Jalview sometimes runs out of memory. This is because of the way that Java
- runs on a computer - what is actually run is a program called a virtual machine
- (the JVM) which executes the java instructions. The JVM has limits on the memory
- that can be allocated to the java program - and you might need to increase them
- if you are working with particularly large datasets.
- If Jalview has not explicitly told you that it has run out of memory, then a
- common sign is that a function that normally works seems to have no effect when
- working with a larger set of sequences (this might include open dialog boxes
- for saving PNG files, or when interpreting the result of a web service calculation).
Jalview Memory Usage Monitor: If you are concerned about memory, or think that things might be behaving - strangely because of a shortage of memory, then you can check this by enabling the - memory usage monitor. This is done by selecting the Tools→Show Memory Usage - option. Once enabled, the memory usage monitor displays the currently - available memory, the total memory, and the percentage free at the - bottom left hand side of the Jalview Desktop window's background.
-Increasing the memory available to Jalview
-The way you increase the memory settings for the JVM depends on which installation
- of Jalview you use:
JavaWS sets the JVM parameters through special tags in the JNLP file. You'll - need to make your own jnlp file and add the following parameter into the - <resources> element. -
-<j2se version="1.4+" initial-heap-size="500M" max-heap-size="1000M"/> -- Save the jnlp file somewhere and then - if you start Jalview through your - web browser, point your browser at the file's url, othewise simply run javaws - with the file location as its argument. The file's url is something like :
-file://<full path to file> -- If jalview doesn't start up, see below. You'll have - to edit the above settings in the JNLP file using a text editor, save it, - and try starting Jalview with it once more. -
You need to change the InstallAnywhere configuration settings for the - application. These are found in different places depending upon which operating - system you have : -
Take a look inside the Jalview program installation directory (this - might be in C:\Program Files\Jalview on windows). You should find a - file called 'Jalview.lax' in it - make a backup, and then add the following - lines to the end of the original file : -
-lax.nl.java.option.java.heap.size.max=1000m -lax.nl.java.option.java.heap.size.initial=500m -- Case and (lack of) spaces are important here! Do not add any spaces after - the m in each line, and do not put any spaces before 'lax'.
The lines you need to change are in the Info.plist file inside - the Jalview.app/Contents directory (which is where the installAnywhere - installation was made) : -
-<key&ht;VMOptions</key&ht; -<array> -! <string>-Xms2M</string> -! <string>-Xmx64M</string> -</array> -- Exchange the above two string tags for : -
-<string>-Xms500M</string> -<string>-Xmx1000M</string> -- -
The 1000m value corresponds to the maximum number of megabytes of space that - java objects can occupy. The 500m is the initial heap size that java will run - in - increasing this can speed up memory allocation if you know you will need - 500 meg of memory to begin with (ie it should speed up loading large alignments). -
-If, after setting the initial and maximum heap size to some large value, you - cannot actually start Jalview, then the max and initial sizes are too big for - your machine (there seems to be a physical limit related to physical RAM - email - the usual address to enlighten us if you know better!). Our experiments found - 1000m to be the biggest setting that could be used on a 1GB machine. Just try - reducing the sizes until Jalview starts up properly!
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