X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhelp%2Fhtml%2Fmemory.html;h=17dc55773614df4b2ae5eca048600e433b56c23c;hb=b72ed01b68a8572022f912687db5be60b53c15cf;hp=4baebf2ce41a1981beea405667ac2018e57d5c22;hpb=ee7fcf8d9d817e079c2f0498d149ec45a21f82dc;p=jalview.git diff --git a/help/help/html/memory.html b/help/help/html/memory.html index 4baebf2..17dc557 100755 --- a/help/help/html/memory.html +++ b/help/help/html/memory.html @@ -30,9 +30,13 @@
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. + physical memory, or 32GB - which ever is smaller.
++ 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,
@@ -61,33 +65,60 @@
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, and
- its behaviour can be altered in a number of different ways:
+ 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:
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.faAlternatively, you can use the standard Jalview command line + jalview.jvmmempc=50 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.
+ /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 http://www.jalview.org/examples/jpred_msa.fasta -annotations http://www.jalview.org/examples/jpred_msa.seq.concise -colour ClustalYou 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.faIn 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) -
+ \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). +