Ubuntu 11.10 64bit mex file compilation

Question

Volker on 20 Apr 2012

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Direct link to this question

https://www.mathworks.com/matlabcentral/answers/36096-ubuntu-11-10-64bit-mex-file-compilation

Hi!

I recently started using MatlabR2011b on Ubuntu, largely for compiling my FORTRAN mex-files for use on linux systems (clusters).

However, I am encountering problems in executing them, after compiling them out of Matlab.

For example, when I compile the supplied example timestwo.F, I get a segmentation violation.

What could be the problem? Could it be, because I am using a newer version of the gcc-compiler? Though the compiling runs without errors.

Here is the error report:

>> timestwo(2.0)
------------------------------------------------------------------------
       Segmentation violation detected at Fri Apr 20 15:56:23 2012
------------------------------------------------------------------------
Configuration:
  Crash Decoding  : Disabled
  Current Visual  : 0x21 (class 4, depth 24)
  Default Encoding: UTF-8
  GNU C Library   : 2.13 stable
  MATLAB Root     : /usr/local/MATLAB/R2011b
  MATLAB Version  : 7.13.0.564 (R2011b)
  Operating System: Linux 3.0.0-17-generic #30-Ubuntu SMP Thu Mar 8 20:45:39 UTC 2012 x86_64
  Processor ID    : x86 Family 6 Model 10 Stepping 7, GenuineIntel
  Virtual Machine : Java 1.6.0_17-b04 with Sun Microsystems Inc. Java HotSpot(TM) 64-Bit Server VM mixed mode
  Window System   : The X.Org Foundation (11004000), display :0
Fault Count: 1
Abnormal termination:
Segmentation violation
Register State (from fault):
  RAX = 00007f05f56a4418  RBX = 00007f05f56a4c60
  RCX = 00007f05f022a270  RDX = 00007f0607285c70
  RSP = 00007f05f56a43f8  RBP = 00007f05f56a4440
  RSI = f56a4a40030d5b68  RDI = 00007f05f56a4420
     R8 = 0000000002c5c9c0   R9 = 00007f0609741480
    R10 = 00007f05f56a4170  R11 = 00007f06072b12f0
    R12 = 00007f05f56a4ba0  R13 = 00007f05f56a4c60
    R14 = 00000000020a5c40  R15 = 00007f05f56a45d0
    RIP = 00007f0607285c70  EFL = 0000000000010212
     CS = 0033   FS = 0000   GS = 0000
Stack Trace (from fault):
[  0] 0x00007f0609a1a5de    /usr/local/MATLAB/R2011b/bin/glnxa64/libmwfl.so+00210398 _ZN2fl4diag15stacktrace_base7captureERKNS0_14thread_contextEm+000158
[  1] 0x00007f0609a1c62d    /usr/local/MATLAB/R2011b/bin/glnxa64/libmwfl.so+00218669
[  2] 0x00007f0609a1c8f5    /usr/local/MATLAB/R2011b/bin/glnxa64/libmwfl.so+00219381 _ZN2fl4diag13terminate_logEPKcRKNS0_14thread_contextEb+000165
[  3] 0x00007f0608a224f5   /usr/local/MATLAB/R2011b/bin/glnxa64/libmwmcr.so+00447733 _ZN2fl4diag13terminate_logEPKcPK8ucontextb+000085
[  4] 0x00007f0608a1f5b4   /usr/local/MATLAB/R2011b/bin/glnxa64/libmwmcr.so+00435636
[  5] 0x00007f0608a20333   /usr/local/MATLAB/R2011b/bin/glnxa64/libmwmcr.so+00439091
[  6] 0x00007f0608a204c7   /usr/local/MATLAB/R2011b/bin/glnxa64/libmwmcr.so+00439495
[  7] 0x00007f0608a2185f   /usr/local/MATLAB/R2011b/bin/glnxa64/libmwmcr.so+00444511
[  8] 0x00007f0608a21a15   /usr/local/MATLAB/R2011b/bin/glnxa64/libmwmcr.so+00444949
[  9] 0x00007f06074fc060              /lib/x86_64-linux-gnu/libpthread.so.0+00065632
[ 10] 0x00007f0607285c70                    /lib/x86_64-linux-gnu/libc.so.6+01289328
[ 11] 0x00007f05ca40ea6a      /home/volker/Dokumente/MATLAB/timestwo.mexa64+00002666 mexfunction_+000220
[ 12] 0x00007f060202c22c     /usr/local/MATLAB/R2011b/bin/glnxa64/libmex.so+00049708 mexRunMexFile+000108
