This sounds very much like a problem I had before switching JRE's. This version has been known to work with Ubuntu 10.10, Ubuntu 10.10, Linux it 2.6.35-32-generic #67-Ubuntu SMP Mon Mar 5 19:39:49 UTC 2012 x86_64 GNU/Linux:
java version "1.6.0_21" Java(TM) SE Runtime Environment (build 1.6.0_21-b06) Java HotSpot(TM) 64-Bit Server VM (build 17.0-b16, mixed mode) Tim Coalson believed the problem was somehow related to a cache size. Once it reached that cache size, then java performance plummeted, as you saw. Switching JRE's fixed the problem, and I don't have a non-java TFCE version I can send you. On Jan 22, 2014, at 4:27 PM, Eshita Shah <[email protected]> wrote: > Yes, it works fine at 1000 iterations. I am trying to run 5000. It seems to > get really slow after 1000, but continues on to about 2600 until it crashes. > > > On Wed, Jan 22, 2014 at 2:13 PM, Donna Dierker <[email protected]> > wrote: > How many iterations did you specify? Have you tried it with 1000 iterations? > > > On Jan 22, 2014, at 3:09 PM, Eshita Shah <[email protected]> wrote: > > > Hi Donna, > > > > I have been trying to allocate more memory to caret_stats so it can run > > java properly without crashing. However, this has not worked. I just > > downloaded the JRE you provided, and it is actually the same one that I am > > using. > > > > Do you think there is another source of this problem? > > > > Thank you, > > Eshita > > > > > > On Wed, Jan 15, 2014 at 7:23 PM, Donna Dierker > > <[email protected]> wrote: > > At the end of the TFCE processing, you should get a text file named > > something like *report.txt, along with a *ignif*metric. If you don't, then > > it's not finishing normally. > > > > How many iterations are you using? If it doesn't finish overnight with 5k > > iterations, then it might be your java runtime engine. Before I started > > using this one, my java runtime engine just hung or grinded to a near halt > > after a few thousand iterations: > > > > http://brainmap.wustl.edu/pub/donna/US/WVU/linux_java.zip > > login pub > > password download > > > > You can use others; just be aware that the JRE can be an obstacle. > > > > > > On Jan 15, 2014, at 3:32 PM, Eshita Shah <[email protected]> wrote: > > > > > Hi Donna, > > > > > > I am running a script you sent me a while ago, which uses caret_stats to > > > run ANOVA and then TFCE for significant cluster analysis. I am noticing > > > that the output files generated after running the script do not match up > > > to the expected outputs. I am seeing files such as ".metric.data1", > > > ".metric.data2", etc. I'm not sure where they are coming from - my hunch > > > is that the script is being aborted at some point (because I am not > > > getting any of the TFCE outputs), but I'm not exactly sure why these > > > files would be generated or what they are. > > > > > > Please let me know if you have any ideas. > > > > > > Thank you, > > > Eshita > > > > > > -- > > > Eshita Shah > > > University of California, Los Angeles | 2014 > > > B.S. Neuroscience > > > [email protected] > > > > > > > > > _______________________________________________ > > > caret-users mailing list > > > [email protected] > > > http://brainvis.wustl.edu/mailman/listinfo/caret-users > > > > > > _______________________________________________ > > caret-users mailing list > > [email protected] > > http://brainvis.wustl.edu/mailman/listinfo/caret-users > > _______________________________________________ > > caret-users mailing list > > [email protected] > > http://brainvis.wustl.edu/mailman/listinfo/caret-users > > > _______________________________________________ > caret-users mailing list > [email protected] > http://brainvis.wustl.edu/mailman/listinfo/caret-users > > > > -- > Eshita Shah > University of California, Los Angeles | 2014 > B.S. Neuroscience > [email protected] > > > _______________________________________________ > caret-users mailing list > [email protected] > http://brainvis.wustl.edu/mailman/listinfo/caret-users _______________________________________________ caret-users mailing list [email protected] http://brainvis.wustl.edu/mailman/listinfo/caret-users
