To Run Mesquite on Linux

SYSTEM REQUIREMENTS
To run Mesquite, you need Java installed.  The version of Mesquite you have here runs on Java 1.8 or higher. If Mesquite doesn't work, you may need to try different versions of Java. Occasionally a new version of Java is released that has bugs, or adds a requirement that is not backwards-compatible, and Mesquite will be unable to run. 

There is a bug in Oracle Java versions 11 to 16 (at least) on Linux that causes Mesquite to crash during startup with a StackOverflowError. The only workaround we know is to use Mesquite on Linux only with Java version 8 (i.e. 1.8) which is available from java.com. You may need to make adjustments so that your system knows to use Java 8 (e.g., see instructions here http://www.ormbunkar.se/aliview/#java8install, or see below).

RUNNING MESQUITE
Run Mesquite by double clicking mesquite.sh or running mesquite.sh from the command line like this:
	./mesquite.sh

You may want to edit this to request more memory using  options like "-Xmx1000M -Xss4m" (see below).

Alternatively, run it from the command line by cd'ing into Mesquite_Folder and then giving a command like this:

   java -Xmx1000M -Xss4m -Djava.library.path=lib -Djri.ignore.ule="yes" -jar Mesquite.jar

The part -Xmx1000M indicates how much heap memory to give to Mesquite in general. With more heap memory Mesquite can handle more trees, bigger matrices, bigger charts, and so on.

The part -Xss4m indicates how much stack memory to give to each thread.  With more stack memory, Mesquite can handle bigger trees, e.g. more than 5000 taxa.  To be able to handle 10000 taxa, you may need to increase this to 4m

Here is an example configuration:

	java -Xmx4000M -Xss16m -d64 -Djava.library.path=lib -Djri.ignore.ule="yes" -jar Mesquite.jar

This gives much memory to Mesquite, but 4000 MB (= 4 GB) memory exceeds the ability of 32 bit Java.  For that reason the command -d64 was added, to indicate you want to use 64 bit java.  

If you run Mesquite directly from the command line, you can replace ÒjavaÓ by the full path to the Java 1.8 jre or jdk.  That will allow you to have multiple versions of Java on your computer, have Java 16 or some other newer version as the default, but still run Mesquite on Java 1.8.