Maximum memory size/preformance

[Knox Long]

I am having a problem getting a program that I have which requires a large amount of memory to run at the speed I think it should a recently installed version of ubuntu.   The same program compiled in exactly the same way under Cygwin runs more than 5x faster on the same machine (which has 128 GB of ram).  This program requires a lot of memory due to the fact that it has a set of very large structures (that describe the physical conditions at different points in the wind of quasar).  The result is the program requires several GB of memory.

I suspect the reason that the program runs more slowly using Ubuntu is that the amount of physical memory being used is too small.  Even though I have succeeded in using ulimit to set the max locked memory to unlimited, it does not change the fact that top says only 670 MB of resident is being used, while the virtual memory is more than a GB.  (Unfortunately, I cannot check in Cygwin that this is the problem, because on Cygwin the top command produces quite different outputs.

If anyone has any thoughts about this I would appreciate it.  (Note that I am not an expert in linux or especially ubuntu).

Thanks
Knox
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