<html>\r
<head><title>Memory Settings</title></head>\r
<body>\r
-<h2> \r
+<h2>\r
<center>\r
- <strong>Memory Usage Settings for Jalview</strong> \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
+<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
+ 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
+<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
+ <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 <a href="jalviewjnlp.html">make your own jnlp file</a> 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
+ 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
+ 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
+ <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
+ <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
+ 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
+ <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>-Xmx64M</string>\r
</array>\r
</pre>\r
- Exchange the above two string tags for : \r
+ Exchange the above two string tags for :\r
<pre>\r
<string>-Xms500M</string>\r
<string>-Xmx1000M</string>\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
+ 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
+<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
+<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
git://source.jalview.org / jalview.git / blobdiff