X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhelp%2Fhtml%2Fmemory.html;h=17dc55773614df4b2ae5eca048600e433b56c23c;hb=5a8552c431758f7cb4fdca50f6d50996d13e23bc;hp=396507b3ea07f2d2fc06a7409688b510437cea38;hpb=ab1dce80c1a6f45b2071016f1ce07a3466d81a2e;p=jalview.git diff --git a/help/help/html/memory.html b/help/help/html/memory.html index 396507b..17dc557 100755 --- a/help/help/html/memory.html +++ b/help/help/html/memory.html @@ -28,24 +28,22 @@ 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, or 32GB - which ever is smaller.

- 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). + This behaviour might not be ideal if you are working on a machine + that runs other memory intensive processes, and (since + Jalview 2.11.2) can be changed via the Startup Preferences panel. +

+

+ 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 @@ -58,108 +56,109 @@ 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:

For linux and other unixes you will have to install a Java 1.8 + JRE (we recommend the ones found at https://adoptopenjdk.net/)
+
You will also need to reference the "appdir" release + folder with all of the Jalview jar files. + Assuming the java (or java.exe on Windows) + commands are available to you, you can run, e.g. 
       java -Xmx1500m -cp "/PATH_TO_RELEASE_DIR/*" jalview.bin.Jalview
-
- or on Windows - 
+
Or on Windows 
       java.exe -Xmx1500m -cp "\PATH_TO_RELEASE_DIR\*" jalview.bin.Jalview
-
- Note that the classpath argument wildcard must be simply a '*' and not '*.jar'. This is a limitation of Java. -

-

- You can also add other Jalview command line arguments as above after the jalview.bin.Jalview class name (you cannot use jvl files if launching Jalview in this way). - - - + Note: for this to work the classpath argument wildcard must be simply + a '*' and not '*.jar'.

+ You can also add other Jalview + command line arguments as above after the jalview.bin.Jalview + class name, but you cannot use jvl files + if launching Jalview in this way. -