Usage

To run Trinity after you load the module use the Trinity command.

Local Drive Use

Warning

You must use local scratch directories on compute nodes for Trinity output and then only copy the results back to your /blue/ directory tree. Local scratch directory for a job is available via the $TMPDIR variable provided by SLURM. Put the output directory under $TMPDIR and then copy that directory to your /blue space at the end of the job. If you do not use $TMPDIR for staging out the Trinity output directory your job(s) could be cancelled without warning. See Temporary Directories for more information.

Java Heap Memory

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 a command that looks like

export _JAVA_OPTIONS="-Xmx2g"

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 than the amount of memory you requested from the batch system.

The default Butterfly memory setting in the Trinity script is -Xmx20G, so plan your job resource request accordingly.