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TrakEM2

1,900 bytes added, 12:03, 25 February 2010
fiji arguments for heavy-duty tasks
* Create new projects from "File - New - TrakEM2 (blank)"
* Open an existing project by dragging its .xml file onto the toolbar, or via "File - Open".
 
== Running fiji for heavy-duty, memory-intensive, high-performance TrakEM2 tasks ==
 
The following configuration has been tested in a machine with 8 CPU cores and 16 Gb of RAM, running Ubuntu 8.04 "Hardy":
 
./fiji -Xms10g -Xmx10g -Xincgc -XX:MaxPermSize=512m -XX:PermSize=512m
-XX:NewRatio=5 -XX:CMSTriggerRatio=50 -XX:+UseCompressedOops --
 
Put all the above in one line.
 
What the JVM flags mean:
 
* -Xms10g : use an initial heap size of 10 Gb (i.e. start fiji with 10 Gb of RAM preallocated to it)
* -Xmx10g: use a maximum heap size of 10 Gb. Note it's the same amount as the intial heap size, so that the heap cannot be resized.
* -Xincgc : use the incremental garbage collector. Clean up unused memory in the concurrent mark-sweep generation (i.e. not the super-new generation of allocated objects) using parallel threads.
* -XX:MaxPermSize=512m : set the heap size allocated to objects that don't need to be garbage often to half a gygabyte. The default is only 32m, which proves insufficient.
* -XX:PermSize=512m : preallocate the heap for the permanent objects directly to its maximum, half a gygabyte, so it doesn't ever have to be resized.
* XX:NewRatio=5 : Set the ratio of ephemeral versus more long-lived objects to 5 (the default is 9 or more in 64-bit Sun JVMs).
* XX:CMSTriggerRatio=50 : run the parallel garbage collector when the ratio of free versus non-free heap space is 50 % (the default is 92% in 64-bit JVM, which may incur in pauses and undesirable full sweeps).
* XX:+UseCompressedOops : use 32-bit pointers when possible, in a 64-bit JVM. This can cut the memory footprint by half in many cases.
* The ending double hyphen "--" is to specify all of these are JVM arguments, not fiji/ImageJ arguments.
 
 
With the above settings, we have succesfully registered 77,000 image tiles corresponding to 459 serial sections, using the "Align multi-layer mosaic" TrakEM2 command.
== Documentation ==
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