java.lang.OutofMemoryError: Java heap space

Jackson Lima jacksonlima at gmail.com
Wed May 30 16:13:35 UTC 2007


Hi to all!
I am trying to run the TreeAnnotator program, that sumariza the
phylogenetics trees generated by the BEAST. The two programs run in
java, try to run the program and it it gives this message of error:

"java.lang.OutofMemoryError: Java heap space"

The code standard of the TreeAnnotator is:
#!/bin/sh

  if [ -z "$BEAST" ]; then
         LS_OUT=$(ls -l "$0")' -> '"$0"
         FILENAME0=${LS_OUT#*-> }
         FILENAME=${FILENAME0% -> *}
         BEAST=`dirname "$FILENAME"`/..
  fi

  BEAST_LIB=$BEAST/lib
         java -Xms64m -Xmx256m -Djava.library.path=$BEAST_LIB -cp
$BEAST_LIB/beast.jar dr.app.tools.TreeAnnotator $*

In the page of the program
(http://beast.bio.ed.ac.uk/Increasing_Memory_Usage) the author
suggests to modify the code of the TreeAnnotator,  the parameters -
Xmx and - Xms, I tried - Xms1024m - Xmx1024m but I did not obtain
success when run the program, therefore this message of error:

"Error occurred during initialization of VM
Could not reserve enough space for object heap
Could not create the Java virtual machine.
Exit 1
"
But my limits are:

cputime      unlimited
filesize     unlimited
datasize     2097152 kbytes
stacksize    2097152 kbytes
coredumpsize unlimited
memoryuse    unlimited
vmemoryuse   unlimited
descriptors  11095
memorylocked unlimited
maxproc      5547
sbsize       unlimited

 The CPU:
FreeBSD  6.2-RELEASE-p3 FreeBSD 6.2-RELEASE-p3 #1: Thu Apr 26 13:14:47 UTC 2007
/usr/obj/usr/src/sys/GENERIC  i386

Have 4 Gb of Memory.

Thanks.

Jackson Lima

Ps: Sorry my poor english.


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