X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhelp%2Fhtml%2Fmemory.html;h=0374dcba23fb31286bb95fe8dbe09ecb3ce9b169;hb=8554d8662434979c3a0bdebcc6a2cd837f2afd7c;hp=b784451fcfe9925c2ae862ff52b1037ae270908b;hpb=9c2db0c1bb8cbfc7fac9e783f1b43e379c060dad;p=jalview.git diff --git a/help/help/html/memory.html b/help/help/html/memory.html index b784451..0374dcb 100755 --- a/help/help/html/memory.html +++ b/help/help/html/memory.html @@ -28,24 +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 (default settings are - to try and use up to 90% of physical memory available to it). - Sometimes it may require more memory, or if you are working in a - shared memory environment you may want to limit the maximum amount - of memory that it might use. - This has to be set at the time 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 - 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 @@ -58,81 +52,96 @@ 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. - This default setting can be altered in a number of different ways, depending on how you prefer to launch Jalview and how specific you want to be with the maximum memory setting. + 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:

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