|Known Problems and Limitations:
1. Until Java 5 the default amount of memory allocated a Java virtual machine was 64M. This is not nearly enough.
2. The amount of memory can be increases on the command line that starts Java. The scripts that come in the Jarnal installation package use 192M. This is set on the command line by the command line switch -Xms192m. This should be enough for most purposes, but you can increase it if necessary.
3. As of Java 5 some machines are classed as "servers". If you run java -h from a command line and see The default VM is server, because you are running on a server-class machine mixed in with the information it prints out then the default amount of memory is not 64M, it is 1/4 the total amount of physical memory on your machine up to a maximum of 1G. For example, on one machine I have 4G memory; it is a server class machine. If I run Java without setting the memory - deleting the switch -Xms192m from the command line script - then Java runs with 1G of memory, quite a lot more than 192M.
4. If you want to use very large files (100+ page pdf documents) 192M is not enough memory. If you have a modern machine with 2-4G of physical memory, try setting the memory to 1-2G. I got very good performance on large documents with -Xms1920m, 10 times the usual setting.
Thanks to Marco Poletti for helping figure this out.