Segmentation violation in MATLAB 2021b on linux

Hi all! I'm struggling from segmentation violation error when I run matlab code on linux.

I found similar error with this on google, but I can't fix this problem in that way since don't have sudo authority.

How can I fix this problem without sudo authority?

My code is:

% fix the random number generator
rng(2406,'twister')

% get path of rDCM toolbox
P        = mfilename('fullpath');
rDCM_ind = strfind(P,fullfile('/tapas/rDCM','code'));
addpath('/scratch/08491/sangyoon/tapas/rDCM/code');
addpath('/scratch/08491/sangyoon/tapas/rDCM/misc');

%% make file name list ; i think this code causes problem..
folder_name = '/scratch/08491/sangyoon/rDCM_input';
list = dir(folder_name);
fprintf(list.name);
%% make iteration (with just one person)
for i = 4:4
    % 1 load input
    %Y = load(fullfile(P(1:rDCM_ind-1), '/rDCM_input', list(i).name));
    Y = load(fullfile('/scratch/08491/sangyoon/rDCM_input', list(i).name));
    % 2 generate DCM
    DCM = tapas_rdcm_model_specification(Y, [], []);
    
    % 3 specify the options for the rDCM analysis
    input_options.SNR             = 3; %we have to find it.
    input_options.y_dt            = 0.8; % found TR from json file
    input_options.p0_all          = 0.15;  % single p0 value (for computational efficiency)
    input_options.iter            = 100;
    input_options.filter_str      = 5;
    input_options.restrictInputs  = 0;
    input_options.u_shift = 0;
    input_options.DCM = DCM;
    input_options.type = 'r';
    input_options.padding = 0;
    input_options.visualize           = 1;
    input_options.compute_signal      = 1;
    
    % 4 run rDCM analysis with sparsity constraints (performs model inversion)
    [output] = tapas_rdcm_estimate(DCM, 'r', input_options, 2);
    
    % 5 save result of rDCM analysis
    output_name = strcat('/scratch/08491/sangyoon/rDCM_output/rDCM_result_', list(i).name);
    result = output.Ep.A;
    save(output_name, 'result');
    
end

I attached error message below.

Thanks!

Sincerely, Stella

--------------------------------------------------------------------------------
Segmentation violation detected at 2022-01-29 04:36:49 -0600
--------------------------------------------------------------------------------

Configuration:
Crash Decoding           : Disabled - No sandbox or build area path
Crash Mode               : continue (default)
Default Encoding         : UTF-8
Deployed                 : false
GNU C Library            : 2.17 stable
Graphics Driver          : Unknown software 
Graphics card 1          : 0x102b ( 0x102b ) 0x536 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    : 1496533
MATLAB Root              : /home1/apps/matlab/2021b
MATLAB Version           : 9.11.0.1809720 (R2021b) Update 1
OpenGL                   : software
Operating System         : "CentOS Linux release 7.6.1810 (Core) "
Process ID               : 333617
Processor ID             : x86 Family 6 Model 85 Stepping 4, GenuineIntel
Session Key              : d09989e8-3aaf-4a93-8dc0-74d009870600
Static TLS mitigation    : Disabled: Unnecessary
Window System            : No active display

Fault Count: 1


Abnormal termination:
Segmentation violation

Current Thread: 'MCR 0 interpret' id 47786220611328

Register State (from fault):
RAX = 4000000000000000  RBX = 00002b7618b40260
RCX = 00002b7795b8e180  RDX = 00002b7618b40260
RSP = 00002b7618b3dd40  RBP = 00002b7618b400c0
RSI = 00002b7795b8cde0  RDI = 00002b7618b40248

R8 = 00002b7618b40260   R9 = 0000000000000031
R10 = c0326376cb88a02e  R11 = 00002b77c0238fa0
R12 = 00002b7618b40248  R13 = 00002b7795b8e180
R14 = 00002b7618b40260  R15 = 0000000000000031

