X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhelp%2Fhtml%2Fmemory.html;h=17dc55773614df4b2ae5eca048600e433b56c23c;hb=d8fcaf315395d614059f4345c20ff2f86a4476f1;hp=b784451fcfe9925c2ae862ff52b1037ae270908b;hpb=9c2db0c1bb8cbfc7fac9e783f1b43e379c060dad;p=jalview.git diff --git a/help/help/html/memory.html b/help/help/html/memory.html index b784451..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 @@ -58,81 +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:
- 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 -- - - +
jalview
command line launch
+ --jvmmemmax=MAXMEMORY
and --jvmmempc=PERCENT
. MAXMEMORY
should be an integer optionally followed by one of k
, m
, g
, t
. PERCENT
should be an integer between 1 and 100.
-
++ 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'.