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POHow to load a sliding diagonal vector from data stored column-wise with SSE
 

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  1. POHow to load a sliding diagonal vector from data stored column-wise with SSE
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    <p>The sliding diagonal vector contains 16 elements, each one an 8-bit unsigned integer.</p> <p>Without SSE and a bit simplified it would have looked like this in C:</p> <pre class="lang-c prettyprint-override"><code>int width=1000000; // a big number uint8_t matrix[width][16]; fill_matrix_with_interesting_values(&amp;matrix); for (int i=0; i &lt; width - 16; ++i) { uint8_t diagonal_vector[16]; for (int j=0; j&lt;16; ++j) { diagonal_vector[j] = matrix[i+j][j]; } do_something(&amp;diagonal_vector); } </code></pre> <p>but in my case I can only load column-wise (vertically) from the matrix with the <code>_mm_load_si128</code> intrinsics function. The sliding diagonal vector is moving horizontally so I need to load 16 column vectors in advance and use one element from each of those column vectors to create the diagonal vector.</p> <p>Is it possible to make a fast low-memory implementation for this with SSE?</p> <p><strong>Update Nov 14 2016:</strong> Providing some more details. In my case I read single-letter codes from a text file in <a href="https://en.wikipedia.org/wiki/FASTA_format" rel="nofollow noreferrer">FASTA format</a>. Each letter represents a certain amino acid. Each amino acid has a specific column vector associated with it. That column vector is looked up from a constant table (a <a href="https://en.wikipedia.org/wiki/BLOSUM" rel="nofollow noreferrer">BLOSUM</a> matrix). In C code it would look like this</p> <pre class="lang-c prettyprint-override"><code>while (uint8_t c = read_next_letter_from_file()) { column_vector = lookup_from_const_table(c) uint8_t diagonal_vector[16]; ... rearrange the values from the latest column vectors into the diagonal_vector ... do_something(&amp;diagonal_vector) } </code></pre>
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