RIP = 00002b77c0238ff6  EFL = 0000000000010206

CS = 0033   FS = 0000   GS = 0000

Stack Trace (from fault):
[  0] 0x00002b77c0238ff6 /opt/intel/compilers_and_libraries_2018.2.199/linux/mkl/lib/intel64/libmkl_intel_thread.so+02293750 mkl_blas_zdotu+00000086
[  1] 0x00002b77b6889d72 /opt/intel/compilers_and_libraries_2018.2.199/linux/mkl/lib/intel64/libmkl_intel_ilp64.so+01514866 ZDOTU+00000162
[  2] 0x00002b75f1e1ec5b /home1/apps/matlab/2021b/bin/glnxa64/libmwmathlinalg.so+03681371
[  3] 0x00002b75eca487a5 /home1/apps/matlab/2021b/bin/glnxa64/libmwm_lxe.so+10782629
[  4] 0x00002b75eca48da7 /home1/apps/matlab/2021b/bin/glnxa64/libmwm_lxe.so+10784167
[  5] 0x00002b75eca48e99 /home1/apps/matlab/2021b/bin/glnxa64/libmwm_lxe.so+10784409
[  6] 0x00002b75eccec833 /home1/apps/matlab/2021b/bin/glnxa64/libmwm_lxe.so+13551667
[  7] 0x00002b75eccf0827 /home1/apps/matlab/2021b/bin/glnxa64/libmwm_lxe.so+13568039
[  8] 0x00002b75ec8eee50 /home1/apps/matlab/2021b/bin/glnxa64/libmwm_lxe.so+09367120
[  9] 0x00002b7689221c41                                   <unknown-module>+00000000
[ 10] 0x00002b75ec8d81e4 /home1/apps/matlab/2021b/bin/glnxa64/libmwm_lxe.so+09273828
[ 11] 0x00002b75ec8dbca0 /home1/apps/matlab/2021b/bin/glnxa64/libmwm_lxe.so+09288864
[ 12] 0x00002b75ecb0b726 /home1/apps/matlab/2021b/bin/glnxa64/libmwm_lxe.so+11581222
[ 13] 0x00002b75ecbf4d8d /home1/apps/matlab/2021b/bin/glnxa64/libmwm_lxe.so+12537229
[ 14] 0x00002b75ecbf6205 /home1/apps/matlab/2021b/bin/glnxa64/libmwm_lxe.so+12542469
[ 15] 0x00002b749ff4cdf0 /home1/apps/matlab/2021b/bin/glnxa64/libmwm_dispatcher.so+01236464 _ZN8Mfh_file20dispatch_file_commonEMS_FviPP11mxArray_tagiS2_EiS2_iS2_+00000208
[ 16] 0x00002b749ff4e3f3 /home1/apps/matlab/2021b/bin/glnxa64/libmwm_dispatcher.so+01242099
[ 17] 0x00002b749ff4e8c1 /home1/apps/matlab/2021b/bin/glnxa64/libmwm_dispatcher.so+01243329 _ZN8Mfh_file8dispatchEiPSt10unique_ptrI11mxArray_tagN6matrix6detail17mxDestroy_deleterEEiPPS1_+00000033
[ 18] 0x00002b75ecc06e44 /home1/apps/matlab/2021b/bin/glnxa64/libmwm_lxe.so+12611140
[ 19] 0x00002b75ecc094e2 /home1/apps/matlab/2021b/bin/glnxa64/libmwm_lxe.so+12621026
[ 20] 0x00002b75ecd6315d /home1/apps/matlab/2021b/bin/glnxa64/libmwm_lxe.so+14037341
[ 21] 0x00002b75ecd54e9a /home1/apps/matlab/2021b/bin/glnxa64/libmwm_lxe.so+13979290
[ 22] 0x00002b75ecce3d5d /home1/apps/matlab/2021b/bin/glnxa64/libmwm_lxe.so+13516125
[ 23] 0x00002b75ecce3e30 /home1/apps/matlab/2021b/bin/glnxa64/libmwm_lxe.so+13516336
[ 24] 0x00002b75ec7abd40 /home1/apps/matlab/2021b/bin/glnxa64/libmwm_lxe.so+08043840
