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POwhat will cause a segfault when calling mxCreateDoubleMatrix()?
 

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  1. POwhat will cause a segfault when calling mxCreateDoubleMatrix()?
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    <p>I'm linking with matlab to write matfiles from within my C code.<br> When running the following code, i get a segfault (on the first line):</p> <pre><code>pPressure_a = mxCreateDoubleMatrix((MWSIZE)2, (MWSIZE)dim, mxREAL); if(pPressure_a == NULL){ fatal("Memory alocation error."); } copyDoubleToPtr2D(temp2D_a, mxGetPr(pPressure_a), dim, 2); matPutVariable(matfile, "p", pPressure_a); mxDestroyArray(pPressure_a); </code></pre> <p>In the above snippet, "MWSIZE" is #defined as int32_t, as I'm compiling this with matlab R14, but the #define allows changing this easily for use with other versions. Using gdb, I have confirmed that when the first line is called pPressure_a = 0x0; and dim = 501, which are perfectly valid values.</p> <h2>Here is the backtrace:</h2> <pre><code>Program received signal SIGSEGV, Segmentation fault. 0x00007ffff73eeb5d in ?? () from /lib/libc.so.6 (gdb) bt #0 0x00007ffff73eeb5d in ?? () from /lib/libc.so.6 #1 0x00007ffff73f103e in malloc () from /lib/libc.so.6 #2 0x00007ffff7730e35 in ?? () from /usr/local/matlabr14/bin/glnxa64/libut.so #3 0x00007ffff7731600 in ?? () from /usr/local/matlabr14/bin/glnxa64/libut.so #4 0x00007ffff7730046 in utCalloc () from /usr/local/matlabr14/bin/glnxa64/libut.so #5 0x00007ffff7236c76 in mxCreateNumericMatrix () from /usr/local/matlabr14/bin/glnxa64/libmx.so #6 0x00007ffff7237620 in mxCreateDoubleMatrix () from /usr/local/matlabr14/bin/glnxa64/libmx.so #7 0x0000000000412c28 in calcCohAcoustPress (settings=0x646ab0) at /home/eey/models/cTraceo/./calcCohAcoustPress.c:324 #8 0x0000000000413736 in main (argc=2, argv=0x7fffffffe038) at cTraceo.c:137 (gdb) f 7 #7 0x0000000000412c28 in calcCohAcoustPress (settings=0x646ab0) at /home/eey/models/cTraceo/./calcCohAcoustPress.c:324 324 pPressure_a = mxCreateDoubleMatrix((MWSIZE)2, (MWSIZE)dim, mxREAL); </code></pre> <hr> <p>I'm calling mxCreateDoubleMatrix() in the same way (several times) earlier in the code, and have never had problems.</p> <p>What can be causing this?</p> <p><strong>EDIT</strong>: Running valgrind produces several blocks like this:</p> <pre><code>==17538== Conditional jump or move depends on uninitialised value(s) ==17538== at 0x4E560B8: csqrt (s_csqrt.c:66) ==17538== by 0x40E149: solveDynamicEq (in cTraceo/bin/cTraceo-64b.bin) ==17538== by 0x411BA5: calcCohAcoustPress (in cTraceo/bin/cTraceo-64b.bin) ==17538== by 0x413555: main (in cTraceo/bin/cTraceo-64b.bin) </code></pre> <p>And ends with this:</p> <pre><code>Invalid read of size 8 ==17538== at 0x412A3F: calcCohAcoustPress (in cTraceo/bin/cTraceo-64b.bin) ==17538== by 0x413555: main (in cTraceo/bin/cTraceo-64b.bin) ==17538== Address 0x86a3050 is 0 bytes after a block of size 16 alloc'd ==17538== at 0x4C2815C: malloc (vg_replace_malloc.c:236) ==17538== by 0x401781: mallocDouble2D (in cTraceo/bin/cTraceo-64b.bin) ==17538== by 0x41296D: calcCohAcoustPress (in cTraceo/bin/cTraceo-64b.bin) ==17538== by 0x413555: main (in cTraceo/bin/cTraceo-64b.bin) ==17538== ==17538== Invalid write of size 8 ==17538== at 0x412A43: calcCohAcoustPress (in cTraceo/bin/cTraceo-64b.bin) ==17538== by 0x413555: main (in cTraceo/bin/cTraceo-64b.bin) ==17538== Address 0x0 is not stack'd, malloc'd or (recently) free'd ==17538== Process terminating with default action of signal 11 (SIGSEGV) ==17538== Access not within mapped region at address 0x0 ==17538== at 0x412A43: calcCohAcoustPress (in cTraceo/bin/cTraceo-64b.bin) ==17538== by 0x413555: main (in cTraceo/bin/cTraceo-64b.bin) ==17538== If you believe this happened as a result of a stack ==17538== overflow in your program's main thread (unlikely but ==17538== possible), you can try to increase the size of the ==17538== main thread stack using the --main-stacksize= flag. ==17538== The main thread stack size used in this run was 8388608. ==17538== Invalid free() / delete / delete[] ==17538== at 0x4C27D71: free (vg_replace_malloc.c:366) ==17538== by 0x58FAA0A: free_mem (in /lib/libc-2.12.1.so) ==17538== by 0x58FA5A1: __libc_freeres (in /lib/libc-2.12.1.so) ==17538== by 0x4A2366B: _vgnU_freeres (vg_preloaded.c:62) ==17538== by 0x7FEFFFD27: ??? ==17538== by 0x413555: main (in cTraceo/bin/cTraceo-64b.bin) ==17538== Address 0x41508a0 is not stack'd, malloc'd or (recently) free'd </code></pre> <p>Sadly, I'm new to valgrind and don't actually know what that means... :p</p>
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    1. USEmanuel Ey
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      1. POwhat will cause a segfault when calling mxCreateDoubleMatrix()?
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    1. COPerhaps some memory-stomping problem has occurred earlier, and corrupted data structures used by `malloc`. If you're on Linux, setting the environment variable `MALLOC_CHECK_` to 3 before running MATLAB may make the C library do extra checks and call `abort` if it spots an inconsistency.
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      1. POwhat will cause a segfault when calling mxCreateDoubleMatrix()?
      1. USGareth McCaughan
    2. COTry running it in valgrind to see if you're overwriting memory elsewhere. valgrind ./prog_name
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      1. POwhat will cause a segfault when calling mxCreateDoubleMatrix()?
      1. USDavidMFrey
    3. CO@Gareth McCaughan: No effect. @DavidMFrey: I'm gonna give it a try.
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      1. POwhat will cause a segfault when calling mxCreateDoubleMatrix()?
      1. USEmanuel Ey
 

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