</h2>
<p>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.</p>
+ <p>
+ This behaviour might not be ideal if you are working on a machine
+ that runs other memory intensive processes, and (<em>since
+ Jalview 2.11.2</em>) can be changed via the <a
+ ref="preferences.html#startup">Startup Preferences</a> panel.
+ </p>
<p>
<em>Signs that Jalview is Running out of Memory</em><br /> If
Jalview has not explicitly told you that it has run out of memory,
</p>
<ul>
- <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>
+ <li><em><font size="3">Jalview's Startup
+ Preferences panel</font></em> <br /> The easiest way to launch Jalview
+ with a different percentage of physical memory available is to
+ adjust your user preferences via the <a
+ ref="preferences.html#startup">Startup Preferences</a> panel.</li>
+ <li><em><font size="3">JVL file</font></em> <br />Another way
+ to adjust launch settings is with 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
+ 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>
+ /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</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 (or can limit the amount) of memory to be allocated to Jalview in conjunction with the jalview.jvmmempc setting.
<br/><br/>
</li>
- <li><em><font size="3"><a name="jar">Command line arguments when using the executable jar (jalview-all.jar)</a></em><br/>
- If you are using the Jalview standalone executable jar, (usually named <em>jalview-all-....jar</em> with a Jalview and Java version designation),
- then you can set the <em>jvmmempc</em> and <em>jvmmemmax</em> values using application command line arguments <em>-jvmmempc=N</em>
- and <em>-jvmmemmax=M</em> respectively, e.g.
+ <li><em><font size="3"><a name="jar">Command line arguments when using the executable jar (jalview-all.jar) or jalview.bin.Launcher</a></em><br/>
+ If you are using the Jalview standalone executable jar (usually named <em>jalview-all-....jar</em> with a Jalview and Java version designation) or using <em>jalview.bin.Launcher</em> to start Jalview,
+ then you can set the <em>jvmmempc</em> and <em>jvmmemmax</em> values using application command line arguments <em>-jvmmempc=PERCENT</em>
+ and <em>-jvmmemmax=MAXMEMORY</em> respectively. <em>PERCENT</em> should be an integer between 1 and 100, and MAXMEMORY should be an amount of memory in bytes, or you can append a "k", "m", "g", or "t" to use units of kilobytes, megabytes, gigabytes or terabytes, e.g.
<pre>java -jar jalview-all-2.11.1.0-j1.8.jar -jvmmempc=50 -jvmmemmax=20g</pre>
(this example will launch Jalview with a maximum heap size of the smaller of 20GB or 50% of physical memory detected).
+ <br/>The default value for jvmmempc is 90, whilst the default value for jvmmemmax is 32g if Jalview can determine a total physical memory size of the host system, and a more cautious 8g if Jalview is unable to determine a total physical memory size.
<br/><br/>
</li>
<li><em><font size="3"><a name="jvm"/>Directly opening Jalview
git://source.jalview.org / jalview.git / blobdiff