[ 25] 0x00002b75ec7add64 /home1/apps/matlab/2021b/bin/glnxa64/libmwm_lxe.so+08052068
[ 26] 0x00002b75ec7aadf1 /home1/apps/matlab/2021b/bin/glnxa64/libmwm_lxe.so+08039921
[ 27] 0x00002b75ec7a0ca5 /home1/apps/matlab/2021b/bin/glnxa64/libmwm_lxe.so+07998629
[ 28] 0x00002b75ec7a1191 /home1/apps/matlab/2021b/bin/glnxa64/libmwm_lxe.so+07999889
[ 29] 0x00002b75ec7aa63a /home1/apps/matlab/2021b/bin/glnxa64/libmwm_lxe.so+08037946
[ 30] 0x00002b75ec7aa736 /home1/apps/matlab/2021b/bin/glnxa64/libmwm_lxe.so+08038198
[ 31] 0x00002b75ec8d8d7b /home1/apps/matlab/2021b/bin/glnxa64/libmwm_lxe.so+09276795
[ 32] 0x00002b75ec8dbca0 /home1/apps/matlab/2021b/bin/glnxa64/libmwm_lxe.so+09288864
[ 33] 0x00002b75ecb0b726 /home1/apps/matlab/2021b/bin/glnxa64/libmwm_lxe.so+11581222
[ 34] 0x00002b75ecab76bc /home1/apps/matlab/2021b/bin/glnxa64/libmwm_lxe.so+11237052
[ 35] 0x00002b75ecab837c /home1/apps/matlab/2021b/bin/glnxa64/libmwm_lxe.so+11240316
[ 36] 0x00002b75ecb598d4 /home1/apps/matlab/2021b/bin/glnxa64/libmwm_lxe.so+11901140
[ 37] 0x00002b75ecb59c0d /home1/apps/matlab/2021b/bin/glnxa64/libmwm_lxe.so+11901965
[ 38] 0x00002b755baf4600 /home1/apps/matlab/2021b/bin/glnxa64/libmwm_interpreter.so+01361408 _Z51inEvalCmdWithLocalReturnInDesiredWSAndPublishEventsRKNSt7__cxx1112basic_stringIDsSt11char_traitsIDsESaIDsEEEPibbP15inWorkSpace_tagN9MathWorks3lxe10EvalSourceE+00000064
[ 39] 0x00002b7323f007ff   /home1/apps/matlab/2021b/bin/glnxa64/libmwiqm.so+00923647 _ZNK3iqm18InternalEvalPlugin24inEvalCmdWithLocalReturnERKNSt7__cxx1112basic_stringIDsSt11char_traitsIDsESaIDsEEEP15inWorkSpace_tag+00000095
[ 40] 0x00002b7323f016ed   /home1/apps/matlab/2021b/bin/glnxa64/libmwiqm.so+00927469 _ZN3iqm18InternalEvalPlugin7executeEP15inWorkSpace_tag+00000237
[ 41] 0x00002b741ff029b5   /home1/apps/matlab/2021b/bin/glnxa64/libmwmcr.so+00932277
[ 42] 0x00002b7323ee93af   /home1/apps/matlab/2021b/bin/glnxa64/libmwiqm.so+00828335
[ 43] 0x00002b7323eba2a1   /home1/apps/matlab/2021b/bin/glnxa64/libmwiqm.so+00635553
[ 44] 0x00002b7323eba581   /home1/apps/matlab/2021b/bin/glnxa64/libmwiqm.so+00636289
[ 45] 0x00002b72bf9ab44e /home1/apps/matlab/2021b/bin/glnxa64/libmwmlutil.so+08614990 _ZNK14cmddistributor16IIPRunNowMessage7deliverERKN10foundation7msg_svc8exchange7RoutingE+00000030
[ 46] 0x00002b72beaf7525    /home1/apps/matlab/2021b/bin/glnxa64/libmwms.so+02626853 _ZN10foundation7msg_svc8exchange12MessageQueue7deliverERKN7mwboost10shared_ptrIKNS1_8EnvelopeEEE+00000197
[ 47] 0x00002b72beaf9dda    /home1/apps/matlab/2021b/bin/glnxa64/libmwms.so+02637274
