On Aug 21, 2006, at 7:21 AM, Rolf Huehne wrote: Frieda Reichsman wrote: does anyone know if there a way to re-set Java's memory to avoid the "Java.lang out of memory error" that results from re-loading a page with an applet many times?
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The only definite way I know of, to free the memory of previous Jmol page loads, is to quit the browser and usually automatically the JavaVM with it.
Hi Rolf,
Yes, this is what I seek to avoid. Since it is not very nice, if you have to do this every 15 minutes, I increase the maximum amount of memory the JavaVM is allowed to use. Currently I am using 256 MB as default (having 1 GB physical memory), but I already set it to 1.6 GB to be able to work (successfully) with the largest PDB file available from RCSB (biological unit 1 of '2bvi', 386 MB uncompressed file size) within my Jmol applet interface.
In order to set the maximum memory size you must open the configuration dialog of your Java installation (I don't know where it is hidden on a Mac).
On Mac OSX there is a Java preferences pane accessed through Applications/Utilities/Java/J2SE 5.0/Java Preferences Then there must be something like an 'Advanced Options' section where you can type in some text.
Although it is not under advanced, there is a form for entering text on the General section of the Java preferences. If you want to set the memory size to 256MB you have to type:
-Xmx256m
I just now entered this into the form on the General section, and will report back to the list when I have a sense of whether it is increasing the time between errors.
You can exchange the '256' by any number you like, as long as it doesn't exceed the available virtual memory space. But it is better for the overall performance of your computer to choose a value for your everyday work that is sufficient below the amount of physical memory (RAM).
I can usually work quite a lot before I run into the 'out of memory' problem with 256MB. But this depends of course of the size of the structures you are loading and the number of reloads you perform.
OK, excelllent info, I will update the list with my results in the next few days.
Best, ///////////////////////////////////////////
Frieda Reichsman, PhD Molecules in Motion Interactive Molecular Structures http://www.moleculesinmotion.com
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