[ 13] 0x00007f06020290c9     /usr/local/MATLAB/R2011b/bin/glnxa64/libmex.so+00037065
[ 14] 0x00007f0602029d8e     /usr/local/MATLAB/R2011b/bin/glnxa64/libmex.so+00040334
[ 15] 0x00007f060878f027 /usr/local/MATLAB/R2011b/bin/glnxa64/libmwm_dispatcher.so+00430119 _ZN8Mfh_file11dispatch_fhEiPP11mxArray_tagiS2_+000519
[ 16] 0x00007f060806ddf3 /usr/local/MATLAB/R2011b/bin/glnxa64/libmwm_interpreter.so+01854963
[ 17] 0x00007f06080044b7 /usr/local/MATLAB/R2011b/bin/glnxa64/libmwm_interpreter.so+01422519
[ 18] 0x00007f06080227b6 /usr/local/MATLAB/R2011b/bin/glnxa64/libmwm_interpreter.so+01546166
[ 19] 0x00007f0608027c9c /usr/local/MATLAB/R2011b/bin/glnxa64/libmwm_interpreter.so+01567900
[ 20] 0x00007f0608025262 /usr/local/MATLAB/R2011b/bin/glnxa64/libmwm_interpreter.so+01557090
[ 21] 0x00007f0608025ea1 /usr/local/MATLAB/R2011b/bin/glnxa64/libmwm_interpreter.so+01560225
[ 22] 0x00007f0608088973 /usr/local/MATLAB/R2011b/bin/glnxa64/libmwm_interpreter.so+01964403
[ 23] 0x00007f060878f027 /usr/local/MATLAB/R2011b/bin/glnxa64/libmwm_dispatcher.so+00430119 _ZN8Mfh_file11dispatch_fhEiPP11mxArray_tagiS2_+000519
[ 24] 0x00007f060805e192 /usr/local/MATLAB/R2011b/bin/glnxa64/libmwm_interpreter.so+01790354
[ 25] 0x00007f060801c13b /usr/local/MATLAB/R2011b/bin/glnxa64/libmwm_interpreter.so+01519931
[ 26] 0x00007f0608019b56 /usr/local/MATLAB/R2011b/bin/glnxa64/libmwm_interpreter.so+01510230
[ 27] 0x00007f060801a087 /usr/local/MATLAB/R2011b/bin/glnxa64/libmwm_interpreter.so+01511559
[ 28] 0x00007f0608c6729e /usr/local/MATLAB/R2011b/bin/glnxa64/libmwbridge.so+00119454
[ 29] 0x00007f0608c681de /usr/local/MATLAB/R2011b/bin/glnxa64/libmwbridge.so+00123358 mnParser+000622
[ 30] 0x00007f0608a08d79   /usr/local/MATLAB/R2011b/bin/glnxa64/libmwmcr.so+00343417 _ZN11mcrInstance30mnParser_on_interpreter_threadEv+000041
[ 31] 0x00007f06089e823e   /usr/local/MATLAB/R2011b/bin/glnxa64/libmwmcr.so+00209470
[ 32] 0x00007f06089e82b9   /usr/local/MATLAB/R2011b/bin/glnxa64/libmwmcr.so+00209593
[ 33] 0x00007f05fe7b9026   /usr/local/MATLAB/R2011b/bin/glnxa64/libmwuix.so+00442406
[ 34] 0x00007f05fe7c3ded   /usr/local/MATLAB/R2011b/bin/glnxa64/libmwuix.so+00486893
[ 35] 0x00007f05ff226ec2     /usr/local/MATLAB/R2011b/bin/glnxa64/libuij.so+00237250 _ZSt8for_eachIN9__gnu_cxx17__normal_iteratorIPN5boost8weak_ptrIN4sysq10ws_ppeHookEEESt6vectorIS6_SaIS6_EEEENS4_8during_FIS6_NS2_10shared_ptrIS5_EEEEET0_T_SH_SG_+000066
[ 36] 0x00007f05ff228619     /usr/local/MATLAB/R2011b/bin/glnxa64/libuij.so+00243225
[ 37] 0x00007f05ff22513e     /usr/local/MATLAB/R2011b/bin/glnxa64/libuij.so+00229694 _Z25svWS_ProcessPendingEventsiib+000494
[ 38] 0x00007f06089e76cf   /usr/local/MATLAB/R2011b/bin/glnxa64/libmwmcr.so+00206543
[ 39] 0x00007f06089e79ae   /usr/local/MATLAB/R2011b/bin/glnxa64/libmwmcr.so+00207278
[ 40] 0x00007f06089e7b1a   /usr/local/MATLAB/R2011b/bin/glnxa64/libmwmcr.so+00207642
[ 41] 0x00007f06074f3efc              /lib/x86_64-linux-gnu/libpthread.so.0+00032508
[ 42] 0x00007f060722e59d                    /lib/x86_64-linux-gnu/libc.so.6+00931229 clone+000109
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.
If this problem is reproducible, please submit a Service Request via:
    http://www.mathworks.com/support/contact_us/
A technical support engineer might contact you with further information.
Thank you for your help.** This crash report has been saved to disk as /