Difference between revisions of "Trinity"
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{{App_Location|app={{#var:app}}|{{#var:ver}}}} | {{App_Location|app={{#var:app}}|{{#var:ver}}}} | ||
==Available versions== | ==Available versions== | ||
| − | * r20110820, r20120125, r20120317 (EL5) | + | * r20110820, r20120125, r20120317, r20120618 (default) - (EL5) |
| − | * | + | * r20120518, r20120608 (default) - (EL6). |
<!-- --> | <!-- --> | ||
{{#if: {{#var: mod}}|==Using application with environment modules system== | {{#if: {{#var: mod}}|==Using application with environment modules system== | ||
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{{#if: {{#var: exe}}|==How To Run== | {{#if: {{#var: exe}}|==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. | 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. | ||
|}} | |}} | ||
Revision as of 14:34, 30 July 2012
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.