Segmentation fault in CalculateConservation for mkhssp about hssp HOT 4 CLOSED

I suspect that the issue caused by an incorrect use of sizeof:

for (uint32 j = 0; j < sizeof(ri.m_dist); ++j)
    ri.m_dist[j] = m_seq[i] == j ? 1 : 0;

m_dist is declared as follows:

struct MResInfo
{
    ...
    ...
    uint32 m_dist[23];
    ...
    ...
};

sizeof returns the size in bytes of the entire array, not the length as is assumed. This means that the loop exeeds the end of the array, causing the segmentation fault.

Getting the length of an array is notoriously hard (see: http://stackoverflow.com/questions/874169/how-to-get-the-size-of-an-array). The array is created as a fixed size, so the loop should use this to control when it ends.

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This bug was introduced in commit e839fd8 on 01/06/2012.

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This bug only happens when compiled with -O2 (optimisation level 2) is used. When -O0 (no optimisations) is used, the program produces output (whether this is correct is now another question) without crashing.

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This is definitely a bug. When using the hard-coded array-length, the output is correct for 1f2i for which the error was raised.

@jonblack Compilation of the bugged code without optimization results in incorrect output for 1f2i as well.

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