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POReading from stdin blocks at approx. 60 kB
 

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  1. POReading from stdin blocks at approx. 60 kB
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    <p>When transforming files with a self-implemented burrows-wheeler algorithm my program gets stuck when reading files with filesize above 59 kB. Basically I'm starting my program in terminal:</p> <pre><code>./BW encode 4 &lt; test </code></pre> <p>where 4 stands for 4*1024 bytes. As told before when processing files (raw data, textfiles etc.) with filesize under 59 kB no problems occure.</p> <p>code where data is processed and send to stdout:</p> <pre><code>void encodeBlock(unsigned char* str,long length){ unsigned int i, out_rownum; unsigned char **str_matr, *out_str, *prnt_rt_str2, *prnt_rt_str1; str_matr = (unsigned char**) calloc(length,sizeof(unsigned char*)); out_str = (unsigned char*) calloc(length+1,sizeof(unsigned char)); // make matrix with rotationstrings of str (by saving pointer to first character) for(i=0;i&lt;(unsigned int) length;i++){ str_matr[i] = &amp;str[i]; } // sorting matrix glob_strt = &amp;str[0]; glob_length = length; qsort(str_matr,length,sizeof(unsigned char*),strCmpEnc); out_str[length] = '\0'; for(i=0;i&lt;(unsigned int) length;i++){ prnt_rt_str1 = printRotStr(length,&amp;str[0],str_matr[i]); prnt_rt_str2 = printRotStr(length,&amp;prnt_rt_str1[0],&amp;prnt_rt_str1[length-1]); if(memcmp(str,prnt_rt_str2,length) == 0){ out_rownum = i; } out_str[i] = prnt_rt_str1[length-1]; } printf("(%d ",out_rownum); fwrite((unsigned char*) out_str, 1, length, stdout); printf(")\n"); free(prnt_rt_str1); free(prnt_rt_str2); free(str_matr); free(out_str); } </code></pre> <p>and code where data is received from stdin</p> <pre><code>void encode(unsigned short int num, unsigned int block_size){ long b_length,length; unsigned char* buffer; freopen(NULL, "rb", stdin); buffer = (unsigned char*) calloc(block_size+1,sizeof(unsigned char)); length = fread((unsigned char*) buffer, 1, block_size, stdin); if(length == 0){ // file empty }else{ b_length = length; printf("##B-W:%ld##\n",length); while(length == b_length){ buffer[block_size] = '\0'; encodeBlock(buffer,length); length = fread((unsigned char*) buffer, 1, block_size, stdin); } if(length != 0){ printf("##B-W:%ld##\n",length); buffer[length] = '\0'; encodeBlock(buffer,length); } } free(buffer); } </code></pre> <p>When it gets stuck it usually terminates and 'Killed' appears on screen. I'm working on linux OS. </p> <p>Result using valgrind: The program gets stuck and my whole system hangs. I'm not able to see any debugging result because I have to shutdown my system manually. </p> <p>UPDATE: The reason behind the blocked reading (after 59kB) was that there was no space left on the heap due of many mem leaks. I solved this problem and finally reading works fine.</p>
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    1. USKara
    1. USuser1745184
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    1. CO`if(memcmp(str,prnt_rt_str2,length) == 0){` goes beyond your allocated memory. It adresses (length-1)(length) characters. Update: That should have been (length+1)
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      1. POReading from stdin blocks at approx. 60 kB
      1. USwildplasser
    2. CORun the program under `valgrind` and fix the *very first* place where it tells you you accessed uninitialized or unallocated memory. Repeat.
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      1. POReading from stdin blocks at approx. 60 kB
      1. USzwol
    3. COWell, 19 pairs of eyeballs are probably quicker.
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      1. USwildplasser
 

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