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Segmentation fault due to data alignment issue on MIC


Segmentation fault due to data alignment issue on MIC

By : user2956931
Date : November 22 2020, 03:03 PM
around this issue The array 'force' is 64-byte aligned. Thus every access to the force array should be 64-byte aligned i.e. the address of the element that is accessed should be a multiple of 64. At a time using the load_pd instruction, 8 doubles are loaded. (f + k * nd) accesses 3rd element when k=1 and 6th element when k=2 and so on. But the beginning of the 3rd element corresponds to 25th byte which is not a multiple of 64 and that is the reason why a segfault is occurring (similarly for other k values). So the formula (f + k * nd) itself should be changed so that every access using the formula is a multiple of 64.
code :


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Segmentation fault while working with SSE intrinsics due to incorrect memory alignment

Segmentation fault while working with SSE intrinsics due to incorrect memory alignment


By : DineshEtwa
Date : March 29 2020, 07:55 AM
seems to work fine Since sizeof(float) is 4, only every fourth entry in V will be properly aligned. Remember that _mm_load_ps loads four floats at a time. The argument, i.e. the pointer to the first float, needs to be aligned to 16 bytes.
I'm assuming that in your example i is a multiple of four, otherwise _mm_load_ps(&V[i]) would fail.
code :
__m128 v_im1;
__m128 v_i = _mm_load_ps( &V[0] );
__m128 v_ip1 = _mm_load_ps( &V[4] );

for ( i = 4 ; i < dx ; i += 4 ) {

    /* Get the three vectors in this 'frame'. */
    v_im1 = v_i; v_i = v_ip1; v_ip1 = _mm_load_ps( &V[i+4] );

    /* Get the u1..u8 from the example code. */
    __m128 u3 = _mm_shuffle_ps( v_im1 , v_i , 3 + (4<<2) + (0<<4) + (1<<6) );
    __m128 u4 = _mm_shuffle_ps( v_i , v_ip1 , 3 + (4<<2) + (0<<4) + (1<<6) );

    __m128 u1 = _mm_shuffle_ps( u3 , v_i , 1 + (2<<2) + (1<<4) + (2<<6) );
    __m128 u2 = _mm_shuffle_ps( v_i , u4 , 1 + (2<<2) + (1<<4) + (2<<6) );

    __m128 u5 = _mm_shuffle_ps( v_im1 , u3 , 1 + (2<<2) + (1<<4) + (2<<6) );
    __m128 u6 = _mm_shuffle_ps( u4 , v_ip1 , 1 + (2<<2) + (1<<4) + (2<<6) );

    __m128 u7 = v_im1;
    __m128 u8 = v_ip1;

    /* Do your computation and store. */
    ...

    }
strtok segmentation fault, just gives a segmentation fault when the first line of input file is blank

strtok segmentation fault, just gives a segmentation fault when the first line of input file is blank


By : Andrew Sol
Date : March 29 2020, 07:55 AM
help you fix your problem Please use sscanf() instead. Try to avoid strtok() at all costs unless otherwise absolutely neccessary.
Here is a link to source you might find useful
Biopython pairwise alignment results in segmentation fault when run in loop

Biopython pairwise alignment results in segmentation fault when run in loop


By : user1407837
Date : March 29 2020, 07:55 AM
wish help you to fix your issue The segmentation fault isn't happening because you are using a loop, but because you are providing non-ASCII characters as input for an alignment mode that takes ASCII string inputs only. Luckily, Bio.pairwise2.align.globalmx also permits aligning lists that contain arbitrary strings of ASCII and non-ASCII characters as tokens(i.e. aligning lists of strings, such as ['ABC', 'ABD'] with ['ABC', 'GGG'] to produce alignments like
code :
['ABC', 'ABD', '-'  ]
['ABC', '-'  , 'GGG']
['ś', 'w', '-', '-', '-', '-', '-', 'i', 'a', 't', '-', '-']
['-', 'w', 'y', 'r', 'z', 'u', 'c', 'i', '-', '-', 's', 'z']
alignments = pairwise2.align.globalmx(source, targ,1,-0.5)
alignments = pairwise2.align.globalmx(list(source), list(targ), 1, -0.5, gap_char=['-'])
source = 'świat'
targ = 'wyrzucisz'
[(['ś', 'w', '-', '-', '-', '-', '-', 'i', 'a', 't', '-', '-'],
  ['-', 'w', 'y', 'r', 'z', 'u', 'c', 'i', '-', '-', 's', 'z'],
  2.0,
  0,
  12)]
new_alignment = []

for aln in alignment:
    # Convert lists back into strings
    a = ''.join(aln[0])
    b = ''.join(aln[1])

    new_aln = (a, b) + aln[2:]
    new_alignment.append(new_aln)
[('św-----iat--', '-wyrzuci--sz', 2.0, 0, 12)]
Segmentation fault due to memory alignment in SSE

Segmentation fault due to memory alignment in SSE


By : Priyansh reja
Date : March 29 2020, 07:55 AM
this one helps. I don't really know anything about these SSE extensions, but it sounds like you are having trouble aligning your variables. To declare a particular alignment with a variable declaration requires non-portable extensions, varying by your compiler.
For GCC you'd declare your variable something like this:
Segmentation fault issue

Segmentation fault issue


By : Prog12
Date : March 29 2020, 07:55 AM
I wish did fix the issue. The other answers are correct however, you can use better methods in c++ rather than using sprintf
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