Problems running ImageJ on 64x WinXP with max mem set to 6 GB

[Shawn Mikula-2]

hello ImageJ community,
this email may be better addressed to a Java mailing list, but hopefully
someone here can help me out...  To use ImageJ with images of several GB's
in size, I have tried installing the 64x JRE (v1.6) on a 64x WinXP system
with 16 GB RAM, but when I use ImageJ with Xmx option set to 6 GB, I am
receiving a "Could not create the Java virtual machine" error and early
termination of ImageJ.  Has anyone used ImageJ on 64x WinXP systems
successfully using multi-GB size images?  Does anyone have any ideas why
Java is not able to create the Java virtual machine?
thanks.
Shawn



--
Shawn Mikula, Ph.D.,
Center for Neuroscience
University of California-Davis,
1544 Newton Court,
Davis, CA 95618,
Phone: [phone]
Fax: [phone]
mail: [hidden email]
web: http://brainmaps.org
 

[Gabriel Landini]

On Monday 02 June 2008, Shawn Mikula wrote:
> hello ImageJ community,
> this email may be better addressed to a Java mailing list, but hopefully
> someone here can help me out...  To use ImageJ with images of several GB's
> in size, I have tried installing the 64x JRE (v1.6) on a 64x WinXP system
> with 16 GB RAM, but when I use ImageJ with Xmx option set to 6 GB, I am
> receiving a "Could not create the Java virtual machine" error and early
> termination of ImageJ.  Has anyone used ImageJ on 64x WinXP systems
> successfully using multi-GB size images?  Does anyone have any ideas why
> Java is not able to create the Java virtual machine?

This question has been asked many times and there is a number of FAQs with
suggestion in the wiki at the Tudor site.

Cheers,

G.

[Michael Schell]

Hi Shawn,

The problem has  something to do with where ImageJ looks for the  
virtual machine.  I am not a Java expert, so somebody else in the is  
group may be able to explain this better or provide a more elegant  
solution.    However, I got this to work with Tony Collins' MBF-
ImageJ bundle by using the following protocol, and now my RAM  
limitation is eliminated.

1.  Go to this website and download JDK 6 Update 2, the first one on  
the list (this may not be the current version; I did this last autumn).

http://java.sun.com/javase/downloads/index.jsp

2.  After you click the download button, you will get some choices  
for which version.  Click the accept button, then scroll down to the  
last choice, which is:

Windows x64 Platform - Java(TM) SE Development Kit 6 Update 2

3.  After it downloads, install it where the installer defaults:  C:/
programs/Java

4.  Open the MBF-ImageJ folder and discard the Imagej.cfg file and  
also discard the /jre folder.

5.  Also, for some unknown reason, MBF-ImageJ installs a *second* /
jre folder in /programs(x86) [not the same folder as /programs].  
Discard this /jre folder too!

6.  Try to launch ImageJ.  It will freak out and tell you that it  
cannot find a /jre folder

7.  Re-direct it to the new version of Java you just installed,  
i.e.,  dig down through C:\Programs\Java\jdk1.6.0_01\jre\bin\javaw.exe

8.  Select javaw.exe

Now ImageJ will launch and you can assign up to 66% of the total  
RAM.  For my 8 GB system, I have assigned 5 GB

Good luck!

Mike

On Jun 2, 2008, at 1:38 PM, Shawn Mikula wrote:

> hello ImageJ community,
> this email may be better addressed to a Java mailing list, but  
> hopefully someone here can help me out...  To use ImageJ with  
> images of several GB's in size, I have tried installing the 64x JRE  
> (v1.6) on a 64x WinXP system with 16 GB RAM, but when I use ImageJ  
> with Xmx option set to 6 GB, I am receiving a "Could not create the  
> Java virtual machine" error and early termination of ImageJ.  Has  
> anyone used ImageJ on 64x WinXP systems successfully using multi-GB  
> size images?  Does anyone have any ideas why Java is not able to  
> create the Java virtual machine?
> thanks.
> Shawn
>
>
>
> --
> Shawn Mikula, Ph.D.,
> Center for Neuroscience
> University of California-Davis,
> 1544 Newton Court,
> Davis, CA 95618,
> Phone: [phone]
> Fax: [phone]
> mail: [hidden email]
> web: http://brainmaps.org

Michael J. Schell, Ph.D., CIV, USUHS
Assist. Professor
Dept. of Pharmacology
Uniformed Services University
4301 Jones Bridge Rd.
Bethesda, MD  20814-3220
tel:  [phone]
[hidden email]

