<html>
<head>
<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
<style type="text/css" style="display:none;"> P {margin-top:0;margin-bottom:0;} </style>
</head>
<body dir="ltr">
<div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0); background-color: rgb(255, 255, 255);">
Hi,</div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0); background-color: rgb(255, 255, 255);">
<br>
</div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0); background-color: rgb(255, 255, 255);">
I'm working with a 3D DMDA, with 3 dof per "node", used to create a sparse matrix Mat K. The Mat is modified repeatedly by the program, using the commands (in that order) :</div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0); background-color: rgb(255, 255, 255);">
<br>
</div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0); background-color: rgb(255, 255, 255);">
MatZeroEntries(K)<br>
</div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0); background-color: rgb(255, 255, 255);">
In a for loop : MatSetValuesLocal(K, 24, irow, 24, icol, vals, ADD_VALUES)</div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0); background-color: rgb(255, 255, 255);">
MatAssemblyBegin(K, MAT_FINAL_ASSEMBLY)<br>
</div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0); background-color: rgb(255, 255, 255);">
<span style="color: rgb(0, 0, 0); background-color: rgb(255, 255, 255); display: inline !important;">MatAssemblyEnd(K, MAT_FINAL_ASSEMBLY)</span><br>
</div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0); background-color: rgb(255, 255, 255);">
MatDiagonalScale(K, vec1, vec1)<br>
</div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0); background-color: rgb(255, 255, 255);">
MatDiagonalSet(K, vec2, ADD_VALUES)<br>
</div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0); background-color: rgb(255, 255, 255);">
<br>
</div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0); background-color: rgb(255, 255, 255);">
<span style="color: rgb(0, 0, 0); background-color: rgb(255, 255, 255); display: inline !important;">Computing time seems high and I</span><span style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:12pt"> would like to improve it. Running tests
with "-log_view" tells me that MatScale() is the bottle neck (50% of total computing time) . From manual pages, I've tried a few tweaks :</span></div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0); background-color: rgb(255, 255, 255);">
<ul>
<li>DMSetMatType(da, MATMPIBAIJ) : "For problems with multiple degrees of freedom per node, ... BAIJ can significantly enhance performance", Chapter 14.2.4<br>
</li><li>Used MatMissingDiagonal() to confirm there is no missing diagonal entries : "If the matrix Y is missing some diagonal entries this routine can be very slow", MatDiagonalSet() manual</li><li>Tried MatSetOption()</li><ul>
<li>MAT_NEW_NONZERO_LOCATIONS == PETSC_FALSE : to increase assembly efficiency</li><li>MAT_NEW_NONZERO_LOCATION_ERR == PETSC_TRUE : "When true, assembly processes have one less global reduction"<br>
</li><li>MAT_NEW_NONZERO_ALLOCATION_ERR == PETSC_TRUE : "When true, assembly processes have one less global reduction"<br>
</li><li>MAT_USE_HASH_TABLE == PETSC_TRUE : "Improve the searches during matrix assembly"<br>
</li></ul>
</ul>
<div><span style="">According to </span><span style="color: rgb(0, 0, 0); background-color: rgb(255, 255, 255); display: inline !important;">"-log_view"</span><span style="">, assembly is fast (0% of total time), and the use of a DMDA makes me believe preallocation
isn't the cause of performance issue.</span><br>
</div>
<div><br>
</div>
<div><span style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:12pt">I would like to know how could I improve <span style="color: rgb(0, 0, 0); background-color: rgb(255, 255, 255); display: inline !important;">MatScale(). W</span>hat are the best
practices (during allocation, when defining Vecs and Mats, the DMDA, etc.)? Instead of <span style="color: rgb(0, 0, 0); background-color: rgb(255, 255, 255); display: inline !important;">MatDiagonalScale(), s<span style="color: rgb(0, 0, 0); background-color: rgb(255, 255, 255); display: inline !important;">hould
I use another command<span> </span></span>to obtain the same result faster?</span></span><br>
</div>
<div><span style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:12pt"><br>
</span></div>
<div><span style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:12pt">Thank you very much!</span></div>
<div><span style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:12pt"><br>
</span></div>
<div><span style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:12pt">Antoine Côté</span></div>
</div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0); background-color: rgb(255, 255, 255);">
<br>
</div>
</body>
</html>