Trinity

Description

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Trinity contains three applications - Inchworm, Chrysalis, and Butterfly. Template:App Location

Available versions

• r20110820, r20120125, r20120317, r20120618 (default) - (EL5)
• r20120518, r20120608 (default) - (EL6).

Using application with environment modules system

To use trinity with the environment modules system at HPC the following commands are available:

Get module information for trinity:

$module spider trinity

Load the default application module:

$module load trinity

The modulefile for this software adds the directory with executable files to the shell execution PATH and sets the following environment variables:

• HPC_TRINITY_DIR - directory where trinity is located.

How To Run

To run Trinity after you load the module use the "Trinity.pl" perl script, or run_Trinity.sh shell script, which is particularly useful as the optional ALLPATHS-LG software is enabled at UF HPC.

If the run produces an error that states that java could not create a virtual machine due to insufficient heap memory you can set the java memory with an

export _JAVA_OPTIONS="-Xmx2g"

command either at the command line if doing an interactive run on a test node or in the job script. Make sure that the value in the "-Xmx" is less then the amount of memory you requested from the batch system.