[ 48] 0x00002b72beae4343    /home1/apps/matlab/2021b/bin/glnxa64/libmwms.so+02548547
[ 49] 0x00002b72beae665c    /home1/apps/matlab/2021b/bin/glnxa64/libmwms.so+02557532
[ 50] 0x00002b72beae2013    /home1/apps/matlab/2021b/bin/glnxa64/libmwms.so+02539539
[ 51] 0x00002b72bf90e211 /home1/apps/matlab/2021b/bin/glnxa64/libmwmlutil.so+07971345
[ 52] 0x00002b72bf90e4bd /home1/apps/matlab/2021b/bin/glnxa64/libmwmlutil.so+07972029
[ 53] 0x00002b72bc581d03   /home1/apps/matlab/2021b/bin/glnxa64/libmwmvm.so+02538755 _ZN7mwboost6detail8function26void_function_obj_invoker0INS_3_bi6bind_tINS3_11unspecifiedENS4_IS5_NS_8functionIFvvEEENS3_5list0EEENS3_5list1INS_17reference_wrapperINS_7promiseIvEEEEEEEEvE6invokeERNS1_15function_bufferE+00000035
[ 54] 0x00002b72bc5c04ff   /home1/apps/matlab/2021b/bin/glnxa64/libmwmvm.so+02794751 _ZN7mwboost13unique_futureIvE3getEv+00001279
[ 55] 0x00002b741feccf0b   /home1/apps/matlab/2021b/bin/glnxa64/libmwmcr.so+00712459
[ 56] 0x00002b72bc5c7be0   /home1/apps/matlab/2021b/bin/glnxa64/libmwmvm.so+02825184 _ZNK7mwboost9function0IvEclEv+00000032
[ 57] 0x00002b72bc5cf740   /home1/apps/matlab/2021b/bin/glnxa64/libmwmvm.so+02856768 _ZN14cmddistributor15PackagedTaskIIP10invokeFuncIN7mwboost8functionIFvvEEEEENS2_10shared_ptrINS2_13unique_futureIDTclfp_EEEEEERKT_+00000048
[ 58] 0x00002b72bc5cf7e8   /home1/apps/matlab/2021b/bin/glnxa64/libmwmvm.so+02856936 _ZNSt17_Function_handlerIFN7mwboost3anyEvEZN14cmddistributor15PackagedTaskIIP10createFuncINS0_8functionIFvvEEEEESt8functionIS2_ET_EUlvE_E9_M_invokeERKSt9_Any_data+00000024
[ 59] 0x00002b7323f098bb   /home1/apps/matlab/2021b/bin/glnxa64/libmwiqm.so+00960699 _ZN3iqm18PackagedTaskPlugin7executeEP15inWorkSpace_tag+00000091
[ 60] 0x00002b741ff026c5   /home1/apps/matlab/2021b/bin/glnxa64/libmwmcr.so+00931525
[ 61] 0x00002b7323ee93af   /home1/apps/matlab/2021b/bin/glnxa64/libmwiqm.so+00828335
[ 62] 0x00002b7323eb926b   /home1/apps/matlab/2021b/bin/glnxa64/libmwiqm.so+00631403
[ 63] 0x00002b72cffaec02 /home1/apps/matlab/2021b/bin/glnxa64/libmwbridge.so+00302082
[ 64] 0x00002b72cffaf543 /home1/apps/matlab/2021b/bin/glnxa64/libmwbridge.so+00304451
[ 65] 0x00002b72cffb57f2 /home1/apps/matlab/2021b/bin/glnxa64/libmwbridge.so+00329714 _Z22mnGetCommandLineBufferbRbN7mwboost8optionalIKP15inWorkSpace_tagEEbRKNS0_9function2IN6mlutil14cmddistributor17inExecutionStatusERKNSt7__cxx1112basic_stringIDsSt11char_traitsIDsESaIDsEEES4_EE+00000274
[ 66] 0x00002b72cffb5a92 /home1/apps/matlab/2021b/bin/glnxa64/libmwbridge.so+00330386 _Z8mnParserv+00000482
