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
- for saving PNG files, or when interpreting the result of a web service calculation).
Jalview Memory Usage Monitor: 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 Tools→Show Memory Usage - 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.
-Increasing the memory available to Jalview
-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. -
-<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 - with the file location as its argument. The file's url is something like :
++
++ Memory Usage Settings for Jalview + ++ 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 for saving PNG files, or when interpreting the result + of a web service calculation). ++ Jalview Memory Usage Monitor: 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 Tools→Show + Memory Usage 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. +
++ Increasing the memory available to Jalview
+
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 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):
http://www.jalview.org/services/launchApp?jvm-max-heap=2G
+
+ Alternatively, if you want to create your own JNLP file then + please download the latest JNLP file from http://www.jalview.org/webstart/jalview.jnlp and modify the + max-heap-size parameter for the j2se tag in the + <resources> element. e.g. +
+<j2se version="1.7+" initial-heap-size="500M" max-heap-size="1000M"/> +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 :
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. -
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 : -
+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 : +
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'.
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) : -
+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) : + +
<key&ht;VMOptions</key&ht; <array> ! <string>-Xms2M</string> ! <string>-Xmx64M</string> </array> -- Exchange the above two string tags for : -
+Exchange the above two string tags for :
<string>-Xms500M</string> <string>-Xmx1000M</string>- -
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 - reducing the sizes until Jalview starts up properly!
-+
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 + reducing the sizes until Jalview starts up properly!
+