Difference between revisions of "Trinity"

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Trinity contains three applications - Inchworm, Chrysalis, and Butterfly.
 
Trinity contains three applications - Inchworm, Chrysalis, and Butterfly.
 
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==Available versions==
 
* r20110820, r20120125, r20120317, r20120618 (default) - (EL5)
 
* r20120518, r20120608 (default) - (EL6).
 
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{{#if: {{#var: mod}}|==Using application with environment modules system==
 
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{{App_Module|app={{#var:app}}|intel={{#var:intel}}|mpi={{#var:mpi}}}}|}}

Revision as of 02:52, 10 August 2012

Description

trinity website  

Trinity contains three applications - Inchworm, Chrysalis, and Butterfly.

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.