm_lxe.so+09727122
[ 28] 0x00007f98b8a9c5b4 /home/julian/Software/matlab/bin/glnxa64/libmwm_lxe.so+10323380
[ 29] 0x00007f98b8a9c769 /home/julian/Software/matlab/bin/glnxa64/libmwm_lxe.so+10323817
[ 30] 0x00007f98bb7cf8e9 /home/julian/Software/matlab/bin/glnxa64/libmwiqm.so+00588009
[ 31] 0x00007f98bb83113a /home/julian/Software/matlab/bin/glnxa64/libmwiqm.so+00987450 _ZN3iqm14UserEvalPlugin7executeEP15inWorkSpace_tag+00000970
[ 32] 0x00007f98bb8066cf /home/julian/Software/matlab/bin/glnxa64/libmwiqm.so+00812751
[ 33] 0x00007f98bb814136 /home/julian/Software/matlab/bin/glnxa64/libmwiqm.so+00868662
[ 34] 0x00007f98bb7d8b1c /home/julian/Software/matlab/bin/glnxa64/libmwiqm.so+00625436
[ 35] 0x00007f98c0063762 /home/julian/Software/matlab/bin/glnxa64/libmwbridge.so+00300898
[ 36] 0x00007f98c0063fd3 /home/julian/Software/matlab/bin/glnxa64/libmwbridge.so+00303059
[ 37] 0x00007f98c006a366 /home/julian/Software/matlab/bin/glnxa64/libmwbridge.so+00328550 _Z22mnGetCommandLineBufferbRbN7mwboost8optionalIKP15inWorkSpace_tagEEbRKNS0_9function2IN6mlutil14cmddistributor17inExecutionStatusERKNSt7__cxx1112basic_stringIDsSt11char_traitsIDsESaIDsEEES4_EE+00000230
[ 38] 0x00007f98c006a60a /home/julian/Software/matlab/bin/glnxa64/libmwbridge.so+00329226 _Z8mnParserv+00000490
[ 39] 0x00007f98bb6b2bd7 /home/julian/Software/matlab/bin/glnxa64/libmwmcr.so+00973783
[ 40] 0x00007f98d894b8c0 /home/julian/Software/matlab/bin/glnxa64/libmwmvm.so+03250368 _ZNK7mwboost9function0IvEclEv+00000032
[ 41] 0x00007f98d894cab0 /home/julian/Software/matlab/bin/glnxa64/libmwmvm.so+03254960 _ZN14cmddistributor15PackagedTaskIIP10invokeFuncIN7mwboost8functionIFvvEEEEENS2_10shared_ptrINS2_13unique_futureIDTclfp_EEEEEERKT_+00000048
[ 42] 0x00007f98d894cb58 /home/julian/Software/matlab/bin/glnxa64/libmwmvm.so+03255128 _ZNSt17_Function_handlerIFN7mwboost3anyEvEZN14cmddistributor15PackagedTaskIIP10createFuncINS0_8functionIFvvEEEEESt8functionIS2_ET_EUlvE_E9_M_invokeERKSt9_Any_data+00000024
[ 43] 0x00007f98bb8253fb /home/julian/Software/matlab/bin/glnxa64/libmwiqm.so+00939003 _ZN3iqm18PackagedTaskPlugin7executeEP15inWorkSpace_tag+00000091
[ 44] 0x00007f98bb6b03bd /home/julian/Software/matlab/bin/glnxa64/libmwmcr.so+00963517
[ 45] 0x00007f98bb8066cf /home/julian/Software/matlab/bin/glnxa64/libmwiqm.so+00812751
[ 46] 0x00007f98bb7d6845 /home/julian/Software/matlab/bin/glnxa64/libmwiqm.so+00616517
[ 47] 0x00007f98bb7d7240 /home/julian/Software/matlab/bin/glnxa64/libmwiqm.so+00619072
[ 48] 0x00007f98bb696efe /home/julian/Software/matlab/bin/glnxa64/libmwmcr.so+00859902
[ 49] 0x00007f98bb697477 /home/julian/Software/matlab/bin/glnxa64/libmwmcr.so+00861303
[ 50] 0x00007f98bb697677 /home/julian/Software/matlab/bin/glnxa64/libmwmcr.so+00861815
[ 51] 0x00007f98d736e482 /home/julian/Software/matlab/bin/glnxa64/libmwboost_thread.so.1.70.0+00062594
[ 52] 0x00007f98d81704c0                             /lib64/libpthread.so.0+00033984
[ 53] 0x00007f98d7b01133                                   /lib64/libc.so.6+01032499 clone+00000067


This error was detected while a MEX-file was running. If the MEX-file
is not an official MathWorks function, please examine its source code
for errors. Please consult the External Interfaces Guide for information
on debugging MEX-files.

Thank you in advance for your time!

[gizemcaylak]

Hi,
Then, it crashes in called C++ code. Is it possible that because of the chosen parameters, e.g. maximum marginal significance, there are no SNPs chosen (thus leads to segmentation fault)? Since dataset is not available and I cannot reproduce the error, but maybe you can try to debug this in C++ code (by generating the mex file after editing the C++ part for debugging)? I hope this helps. If there is a public data that produces a similar error, I would be able to help more.