Re: TreeAnnotator java.lang.OutOfMemoryError: Java heap space

[pawan jayaswal]

Hey, Meng did u get any solution for you querry? If yes Plz also forward to me bcz I am also facing issue.....

On Tuesday, 16 October 2012 08:47:55 UTC+5:30, meng shengli wrote:

I keep getting an out of memory warning when trying to use 
TreeAnnotator.  This is a large run(Trees 11.6gb). 

I have tried increasing the memory allocated to Java and this is the error that I got on my last attempt.

Any suggestions? If you know please tell me through figure, which will show how I should do.

My computer

Windows 7 version

CPU:
Intel(R)Core(TM)i3-2330M cpu @ 2.20GHz 2.20GHz
RAM:4.00GB(2.92 GM USE)
system:32

 
 

Highest Log Clade Credibility: -200.21090323098244
Collecting node information...
0              25             50             75            100
|--------------|--------------|--------------|--------------|
 *********************************Exception in thread "main" java.lang.OutOfMemoryError: Java heap space
 at java.util.regex.Pattern.compile(Unknown Source)
 at java.util.regex.Pattern.<init>(Unknown Source)
  at java.util.regex.Pattern.compile(Unknown Source)
 at java.lang.String.replaceAll(Unknown Source)
 at dr.app.tools.TreeAnnotator$CladeSystem.collectAttributesForClade(Unknown Source)
 at dr.app.tools.TreeAnnotator$CladeSystem.collectAttributes(Unknown Source)
  at dr.app.tools.TreeAnnotator$CladeSystem.collectAttributes(Unknown Source)
 at dr.app.tools.TreeAnnotator$CladeSystem.collectAttributes(Unknown Source)
 at dr.app.tools.TreeAnnotator$CladeSystem.collectAttributes(Unknown Source)
  at dr.app.tools.TreeAnnotator$CladeSystem.collectAttributes(Unknown Source)
 at dr.app.tools.TreeAnnotator$CladeSystem.collectAttributes(Unknown Source)
 at dr.app.tools.TreeAnnotator$CladeSystem.collectAttributes(Unknown Source)
  at dr.app.tools.TreeAnnotator$CladeSystem.collectAttributes(Unknown Source)
 at dr.app.tools.TreeAnnotator$CladeSystem.collectAttributes(Unknown Source)
 at dr.app.tools.TreeAnnotator$CladeSystem.collectAttributes(Unknown Source)
  at dr.app.tools.TreeAnnotator$CladeSystem.collectAttributes(Unknown Source)
 at dr.app.tools.TreeAnnotator$CladeSystem.collectAttributes(Unknown Source)
 at dr.app.tools.TreeAnnotator.<init>(Unknown Source)
  at dr.app.tools.TreeAnnotator.main(Unknown Source)

 
Would YOU please leave me a suggestion? If you know please tell me through figure, which will show how I should do.
 
 
 
Thank you very much!
 
 
 
Meng  shengli

[Ingo Michalak]

Hi together,

try to subsample your trees file (e.g. using LogCombiner). 10,000 trees are usually sufficient/recommended.

Good luck!

[pawan jayaswal]

Dear Ian,

 

  Thank you very much for your valuable suggestion but Still it is not working in my case and I am getting same error. DO u lyk to say sm thing.........

[Santiago Sanchez]

Hello pawan,

You basically need to run treeannotator with a memory allocation above your tree file size. You can probably use a CPU cluster with lots for memory. If you try to run a 11 GB tree file in treeannotator with a computer that has 4 GB of memory, you will not be able to successfully finish the run because of memory shortage, no matter what memory allocation you give to java.

Cheers,

Santiago

Santiago Sanchez-Ramirez

Ecology and Evolutionary Biology, University of Toronto

Natural History (Mycology), Royal Ontario Museum

100 Queen's Park

Toronto, ON

M5S 2C6

Canada

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[pawan jayaswal]

Dear Santiago,

  Thank you very much for your reply. At present  I am having ~ 4 Gb of tree and 120 GB RAM. But still I am facing memory related issue  with Java. I will really thankful if you will be provide some kind of solution for this.

With Regrds

Pawan

[Ingo Michalak]

Hi Pawan,

In the folder BEAST/bin you find an executable script for TreeAnnotator, which you can open in a text editor for modifications. There you can change the amount of memory allocated to (the java instance hosting) TreeAnnotator. Increase the value to more than your trees file's size and run this very script to start TreeAnnotator. 

Good luck!

[Santiago Sanchez]

Hi Pawan,

If you try to run treeannotator command line with:

java -Xmx6144M -Xms6144M -cp beast.jar dr.app.tools.TreeAnnotator -burnin #### mytrees.trees mymcc.tre

Does it still give you a memory error?

Cheers,

Santiago

Santiago Sanchez-Ramirez

Ecology and Evolutionary Biology, University of Toronto

Natural History (Mycology), Royal Ontario Museum

100 Queen's Park

Toronto, ON

M5S 2C6

Canada

[pawan jayaswal]

Dear Ingo & Santiago,

Yes, I have changed the memory allocated to  treeannotator in bin file. like 

@echo off

setlocal

if ""=="%BEAST%" set BEAST=%~dp0%..

set BEAST_LIB=%BEAST%\lib

java -Xms6144m -Xmx6144m -Djava.library.path="%BEAST_LIB%" -cp "%BEAST_LIB%/beast.jar" dr.app.tools.TreeAnnotator %*

After change, Still i m getting same memory related error. Infact I allocated upto 50 GB memory but the thing is same, Ian. 

Santiago, I have run this through command promt but not  get success.

I hope grp will suggest me sm thing which will work..

Still  i m waiting.

Pawan

[Andrew Rambaut]

Dear Pawan, Ingo & Santiago,

It is not as simple as giving the program enough memory to fit the size of the tree file. If the trees are very variable then the memory required to store all the clades and the data may be much more. I suggest down sampling the tree file to fewer trees using logcombiner. How many sequences are in your trees? How many trees are in the tree file (how long are your chains and how frequently are you sampling)?

Andrew

[pawan jayaswal]

Dear Rambaut,

Case1.

 

   I have used logcompiler option also. Tree file size is 1.9 GB after passing through logcompiler it become 222MB after that I passed this logcompiler file (i.e.222MB) through tree-annotator, it generated 422 MB file. But this file is not responded by figtree.

Case2.

When I tried to run this file in cmd, I got error like could not find or load main class  dr.app.tools.Treeannotator. Would u like to suggest how to run this in command prompt.

Pawan