[ 67] 0x00002b741ff04a07   /home1/apps/matlab/2021b/bin/glnxa64/libmwmcr.so+00940551
[ 68] 0x00002b72bc5c7be0   /home1/apps/matlab/2021b/bin/glnxa64/libmwmvm.so+02825184 _ZNK7mwboost9function0IvEclEv+00000032
[ 69] 0x00002b72bc5cf740   /home1/apps/matlab/2021b/bin/glnxa64/libmwmvm.so+02856768 _ZN14cmddistributor15PackagedTaskIIP10invokeFuncIN7mwboost8functionIFvvEEEEENS2_10shared_ptrINS2_13unique_futureIDTclfp_EEEEEERKT_+00000048
[ 70] 0x00002b72bc5cf7e8   /home1/apps/matlab/2021b/bin/glnxa64/libmwmvm.so+02856936 _ZNSt17_Function_handlerIFN7mwboost3anyEvEZN14cmddistributor15PackagedTaskIIP10createFuncINS0_8functionIFvvEEEEESt8functionIS2_ET_EUlvE_E9_M_invokeERKSt9_Any_data+00000024
[ 71] 0x00002b7323f098bb   /home1/apps/matlab/2021b/bin/glnxa64/libmwiqm.so+00960699 _ZN3iqm18PackagedTaskPlugin7executeEP15inWorkSpace_tag+00000091
[ 72] 0x00002b741ff026c5   /home1/apps/matlab/2021b/bin/glnxa64/libmwmcr.so+00931525
[ 73] 0x00002b7323ee93af   /home1/apps/matlab/2021b/bin/glnxa64/libmwiqm.so+00828335
[ 74] 0x00002b7323eb75bc   /home1/apps/matlab/2021b/bin/glnxa64/libmwiqm.so+00624060
[ 75] 0x00002b7323eb8050   /home1/apps/matlab/2021b/bin/glnxa64/libmwiqm.so+00626768
[ 76] 0x00002b741feecafe   /home1/apps/matlab/2021b/bin/glnxa64/libmwmcr.so+00842494
[ 77] 0x00002b741feed11c   /home1/apps/matlab/2021b/bin/glnxa64/libmwmcr.so+00844060
[ 78] 0x00002b741feed392   /home1/apps/matlab/2021b/bin/glnxa64/libmwmcr.so+00844690
[ 79] 0x00002b72be07f8a7 /home1/apps/matlab/2021b/bin/glnxa64/libmwboost_thread.so.1.72.0+00063655
[ 80] 0x00002b72bcb96dd5                             /lib64/libpthread.so.0+00032213
[ 81] 0x00002b72bd443ead                                   /lib64/libc.so.6+01040045 clone+00000109

** This crash report has been saved to disk as /home1/08491/sangyoon/matlab_crash_dump.333617-1 **



MATLAB is exiting because of fatal error
/tmp/slurmd/job9075502/slurm_script: line 15: 333617 Killed                  matlab -noFigureWindows -nosplash -nodisplay -softwareopengl -batch ABCD_rsfMRI_timeseries_rDCM

[Edric Ellis]

I'm not totally sure what's going wrong here, but I'm a bit surprised by the version of the MKL libraries that are being shown in that crash dump. I suggest contacting MathWorks support directly who ought to be able to help you.

(For what it's worth - I don't think the problem that you linked to is relevant in this case).

[Sangyoon Bae]

thank you Edric! I'll contact to MathWorks support:)

[Shanmugaraj k]

Any working solution for this issue ?