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+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see
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 can obtain a JNLP file with modified memory settings from
+ our service with the following link (replace 2G with desired memory
+ in G or M):
http://www.jalview.org/services/launchApp?jvm-max-heap=2G
+
+ Alternatively, if you want to create your own JNLP file then please + download the latest JNLP file from http://www.jalview.org/webstart/jalview.jnlp + and modify the max-heap-size parameter for the j2se tag in the + <resources> element. e.g. +
+<j2se version="1.7+" initial-heap-size="500M" max-heap-size="1000M"/> +In both cases, you should save your new jnlp file somewhere and + then either point your web browser at the file's url, launch it from + your file browser, or from a terminal window run javaws (located in + your Java installation's bin directory) 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!
++ +