X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhelp%2Fhtml%2Fmemory.html;h=80bffa331cff12eacf38405ac301b6af580cc54e;hb=2f160359d38a4d475b0f96eb7da61f823d9ef7bd;hp=e58339854ee5da1fd70660cdcb740f4ec2bdc866;hpb=883ba618f83573893f1f0b895b0bf84dacccefe5;p=jalview.git diff --git a/help/help/html/memory.html b/help/help/html/memory.html index e583398..80bffa3 100755 --- a/help/help/html/memory.html +++ b/help/help/html/memory.html @@ -28,20 +28,18 @@ Memory Usage Settings for Jalview +

When launched as an Application, Jalview will automatically + configure the amount of memory allocated to the program to be 90% of + physical memory. You may wish to change this behaviour - + particularly if you are working on a machine that runs other memory + intensive processes.

- When launched as an Application, Jalview automatically tries to - maximise the amount of memory allocated to it, but sometimes it may - run 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). + Signs that Jalview is Running out of Memory
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 @@ -54,8 +52,95 @@ window's background.

- Increasing the memory available to Jalview
- Since Jalview 2.11, the program automatically configures the JVM memory settings to set the maximum memory available to Jalview to be 90% of physical memory. -

 

+ Increasing the memory available to Jalview
The + amount of memory allocated is defined wheb Jalview is launched + because of the way that Java runs on a computer - what is actually + run is a program called a Java virtual machine (a JVM) which + executes the java program instructions. The JVM has limits on the + memory that can be allocated to the java program - and it is often + necessary to adjust them if you are working with particularly large + datasets, or need to make room for other processes on the machine.
+
Jalview 2.11 includes a launcher that automatically + configures the proportion of memory allocated to Jalview's JVM. By default it requests up to 90% of available memory whilst ensuring that at least 0.5G is available to the operating system and at least 0.5G is available to the Java runtime platform, or a specified 'maximum memory limit' - which ever is smaller. The amount of memory requested can be altered in a number of different ways: +

+ +