X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=help%2Fhelp%2Fhtml%2Fmemory.html;h=ec57530a42f937fdf5387179d64e7ca4573710ef;hb=639bc5f3126d65cc1de8992b9a0fa0cfb993a9ff;hp=e58339854ee5da1fd70660cdcb740f4ec2bdc866;hpb=883ba618f83573893f1f0b895b0bf84dacccefe5;p=jalview.git diff --git a/help/help/html/memory.html b/help/help/html/memory.html index e583398..ec57530 100755 --- a/help/help/html/memory.html +++ b/help/help/html/memory.html @@ -28,20 +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, 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).
+ 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 @@ -54,8 +56,104 @@ 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
+ jalview.jvmmempc=50In 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.
+ /PATH_TO_JALVIEW/Jalview /path/to/file/mymemorysetting.jvlIf you + want to use a memory setting like this and open a file you can use + both the jvl and alignment files as command line arguments, but + you must put the jvl file first, e.g.
+ /PATH_TO_JALVIEW/Jalview /path/to/file/mymemorysetting.jvl /path/to/alignments/myalignment.fa+ Alternatively, you can use the standard Jalview command line + arguments with or without the jvl file (first), e.g.
+ /PATH_TO_JALVIEW/Jalview /path/to/file/mymemorysetting.jvl -open https://www.jalview.org/examples/jpred_msa.fasta -annotations https://www.jalview.org/examples/jpred_msa.seq.concise -colour Clustal+ You can use command line arguments to control memory settings in + Windows and macOS too:
+ \PATH_TO_JALVIEW\Jalview.exe %HOMEPATH%\mymemorysetting.jvl -open %HOMEPATH%\myalignment.fa+ In macOS you can use the macOS open command like this:
+ open /Applications/Jalview.app --args ~/mymemorysetting.jvl -open ~/myalignment.fa(put + all the Jalview arguments after the --args parameter) +
jalview.jvmmemmax = 32G+ Adjusting this default (via a JVL file, above) will allow larger amounts (or can limit the amount) of memory to be allocated to Jalview in conjunction with the jalview.jvmmempc setting. +
java -jar jalview-all-2.11.1.0-j1.8.jar -jvmmempc=50 -jvmmemmax=20g+ (this example will launch Jalview with a maximum heap size of the smaller of 20GB or 50% of physical memory detected). +
+ -Xmx8gJalview binaries for Windows and macOS are distributed + with their own JVM which you will find in +
\PATH_TO_JALVIEW\release+
/Applications/Jalview.app/Contents/Resources/app/release+ and on linux or unix
/PATH_TO_JALVIEW/release+
+ java -Xmx1500m -cp "/PATH_TO_RELEASE_DIR/*" jalview.bin.Jalview +Or on Windows
+ java.exe -Xmx1500m -cp "\PATH_TO_RELEASE_DIR\*" jalview.bin.Jalview +Note: for this to work the classpath argument wildcard must be simply + a '*' and not '*.jar'.