Memory Settings

X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fmemory.html;fp=help%2Fhtml%2Fmemory.html;h=0000000000000000000000000000000000000000;hb=4f77328104498504339216829abf5ea87e2791ec;hp=9437a60e1c8619787181a43ddd8e1c51356099ba;hpb=2b8c0785318a3528e1876e8e2dd48b7d831eae69;p=jalview.git diff --git a/help/html/memory.html b/help/html/memory.html deleted file mode 100755 index 9437a60..0000000 --- a/help/html/memory.html +++ /dev/null @@ -1,156 +0,0 @@ - - - -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 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. -
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...

- Please Note: We do modify the default memory settings in - Jalview from time to time, so you may find different numbers to - those shown in the examples above. -

- 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!

- We increased the default memory in Jalview 2.10.5 to 1G. To launch - Jalview with the pre 2.10.5 default memory allocation, use the Jalview - 256MB JNLP. -

- -