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<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
*
* This file is part of Jalview.
*
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
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+<head><title>Memory Settings</title></head>
+<body>
+<h2>
+ <center>
+ <strong>Memory Usage Settings for Jalview</strong>
+ </center>
+</h2>
+<p>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.<br>
+ 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).</p>
+ <p><em>Jalview Memory Usage Monitor</em>: 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 <strong>Tools→Show Memory Usage</strong>
+ 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.</p>
+<p><em>Increasing the memory available to Jalview</em><br>
+The way you increase the memory settings for the JVM depends on which installation
+ of Jalview you use:</p>
+<ul>
+ <li><em><font size="3">Web Start Version</font></em>
+ <p>JavaWS sets the JVM parameters through special tags in the JNLP file. You'll
+ need to <a href="jalviewjnlp.html">make your own jnlp file</a> and add the following parameter into the
+ <resources> element.
+ <pre>
+<j2se version="1.5+" initial-heap-size="500M" max-heap-size="1000M"/>
+</pre>
+ 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 :<br>
+ <pre>
+file://<full path to file>
+</pre>
+ If jalview doesn't start up, see <a href="#memsetting">below</a>. 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.
+ <p></li>
+ <li><em><font size="3">Install Anywhere version</font></em>
+ <p> You need to change the InstallAnywhere configuration settings for the
+ application. These are found in different places depending upon which operating
+ system you have :
+ <ul>
+ <li><em>Unix/Windows</em>
+ <p> 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 :
+ <pre>
+lax.nl.java.option.java.heap.size.max=1000m
+lax.nl.java.option.java.heap.size.initial=500m
+</pre>
+ 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'.<br>
+ Also there MUST be a carriage return after the final line.
+ <p></p>
+ </li>
+ <li><em>Mac OSX</em>
+ <p>The lines you need to change are in the <em>Info.plist</em> file inside
+ the <em>Jalview.app/Contents</em> directory (which is where the installAnywhere
+ installation was made) :
+ <pre>
+<key&ht;VMOptions</key&ht;
+<array>
+! <string>-Xms2M</string>
+! <string>-Xmx64M</string>
+</array>
+</pre>
+ Exchange the above two string tags for :
+ <pre>
+<string>-Xms500M</string>
+<string>-Xmx1000M</string>
+</pre>
+ <p></p>
+ </li>
+ </ul>
+ <li><font size="3"><em>In all cases</em></font><br>
+ Save the file and try to start Jalview in the normal way. If it doesn't start,
+ see below... </li>
+</ul>
+<font size="3"><em>Jalview doesn't start... What do the memory settings mean ?<a name="memsetting"></a></em></font>
+<p> 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).
+</p>
+<p> 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! </p>
+<p> </p>
+</body>
+</html>
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