[Shawn Mikula-2]

thanks Gabriel, Wayne!  From Wayne's email I checked the Memory & Threads
dialog box and sure enough, it said "(32-bit)", even though I had installed
the 64-bit version of Java's JRE.  From Gabriel's email, I checked the Tudor
wiki and read that the Java exe "will be typically installed in 'C:\Program
Files\Java\' (and not 'C:\Program Files (x86)\Java\' which is used for 32bit
applications)", which was the key since the Java path in ImageJ.cfg was set
for "Program Files (x86)", and thus was pointing to a 32-bit Java exe.  Once
I fixed the Java path in ImageJ.cfg to point to the correct Java exe, it
worked with max mem set to 6 GB.
Sorry for beating a dead horse before more carefully checking online FAQ's
and wikis.  Thanks again for your help.
S


----- Original Message -----
From: "Gabriel Landini" <[hidden email]>
To: <[hidden email]>
Sent: Monday, June 02, 2008 10:42 AM
Subject: Re: Problems running ImageJ on 64x WinXP with max mem set to 6 GB

> On Monday 02 June 2008, Shawn Mikula wrote:
>> hello ImageJ community,
>> this email may be better addressed to a Java mailing list, but hopefully
>> someone here can help me out...  To use ImageJ with images of several
>> GB's
>> in size, I have tried installing the 64x JRE (v1.6) on a 64x WinXP system
>> with 16 GB RAM, but when I use ImageJ with Xmx option set to 6 GB, I am
>> receiving a "Could not create the Java virtual machine" error and early
>> termination of ImageJ.  Has anyone used ImageJ on 64x WinXP systems
>> successfully using multi-GB size images?  Does anyone have any ideas why
>> Java is not able to create the Java virtual machine?
>
> This question has been asked many times and there is a number of FAQs with
> suggestion in the wiki at the Tudor site.
>
> Cheers,
>
> G.

----- Original Message -----
From: "Wayne Rasband" <[hidden email]>
To: "Shawn Mikula" <[hidden email]>
Sent: Monday, June 02, 2008 10:50 AM
Subject: Re: Problems running ImageJ on 64x WinXP with max mem set to 6 GB

>> hello ImageJ community,
>> this email may be better addressed to a Java mailing list, but
>> hopefully someone here can help me out...  To use ImageJ with images
>> of several GB's in size, I have tried installing the 64x JRE (v1.6) on
>> a 64x WinXP system with 16 GB RAM, but when I use ImageJ with Xmx
>> option set to 6 GB, I am receiving a "Could not create the Java
>> virtual machine" error and early termination of ImageJ.  Has anyone
>> used ImageJ on 64x WinXP systems successfully using multi-GB size
>> images?  Does anyone have any ideas why Java is not able to create the
>> Java virtual machine?
>> thanks.
>> Shawn
>
> Shawn,
>
> Are you sure that ImageJ is using a 64-bit version of Java? If it is,
> the title of the Edit>Options>Memory & Threads dialog box will be
> "Memory (64-bit)". I have successfully use the Edit>Options>Memory &
> Threads command to set the memory limit to 12000 MB on a 16GB machine
> running XP64 and a 64-bit version of Java.
>
> -wayne
>

[Stephan Preibisch]

Hi Shawn,

actually this is a problem I faced myself before as I have 24GB on my
machine. In all current 64 Bit Java implementations there seems to be a
problem when using more than 13,7GB of RAM.

On the Tudor website they suggest:
-XmxNg -XX:+AggressiveHeap

However this did not work out above the mentionned 13,7GB. Java does not
complain but never allocates more than that, at least on two machines in
our institute (the 24GB Win64/Ubuntu64) and 16GB Mac.

I was able to solve this issue by using the following commands:
-server -Xms23500M -Xmx23500M -XX:+AggressiveHeap

Hope this helps,
Stephan

-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of
Shawn Mikula
Sent: Monday, June 02, 2008 1:38 PM
To: [hidden email]
Subject: Problems running ImageJ on 64x WinXP with max mem set to 6 GB

hello ImageJ community,
this email may be better addressed to a Java mailing list, but hopefully
someone here can help me out...  To use ImageJ with images of several GB's
in size, I have tried installing the 64x JRE (v1.6) on a 64x WinXP system
with 16 GB RAM, but when I use ImageJ with Xmx option set to 6 GB, I am
receiving a "Could not create the Java virtual machine" error and early
termination of ImageJ.  Has anyone used ImageJ on 64x WinXP systems
successfully using multi-GB size images?  Does anyone have any ideas why
Java is not able to create the Java virtual machine?
thanks.
Shawn



--
Shawn Mikula, Ph.D.,
Center for Neuroscience
University of California-Davis,
1544 Newton Court,
Davis, CA 95618,
Phone: [phone]
Fax: [phone]
mail: [hidden email]
web: http://brainmaps.org