--- /dev/null
+<html>\r
+<head><title>Memory Settings</title></head>\r
+<body>\r
+<h2> \r
+ <center>\r
+ <strong>Memory Usage Settings for Jalview</strong> \r
+ </center>\r
+</h2>\r
+<p>Jalview sometimes runs out of memory. This is because of the way that Java \r
+ runs on a computer - what is actually run is a program called a virtual machine \r
+ (the JVM) which executes the java instructions. The JVM has limits on the memory \r
+ that can be allocated to the java program - and you might need to increase them \r
+ if you are working with particularly large datasets.<br>\r
+ If Jalview has not explicitly told you that it has run out of memory, then a \r
+ common sign is that a function that normally works seems to have no effect when \r
+ working with a larger set of sequences (this might include open dialog boxes \r
+ for saving PNG files, or when interpreting the result of a web service calculation).</p>\r
+<p>The way you increase the memory settings for the JVM depends on which installation \r
+ of Jalview you use:</p>\r
+<ul>\r
+ <li><em><font size="3">Web Start Version</font></em> \r
+ <p>JavaWS sets the JVM parameters through special tags in the JNLP file. You'll \r
+ need to make your own jnlp file and add the following parameter into the \r
+ <resources> element. \r
+ <pre>\r
+<j2se version="1.4+" initial-heap-size="500M" max-heap-size="1000M"/>\r
+</pre>\r
+ Save the jnlp file somewhere and then - if you start Jalview through your \r
+ web browser, point your browser at the file's url, othewise simply run javaws \r
+ with the file location as its argument. The file's url is something like :<br>\r
+ <pre>\r
+file://<full path to file>\r
+</pre>\r
+ If jalview doesn't start up, see <a href="#memsetting">below</a>. You'll have \r
+ to edit the above settings in the JNLP file using a text editor, save it, \r
+ and try starting Jalview with it once more. \r
+ <p></li>\r
+ <li><em><font size="3">Install Anywhere version</font></em> \r
+ <p> You need to change the InstallAnywhere configuration settings for the \r
+ application. These are found in different places depending upon which operating \r
+ system you have : \r
+ <ul>\r
+ <li><em>Unix/Windows</em> \r
+ <p> Take a look inside the Jalview program installation directory (this \r
+ might be in C:\Program Files\Jalview on windows). You should find a \r
+ file called 'Jalview.lax' in it - make a backup, and then add the following \r
+ lines to the end of the original file : \r
+ <pre>\r
+lax.nl.java.option.java.heap.size.max=1000m\r
+lax.nl.java.option.java.heap.size.initial=500m\r
+</pre>\r
+ Case and (lack of) spaces are important here! Do not add any spaces after \r
+ the m in each line, and do not put any spaces before 'lax'.\r
+ <p></p>\r
+ </li>\r
+ <li><em>Mac OSX</em> \r
+ <p>The lines you need to change are in the <em>Info.plist</em> file inside \r
+ the <em>Jalview.app/Contents</em> directory (which is where the installAnywhere \r
+ installation was made) : \r
+ <pre>\r
+<key&ht;VMOptions</key&ht;\r
+<array>\r
+! <string>-Xms2M</string>\r
+! <string>-Xmx64M</string>\r
+</array>\r
+</pre>\r
+ Exchange the above two string tags for : \r
+ <pre>\r
+<string>-Xms500M</string>\r
+<string>-Xmx1000M</string>\r
+</pre>\r
+ <p></p>\r
+ </li>\r
+ </ul>\r
+ <li><font size="3"><em>In all cases</em></font><br>\r
+ Save the file and try to start Jalview in the normal way. If it doesn't start, \r
+ see below... </li>\r
+</ul>\r
+<font size="3"><em>Jalview doesn't start... What do the memory settings mean ?<a name="memsetting"></a></em></font> \r
+<p> The 1000m value corresponds to the maximum number of megabytes of space that \r
+ java objects can occupy. The 500m is the initial heap size that java will run \r
+ in - increasing this can speed up memory allocation if you know you will need \r
+ 500 meg of memory to begin with (ie it should speed up loading large alignments). \r
+</p>\r
+<p> If, after setting the initial and maximum heap size to some large value, you \r
+ cannot actually start Jalview, then the max and initial sizes are too big for \r
+ your machine (there seems to be a physical limit related to physical RAM - email \r
+ the usual address to enlighten us if you know better!). Our experiments found \r
+ 1000m to be the biggest setting that could be used on a 1GB machine. Just try \r
+ reducing the sizes until Jalview starts up properly! </p>\r
+<p> </p>\r
+</body>\r
+</html>\r
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