-<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'.<br>\r
- Also there MUST be a carriage return after the final line.\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
+<html>
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * 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/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ -->
+<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 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):<br /> <a
+ href="http://www.jalview.org/services/launchApp?jvm-max-heap=2G">http://www.jalview.org/services/launchApp?jvm-max-heap=2G</a>
+ </p>
+ <p>
+ Alternatively, if you want to create your own JNLP file then
+ please download the latest JNLP file from <a
+ href="http://www.jalview.org/webstart/jalview.jnlp">http://www.jalview.org/webstart/jalview.jnlp</a>
+ and modify the max-heap-size parameter for the j2se tag in the
+ <resources> element. e.g.
+ <pre>
+<j2se version="1.7+" initial-heap-size="500M" max-heap-size="1000M"/>
+</pre> 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 :<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>
git://source.jalview.org / jalview.git / blobdiff