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 +
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.
- 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
+ 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).
The way you increase the memory settings for the JVM depends on which installation +
The way you increase the memory settings for the JVM depends on which installation of Jalview you use:
JavaWS sets the JVM parameters through special tags in the JNLP file. You'll - need to make your own jnlp file and add the following parameter into the - <resources> element. +
JavaWS sets the JVM parameters through special tags in the JNLP file. You'll + need to make your own jnlp file and add the following parameter into the + <resources> element.
<j2se version="1.4+" initial-heap-size="500M" max-heap-size="1000M"/>- 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 + 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 :
file://<full path to file>- If jalview doesn't start up, see below. 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. + If jalview doesn't start up, see below. 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.
You need to change the InstallAnywhere configuration settings for the - application. These are found in different places depending upon which operating - system you have : +
You need to change the InstallAnywhere configuration settings for the + application. These are found in different places depending upon which operating + system you have :
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 : +
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 :
lax.nl.java.option.java.heap.size.max=1000m lax.nl.java.option.java.heap.size.initial=500m- 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'. + 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'.
The lines you need to change are in the Info.plist file inside - the Jalview.app/Contents directory (which is where the installAnywhere - installation was made) : +
The lines you need to change are in the Info.plist file inside + the Jalview.app/Contents directory (which is where the installAnywhere + installation was made) :
<key&ht;VMOptions</key&ht; <array> @@ -64,7 +65,7 @@ lax.nl.java.option.java.heap.size.initial=500m ! <string>-Xmx64M</string> </array>- Exchange the above two string tags for : + Exchange the above two string tags for :
<string>-Xms500M</string>
<string>-Xmx1000M</string>
@@ -73,20 +74,20 @@ lax.nl.java.option.java.heap.size.initial=500m
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). +Jalview doesn't start... What do the memory settings mean ? +
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).
-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 +
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!