- <li><em><font size="3">JVL file</font></em>
- <p>
- The easiest way to launch Jalview with a different percentage of physical memory available is to
- create a text file with extension <em>.jvl</em> and with content that contains the line
- <pre>
- jalview.jvmmempc=50
- </pre>
- Replace the value with the percentage of memory you wish to allocate to Jalview.
- </p>
- <p>
- 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.
- </p>
- <p>
- In Linux or other unix variants you can launch Jalview on the command line and provide your JVL file as an argument with
- <pre>
- /PATH_TO_JALVIEW/Jalview /path/to/file/mymemorysetting.jvl
- </pre>
-
- </p>
- <p>
- If 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 <em>jvl</em> file first, e.g.
- <pre>
- /PATH_TO_JALVIEW/Jalview /path/to/file/mymemorysetting.jvl /path/to/alignments/myalignment.fa
- </pre>
- alternatively, you can use the standard Jalview command line arguments with or without the jvl file (first), e.g.
- <pre>
- /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 Clustal
- </pre>
- </p>
-
- <p>
- You can use command line arguments to control memory settings in Windows and macOS too:
- <br/>
- In Windows you must use, e.g.
- <pre>
- \PATH_TO_JALVIEW\Jalview.exe %HOMEPATH%\mymemorysetting.jvl -open %HOMEPATH%\myalignment.fa
- </pre>
- and in macOS you can use the macOS <em>open</em> command like this:
- <pre>
- open /Applications/Jalview.app --args ~/mymemorysetting.jvl -open ~/myalignment.fa
- </pre>
- (put all the Jalview arguments <em>after</em> the --args parameter).
-
- </p>
+ <li><em><font size="3">JVL file</font></em> <br /> The easiest
+ way to launch Jalview with a different percentage of physical
+ memory available is to create a text file with extension <em>.jvl</em>
+ and a single line to specify the percentage of memory you wish
+ Jalview to request: <pre>
+ jalview.jvmmempc=50</pre> 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. <br /> <br /> In Linux or other
+ unix variants you can launch Jalview on the command line and
+ provide your JVL file as an argument with <pre>
+ /PATH_TO_JALVIEW/Jalview /path/to/file/mymemorysetting.jvl</pre> If 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 <em>jvl</em> file first, e.g. <pre>
+ /PATH_TO_JALVIEW/Jalview /path/to/file/mymemorysetting.jvl /path/to/alignments/myalignment.fa</pre> Alternatively, you can use the standard Jalview command line
+ arguments with or without the jvl file (first), e.g. <pre>
+ /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 Clustal</pre> You can use command line arguments to control memory
+ settings in Windows and macOS too: <br /> In Windows you must
+ use, e.g. <pre>
+ \PATH_TO_JALVIEW\Jalview.exe %HOMEPATH%\mymemorysetting.jvl -open %HOMEPATH%\myalignment.fa</pre> In macOS you can use the macOS <em>open</em> command like this: <pre>
+ open /Applications/Jalview.app --args ~/mymemorysetting.jvl -open ~/myalignment.fa</pre><em>(put all the Jalview arguments <em>after</em> the --args
+ parameter)
+ </em><br/><br/></li>
+ <li><em><font size="3">Maximum memory limit</em><br/>
+ Since 2.11.1.0, Jalview's configuration includes a 'maximum memory limit':
+ <pre>jalview.jvmmemmax = 32G</pre>
+ Adjusting this default (via a JVL file, above) will allow larger amounts of memory to be allocated to Jalview in connjunction with the jalview.jvmmempc setting.