-------- Original Message -------- Subject: Re: Modularity: Evaluate hypothesis in MorphoJ Date: Fri, 10 Feb 2012 21:36:32 +0000 From: hmi hmi <hm...@hotmail.com> To: <morphmet_modera...@morphometrics.org> Dear Dr, Thank you for the suggestions. Will trim it to make it more manageable. Best regards, Helmi ----- Original Message ----- From: "morphmet" <morphmet_modera...@morphometrics.org> To: morphmet <morphmet@morphometrics.org> Date: Sun, 10 Feb 2012 21:09:00 -0000 Subject: Re: Modularity: Evaluate hypothesis in MorphoJ
-------- Original Message -------- Subject: Re: Modularity: Evaluate hypothesis in MorphoJ Date: Wed, 8 Feb 2012 03:54:42 -0500 From: Chris Klingenberg <c...@manchester.ac.uk> Reply-To: c...@manchester.ac.uk Organization: University of Manchester To: morphmet@morphometrics.org 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 <hm...@hotmail.com> > To: morphomet morphometrics.org <morphmet@morphometrics.org> > > > > 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 > -- *************************************************************** Christian Peter Klingenberg Faculty of Life Sciences The University of Manchester Michael Smith Building Oxford Road Manchester M13 9PT United Kingdom Telephone: +44 161 275 3899 Fax: +44 161 275 5082 E-mail: c...@manchester.ac.uk Web: http://www.flywings.org.uk Skype: chris_klingenberg ***************************************************************
