_envc = envc;
_config = getLocalPath(envc.appDir, CONFIG_FILE);
_backupConfig = getLocalPath(envc.appDir, BACKUP_CONFIG_DIR+File.separator+CONFIG_FILE);
- log.warning("Backup config file now", "_backupConfig", _backupConfig, "exists", _backupConfig.exists(), "isReadable", _backupConfig.canRead());
}
/**
ARG: for (int i = 0; i < _jvmargs.size(); i++) {
if (_jvmargs.get(i) instanceof java.lang.String && _jvmargs.get(i).startsWith("-Xmx")) {
_jvmargs.remove(i);
+ break ARG;
}
}
addAll(maxMemHeapArg, _jvmargs);
+ log.info("Max memory set", "maxMemHeapArg", maxMemHeapArg[0]);
}
} else if (jvmmempc != -1) {
- System.out.println("'jvmmempc' value must be in range 0 to 100 (read as '"+Integer.toString(jvmmempc)+"')");
+ log.warning("'jvmmempc' value must be in range 0 to 100 (read as '"+Integer.toString(jvmmempc)+"')");
}
// get the set of optimum JVM arguments
if (j > -1) {
ext = filename.substring(j+1);
}
- if (LOCATOR_FILE_EXTENSION.equals(ext.toLowerCase())) {
+ if (ext != null && LOCATOR_FILE_EXTENSION.equals(ext.toLowerCase())) {
// this file extension should have been dealt with in Getdown class
} else {
_appargs.add(0, "-open");
</h2>
<p>
When launched as an Application, Jalview automatically tries to
- maximise the amount of memory allocated to it, but sometimes it may
- run out of memory. This is because of the way that Java runs on a
- computer - what is actually run is a program called a virtual
- machine (the JVM) which executes the java instructions. The JVM has
- limits on the memory that can be allocated to the java program - and
+ 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.<br> If Jalview has not explicitly told you that
it has run out of memory, then a common sign is that a function that
window's background.
</p>
<p>
- <em>Increasing the memory available to Jalview</em><br>
- 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.
- <p> </p>
+ <em>Increasing the memory available to Jalview</em><br/>
+ 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.
+ </p>
+
+ <ul>
+ <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>
+
+
+ <li><em><font size="3">Directly opening Jalview with a JVM</font></em>
+ <p>
+ Launching Jalview directly with a JVM is entirely possible, but is not recommended as automatic updates and some other default settings will not operate.
+ </p>
+ <p>
+ However by launching Jalview in this way you have full access to the Java command line arguments.
+ In particular you can set the maximum allowed memory with the <em>-Xmx...</em> JVM argument.
+ <br/>
+ <em>-Xmx</em> should be immediately followed (no space or equals) by the maximum amount of memory that you might want to launch Jalview with. This can be specified in bytes as just a number,
+ or in kilobytes, megabytes or gigabytes by following the number with a "k", "m" or "g" respectively. e.g.
+ <pre>
+ -Xmx8g
+ </pre>
+ </p>
+ <p>
+ Jalview binaries for Windows and macOS are distributed with their own JVM which you will find in
+ <ul>
+ <li><em>Windows:</em> .../Jalview/jre/bin/java.exe</li>
+ <li><em>macOS:</em> .../Jalview.app/Contents/Resources/app/jre/Contents/Home/bin/java</li>
+ </ul>
+ For linux and other unixes you will have to install a Java 1.8 JRE (we recommend the ones found at <a href="https://adoptopenjdk.net">https://adoptopenjdk.net/</a>)
+ </p>
+ <p>
+ You will also need to reference the "appdir" release folder with all of the Jalview jar files.
+ <br/>
+ On Windows this will be
+ <pre>\PATH_TO_JALVIEW\release</pre>
+ whereas on macOS it will be
+ <pre>/Applications/Jalview.app/Contents/Resources/app/release</pre>
+ and on linux or unix
+ <pre>/PATH_TO_JALVIEW/release</pre>
+ </p>
+ <p>
+ Assuming the <em>java</em> (or <em>java.exe</em> on Windows) commands are available to you, you can run, e.g.
+ <pre>
+ java -Xmx1500m -cp "/PATH_TO_RELEASE_DIR/*" jalview.bin.Jalview
+ </pre>
+ or on Windows
+ <pre>
+ java.exe -Xmx1500m -cp "\PATH_TO_RELEASE_DIR\*" jalview.bin.Jalview
+ </pre>
+ <em>Note</em> that the classpath argument wildcard must be simply a '*' and not '*.jar'. This is a limitation of Java.
+ </p>
+ <p>
+ You can also add other Jalview command line arguments as above after the <em>jalview.bin.Jalview</em> class name (you cannot use <em>jvl</em> files if launching Jalview in this way).
+ </li>
+
+
+ </ul>
+
</body>
</html>
git://source.jalview.org / jalview.git / commitdiff