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POPython: ctypes + C malloc error. C memory problem or Python/ctypes problem?
 

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  1. POPython: ctypes + C malloc error. C memory problem or Python/ctypes problem?
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    <p>everyone. I'm having a memory allocation error using ctypes and a C code. I'm wondering if the memory problem is inside of C, or caused by an improper use of ctypes. The memory error is</p> <blockquote> <p>python(79698) malloc: <strong>* error for object 0x15627ac08: incorrect checksum for freed object >- object was probably modified after being freed. *</strong> set a breakpoint in malloc_error_break to debug Abort</p> </blockquote> <p>or</p> <blockquote> <p>python(76110,0x7fff70062ca0) malloc: <strong>* error for object 0x7d807e1078907df: pointer being >freed was not allocated *</strong> set a breakpoint in malloc_error_break to debug Abort</p> </blockquote> <p>depending on how I write the "free_some_memory" part of the code below. I won't post a bunch of C code here, but assuming I've written the C code correctly, <em>does my ctypes interface look correct?</em> </p> <p>Also, the failures I'm experiencing don't always happen in the same place in my scripts, for a given version of "free_some_memory". <em>Is it possible that my C code memory management is written poorly such that Python memory management may or may not bungle up (de)allocations?</em> </p> <p>Dunno if this is important, but I'm working on a Mac, Snow Leopard.<br> Any help you can offer would be very appreciated.</p> <p>Best, jkmacc</p> <p>My C code looks like:</p> <pre><code>/**** cfunction.c ****/ int cfun (double *y, char datafile[1024], int byteoffset, int num ) { allocate_some_memory; do_stuff; if ( error_condition ) { free_some_memory; return ( -1 ); } fill_y_here; free_some_memory; return ( 0 ); } </code></pre> <p>My ctypes wrapper looks like:</p> <pre><code>#pyfunction.py import ctypes as C import numpy as np lib = C.CDLL('mylib.dylib') def pyfun(DATAFILE, BYTEOFFSET, NUM): """ DATAFILE: a string file name BYTEOFFSET: an integer NUM: an integer """ #return integer success/failure flag lib.cfun.restype = C.c_int #array memory to be filled inside of C Y = np.empty(NUM,dtype='double',order='C') cDATAFILE = C.create_string_buffer(DATAFILE,1024) cBYTEOFFSET = C.c_int(int(BYTEOFFSET)) cNUM = C.c_int(int(NUM)) flag = lib.cfun(Y.ctypes.data_as(C.POINTER(C.c_double)), \ cDATAFILE,cBYTEOFFSET,cNUM) if flag == -1: print("Something went wrong.") return -1 else: return Y </code></pre>
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    1. USjkmacc
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    1. COYou need to post the actual code for cfunction.c, not pseudo-code.
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      1. POPython: ctypes + C malloc error. C memory problem or Python/ctypes problem?
      1. USHeath Hunnicutt
    2. COThe Python code is fine. Post the C code. Note that you can pass strings, ints, pointers directly to C functions without putting them in ctypes types (pass DATAFILE, BYTEOFFSET, NUM directly without the cDATAFILE, etc. translations.
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      1. POPython: ctypes + C malloc error. C memory problem or Python/ctypes problem?
      1. USMark Tolonen
    3. COThanks for looking this over. I'll produce a minimal example of the C that generates the problem, as I can't post the full code.
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      1. POPython: ctypes + C malloc error. C memory problem or Python/ctypes problem?
      1. USjkmacc
 

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