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="1.5+" 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!
++ +