Memory Settings

From bb712bf37621ce1bee698ecd847845bcdf4e3269 Mon Sep 17 00:00:00 2001 From: amwaterhouse Date: Thu, 15 Sep 2005 14:09:08 +0000 Subject: [PATCH] Memory settings added to help --- help/help.jhm | 1 + help/helpTOC.xml | 2 +- help/html/memory.html | 93 +++++++++++++++++++++++++++++++++++++++++++++++++ 3 files changed, 95 insertions(+), 1 deletion(-) create mode 100755 help/html/memory.html diff --git a/help/help.jhm b/help/help.jhm index 7d884b3..1690f5e 100755 --- a/help/help.jhm +++ b/help/help.jhm @@ -55,6 +55,7 @@ + diff --git a/help/helpTOC.xml b/help/helpTOC.xml index 0f476a5..5c48b5a 100755 --- a/help/helpTOC.xml +++ b/help/helpTOC.xml @@ -51,8 +51,8 @@ - + diff --git a/help/html/memory.html b/help/html/memory.html new file mode 100755 index 0000000..8dd2b58 --- /dev/null +++ b/help/html/memory.html @@ -0,0 +1,93 @@ + +Memory Settings + +

+ + 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).

The way you increase the memory settings for the JVM depends on which installation + of Jalview you use:

Web Start Version +
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 :
+
```
+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. +
Install Anywhere version +
You need to change the InstallAnywhere configuration settings for the + application. These are found in different places depending upon which operating + system you have : +
- Unix/Windows +
  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'. +
  +
- Mac OSX +
  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 : +
```
+<string>-Xms500M</string>
+<string>-Xmx1000M</string>
+
```
  +
  +
+
In all cases
+ Save the file and try to start Jalview in the normal way. If it doesn't start, + see below...

+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 + reducing the sizes until Jalview starts up properly!

+ + -- 1.7.10.2