Re: [Jmol-developers] Loop speed optimization potential

[Rolf H. <rh...@fl...>]

Am 03.04.15 um 03:55 schrieb Robert Hanson:
> Rolf, you are definitely pushing the limit there, I think. What exactly
> happens inside the loop you are really interested in using? If it is
> anything much, then the looping itself is going to be insignificant
> compared to the other processing.
>
Bob, the commands inside the loops take about two thirds of the whole 
time (see simplified example below with constant subnodeCount). So the 
loops take about one third and a loop speedup of a factor of 10 could 
reduce the overhead running time by 30% (e.g.: 2 minutes instead of 
three minutes or two hours instead of three hours).

I might also try a different optimization called 'Octree' which is said 
to be more efficient than the 'grid' optimization below to identify 
pseudoatom pairs near enough to each other for having significant 
influence onto each other.

I also considered implementing the algorithm in Javascript instead of 
Jmolscript to compensate for the slower JSmol speed. But it  must also 
work in the Java applet and the application. And I would rather like to 
avoid any "dangerous" methods of variable exchange between Javascript 
and Jmol.

Angel, reversing the loop doesn't change anything in Jmol/Java. I havn't 
checked Jmol/HTML5 yet.

-------- Simplified Example -------------
function sTest1(iMax) {
   var gridKeyList = [];
   var gridMembers = {};
   for (var  i=iMax; i>=1; i--) {
     var gridKey = "val" + i;
     gridKeyList[i] = gridKey;
     gridMembers[gridKey] = {};
     var averageMemberCount = 3;
     var nodeNoToIndex = {"1": 1, "2": 2, "3": 3};
     for (var j=averageMemberCount; j>=1; j--) {
        gridMembers[gridKey].[j] = j;
     }
   }
   var pairKeys = {};
   var counter2 = 0;
   var gridKeyCount = gridKeyList.size;
   if (gridKeyCount > 0) {
    var startTime = now();
    for (var gridKey in gridKeyList) {
       var subNodeList = gridMembers[gridKey].keys;
       var subNodeCount = subNodeList.size;
       for (var si=1; si<subNodeCount; si++) {
         var nodeNo1 = subNodeList[si];
         var i = nodeNoToIndex[nodeNo1];
         for (var sj=subNodeCount; sj>si; sj--) {
           var nodeNo2 = subNodeList[sj];
           var pairKey = "" + nodeNo1 + "|" + nodeNo2;
           counter2++;
           if (pairKeys[pairKey].size == 0) {
           }
         }
       }
     }
   }
   var duration = now(startTime);
   print "Loop size=" + iMax + "; Counter=" + counter2 + "; Total time=" 
+ duration + " ms;";
}
----------------------------

Regards,
Rolf