* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
---!>
-<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="1.4+" 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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