Memory Settings

From af2e52a8a12ccafb733ca34eb0bbc313c3771900 Mon Sep 17 00:00:00 2001 From: jprocter Date: Fri, 11 Jan 2008 13:54:27 +0000 Subject: [PATCH] jalview memory monitor instructions added --- help/html/memory.html | 195 +++++++++++++++++++++++++------------------------ 1 file changed, 101 insertions(+), 94 deletions(-) diff --git a/help/html/memory.html b/help/html/memory.html index ba1a72c..10ef708 100755 --- a/help/html/memory.html +++ b/help/html/memory.html @@ -1,94 +1,101 @@ - -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'.
  - Also there MUST be a carriage return after the final line. -
  -
- 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!

- - + +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).

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:

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'.
  + Also there MUST be a carriage return after the final line. +
  +
- 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