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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!
++ +