Size of tree accepted

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What steps will reproduce the problem?
1. I ran leaf stability index for a set of 700 trees of about 300 taxa
2. Also tried running it for a smaller number of trees (10) but with same 
300 taxa

What is the expected output? What do you see instead?
Instead of leaf stability indices, I get (for full trees):
Exception in thread "main" java.lang.OutOfMemoryError: Java heap space
        at java.util.ArrayList.<init>(Unknown Source)
        at java.util.ArrayList.<init>(Unknown Source)
        at jade.tree.Node.<init>(Node.java:39)
        at jade.tree.TreeReader.readTree(TreeReader.java:50)
        at phyutility.mainrunner.Main.leafStab(Main.java:554)
        at phyutility.mainrunner.Main.runArgs(Main.java:359)
        at phyutility.mainrunner.Main.<init>(Main.java:66)
        at phyutility.mainrunner.Main.main(Main.java:1509)

and (for reduced number of trees):
Exception in thread "main" java.lang.OutOfMemoryError: Java heap space
        at jade.math.NChooseM.iterate(NChooseM.java:68)
        at phyutility.leafstability.Runner.initializeRun(Runner.java:47)
        at phyutility.leafstability.Runner.<init>(Runner.java:23)
        at phyutility.mainrunner.Main.leafStab(Main.java:560)
        at phyutility.mainrunner.Main.runArgs(Main.java:359)
        at phyutility.mainrunner.Main.<init>(Main.java:66)
        at phyutility.mainrunner.Main.main(Main.java:1509)

What version of the product are you using? On what operating system?
Phyutility 2.2 on Windows XP

Please provide any additional information below.
I tried increasing the memory allocation using the java command but even 
after increasing it to 1GB I still get the same error message. Am not sure 
if the memory allocation increase didn't work or the program still can't 
handle the trees.

Original issue reported on code.google.com by nanthin...@gmail.com on 25 Apr 2008 at 11:46

[GoogleCodeExporter]

This is going to be a problem with large trees, but I am exploring solutions.

Original comment by blackrim on 8 Apr 2010 at 2:47

• Changed state: Accepted

[GoogleCodeExporter]

I'm getting the same error:

Exception in thread "main" java.lang.OutOfMemoryError: Java heap space

when thinning a data set of 90.000 trees down to 1000. 
I'm trying to increase the memory using the command (while in phyutility 
diretory)

java -Xms32m -Xmx15000m phyutility

but get the following error

Exception in thread "main" java.lang.NoClassDefFoundError: phyutility
Caused by: java.lang.ClassNotFoundException: phyutility
    at java.net.URLClassLoader$1.run(URLClassLoader.java:200)
    at java.security.AccessController.doPrivileged(Native Method)
    at java.net.URLClassLoader.findClass(URLClassLoader.java:188)
    at java.lang.ClassLoader.loadClass(ClassLoader.java:315)
    at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:330)
    at java.lang.ClassLoader.loadClass(ClassLoader.java:250)
    at java.lang.ClassLoader.loadClassInternal(ClassLoader.java:398)

I'm using Phyutility 2.2 on Mac OSX 10.6.3

What am I doing wrong? 
Thanks!

Original comment by lceg...@gmail.com on 31 May 2010 at 10:38

[GoogleCodeExporter]

I got it to work by using the command
java -Xmx3900m -jar Phyutility.jar -tt 9000 -in file.tre -out file.tre
I guess I'll just have to increase the heap memory this way whenever I need the 
extra
boost which is not often at all.

One question though, is it possible to have the processor do the work and not 
the RAM
memory? It's taking for ever (over 15 hours) and my computer is way too slow 
when
this is running!

Thanks

Original comment by lceg...@gmail.com on 1 Jun 2010 at 4:01

[GoogleCodeExporter]

I am working on trying to make the memory use more efficient. Definitely at 
this point it isn't that RAM is doing the work, but it does take quite a bit of 
RAM depending on the size of the tree. Anyway, working on this. 

Original comment by blackrim on 29 Jan 2012 at 11:29