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).
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
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.
The easiest way to launch Jalview with a different percentage of physical memory available is to create a text file with extension .jvl and with content that looks like
jalview.jvmmempc=50
Replace the value with the percentage of memory you wish to allocate to Jalview.
In Windows and in macOS you can then launch Jalview by double clicking on this file, and your memory setting will be used instead of the default value of 90.
In Linux or other unix variants you can launch Jalview on the command line and provide your JVL file as an argument with
/PATH_TO_JALVIEW/Jalview /path/to/file/mymemorysetting.jvl
If you want to use a memory setting like this and open a file you can use both files as arguments in the command line, but you must put the jvl file first, e.g.
/PATH_TO_JALVIEW/Jalview /path/to/file/mymemorysetting.jvl /path/to/alignments/myalignment.fa