3 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
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23 <title>Memory Settings</title>
28 <strong>Memory Usage Settings for Jalview</strong>
31 <p>When launched as an Application, Jalview will automatically
32 configure the amount of memory allocated to the program to be 90% of
33 physical memory. You may wish to change this behaviour -
34 particularly if you are working on a machine that runs other memory
37 <em>Signs that Jalview is Running out of Memory</em><br /> If
38 Jalview has not explicitly told you that it has run out of memory,
39 then a common sign is that a function that normally works seems to
40 have no effect when working with a larger set of sequences (this
41 might include open dialog boxes for saving PNG files, or when
42 interpreting the result of a web service calculation).
45 <em>Jalview Memory Usage Monitor</em>: If you are concerned about
46 memory, or think that things might be behaving strangely because of
47 a shortage of memory, then you can check this by enabling the memory
48 usage monitor. This is done by selecting the <strong>Tools→Show
49 Memory Usage</strong> option. Once enabled, the memory usage monitor
50 displays the currently available memory, the total memory, and the
51 percentage free at the bottom left hand side of the Jalview Desktop
55 <em>Increasing the memory available to Jalview</em><br /> The
56 amount of memory allocated is defined wheb Jalview is launched
57 because of the way that Java runs on a computer - what is actually
58 run is a program called a Java virtual machine (a JVM) which
59 executes the java program instructions. The JVM has limits on the
60 memory that can be allocated to the java program - and it is often
61 necessary to adjust them if you are working with particularly large
62 datasets, or need to make room for other processes on the machine.<br />
63 <br />Jalview 2.11 includes a launcher that automatically
64 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:
68 <li><em><font size="3">JVL file</font></em> <br /> The easiest
69 way to launch Jalview with a different percentage of physical
70 memory available is to create a text file with extension <em>.jvl</em>
71 and a single line to specify the percentage of memory you wish
72 Jalview to request: <pre>
73 jalview.jvmmempc=50</pre> In Windows and in macOS you can then launch Jalview by
74 double clicking on this file, and your memory setting will be used
75 instead of the default value. <br /> <br /> In Linux or other
76 unix variants you can launch Jalview on the command line and
77 provide your JVL file as an argument with <pre>
78 /PATH_TO_JALVIEW/Jalview /path/to/file/mymemorysetting.jvl</pre> If you want to use a memory setting like this and open a
79 file you can use both the jvl and alignment files as command line
80 arguments, but you must put the <em>jvl</em> file first, e.g. <pre>
81 /PATH_TO_JALVIEW/Jalview /path/to/file/mymemorysetting.jvl /path/to/alignments/myalignment.fa</pre> Alternatively, you can use the standard Jalview command line
82 arguments with or without the jvl file (first), e.g. <pre>
83 /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
84 settings in Windows and macOS too: <br /> In Windows you must
86 \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>
87 open /Applications/Jalview.app --args ~/mymemorysetting.jvl -open ~/myalignment.fa</pre><em>(put all the Jalview arguments <em>after</em> the --args
90 <li><em><font size="3">Maximum memory limit</em><br/>
91 Since 2.11.1.0, Jalview's configuration includes a 'maximum memory limit':
92 <pre>jalview.jvmmemmax = 32G</pre>
93 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.
96 <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/>
97 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,
98 then you can set the <em>jvmmempc</em> and <em>jvmmemmax</em> values using application command line arguments <em>-jvmmempc=PERCENT</em>
99 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.
100 <pre>java -jar jalview-all-2.11.1.0-j1.8.jar -jvmmempc=50 -jvmmemmax=20g</pre>
101 (this example will launch Jalview with a maximum heap size of the smaller of 20GB or 50% of physical memory detected).
102 <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.
105 <li><em><font size="3"><a name="jvm"/>Directly opening Jalview
106 with a JVM</font></em> <br /> Launching Jalview directly with a JVM is
107 entirely possible, but is not recommended for regular interactive
108 use because it bypasses Jalview's launcher which also handles
109 automatic updates and configuration of other aspects of Jalview
110 operation. <br /> However by launching Jalview in this way you
111 have full access to the Java command line arguments. In particular
112 you can set the maximum allowed memory with the <em>-Xmx...</em>
113 JVM argument. <br /> <em>-Xmx</em> should be immediately followed
114 (no space or equals) by the maximum amount of memory specified in
115 bytes, or in kilobytes, megabytes or gigabytes by following the
116 number with a "k", "m" or "g" respectively. <br />For example: <pre>
117 -Xmx8g</pre>Jalview binaries for Windows and macOS are distributed
118 with their own JVM which you will find in
120 <li><em>Windows:</em> .../Jalview/jre/bin/java.exe</li>
122 .../Jalview.app/Contents/Resources/app/jre/Contents/Home/bin/java</li>
123 </ul> For linux and other unixes you will have to install a Java 1.8
124 JRE (we recommend the ones found at <a
125 href="https://adoptopenjdk.net">https://adoptopenjdk.net/</a>) <br />
126 <br /> You will also need to reference the "appdir" release
127 folder with all of the Jalview jar files.
129 <li>On Windows this will be <pre>\PATH_TO_JALVIEW\release</pre>
131 <li>On macOS it will be <pre>/Applications/Jalview.app/Contents/Resources/app/release</pre>
132 and on linux or unix <pre>/PATH_TO_JALVIEW/release</pre>
134 </ul> Assuming the <em>java</em> (or <em>java.exe</em> on Windows)
135 commands are available to you, you can run, e.g. <pre>
136 java -Xmx1500m -cp "/PATH_TO_RELEASE_DIR/*" jalview.bin.Jalview
137 </pre> Or on Windows <pre>
138 java.exe -Xmx1500m -cp "\PATH_TO_RELEASE_DIR\*" jalview.bin.Jalview
139 </pre> <em>Note:</em> for this to work the classpath argument wildcard <strong>must</strong> be simply
140 a '*' and not '*.jar'. <br /> <br />
141 You can also add other <a href="features/commandline.html">Jalview
142 command line arguments</a> as above after the <em>jalview.bin.Jalview</em>
143 class name, but <strong>you cannot use <em>jvl</em> files
144 </strong> if launching Jalview in this way.</li>