Memory Settings

X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=help%2Fhtml%2Fmemory.html;h=9437a60e1c8619787181a43ddd8e1c51356099ba;hb=bc18effe68ba80213a6d03ca7e6175adc6be71d6;hp=e18e273bc6e63d17a8266460e4a4915b193850f3;hpb=6ab4ef1cc71ff9d28a21a139db69e4a8351a3fb5;p=jalview.git diff --git a/help/html/memory.html b/help/html/memory.html index e18e273..9437a60 100755 --- a/help/html/memory.html +++ b/help/html/memory.html @@ -1,18 +1,156 @@ + * You should have received a copy of the GNU General Public License + * along with Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. + --> + +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. +

+ +