-------- Original Message -------- Subject: Re: Modularity: Evaluate hypothesis in MorphoJ Date: Wed, 8 Feb 2012 03:54:42 -0500 From: Chris Klingenberg <[email protected]> Reply-To: [email protected] Organization: University of Manchester To: [email protected] Dear Helmi Hmm, I can only guess what makes your computer grind away like this, but here is what I suspect. You start with 49 landmarks and your hypothesis divides them into two modules of 18 and 49. There are a lot of ways of doing that (the combinatorial calculator on the web that comes up first on Google says that there are something like 1.155E13 possiblities: 11.55 trillion!). So if you choose to do the complete enumeration of all possible partition, your computer will be busy for a long time! OK, the restriction to contiguous partitions reduces the possible number of allowed partitions, but that comes with some extra computational effort. The message is: use a smaller number of partitions. For example, start with the default of 10,000 and see how long it takes. Then maybe try with 100,000 or a million (which will take about 10 or 100 times as long) -- almost surely, the distributions of RV coefficients will be very similar. I hope this is helpful. Best wishes, Chris On 2/7/2012 9:57 PM, morphmet wrote:
-------- Original Message -------- Subject: Modularity: Evaluate hypothesis in MorphoJ Date: Fri, 3 Feb 2012 05:28:08 -0500 From: hmi hmi <[email protected]> To: morphomet morphometrics.org <[email protected]> Dear Morphometricans, I am trying the modularity: evaluate hypothesis function following the user guide in MorphoJ (1.03d and 1.04a) on two separate Windows 7-64bit machines (core-i5 8gb ram and core2 quad 8gb ram-both with 4 CPU cores) for both 2D and 3D data. Both have the 32-bit java console installed. The calculations work well for 2D data (25 landmarks) with few seconds lag. The characteristics of the 3D data are: 49 landmarks (80 specimens) with two partitions, where 18 landmarks are placed in the second partition. The contiguous partitions only box ticked and full enumeration of partitions selected. The 49 landmarks originated from a 200 landmark (80 specimens) morphoJ file. After selecting this operation, I notice the total CPU usage of the javaw.exe*32.exe in the task manager goes up to 25% and stays at 25% for one modularity operation. So if I made another modularity test, the CPU usage will be 50%. I do not see anything come out in the "Results" and "Graphics" tab of MorphoJ. When I move the mouse cursor on MorphoJ, it does show MorphoJ busy calculating the data. I left the computer on overnight, I see the CPU usage is still 25% with MorphoJ busy with the calculations. I've tried different analyis in MorphoJ while waiting for the modularity test and MorphoJ can work on other data and the output is generated after few seconds lag which shows that the software is not frozen. However, no analysis done after the modularity test could be save as the modularity test itself is not completed. I've also tried increasing CPU usage process priority to high and realtime but that did not improve the processing time. There does not seem to be any difference in the processing time regardless of type of CPU usage. The ram usage is not affected and stays about 142 mb. Is there something wrong with my data? Does anyone know how to make the calculations faster? Grateful for the help. Regards, Helmi Pritam University of Dundee
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