treeannotator v2.2.1 windows command line increase memory solution

[Justin]

Dear All,

Just a heads up if you're running into this problem on Windows.  I had a tree with a bunch of nodes, so treeannotator was crashing out with a 'java.lang.OutOfMemoryError: Java heap space' on my 32 bit java machine, or a 'java.lang.OutOfMemoryError: GC overhead limit exceeded' on my 64 bit java machine.  This was after I re-sampled down with LogCombiner to a # of trees <10,000. 

There was a command line solution for the utility programs in beast 1.8, but here it is for Beast 2.2.  The FAQ just deals with the main Beast program.

Open up cmd with admin privileges on a computer with 64-bit Java 8.  Navigate to your beast folder.  Then run the following:

java -Xms1000m -Xmx2000m -Djava.library.path=.\lib -cp .\lib\beast.jar beast.app.treeannotator.TreeAnnotatorLauncher

-Xms can set, and it's the initial Java heap size
-Xmx can set, and its the max Java heap size.

Hope that helps!

Justin

[alicia alvarez]

Dear Justin
I tried to use the command that you suggested but I get this message: Unrecognized option: -cp.\lib\beast.jar

Can you help me?
Thanks
Alicia

[Sere Bix]

Did you forgot the space betwenn -cp and .\lib\beast.jar? -cp is an optional command were you need to define a path for the library in use.

[alicia alvarez]

Dear Sere Bix

Thank you! Yes, I did not notice initially that I should use space after -cp.

Another question: I tried to run TreeAnnot with this setting (Xms1000m -Xmx2000m) but I still has the same error "GC overhead limit exceeded"

how much more can you increase the memory given to java?

I have 10,000 trees obtained from a single run in Beast. I do not know if this is too much ofr if I should make a run saving a lesser amount of trees?

Thank you

Best

Alicia