Lonestar6 Directories

Diagram of Lonestar6 directories and what connects to what, and how fast

Lonestar6 is a collection of 560 computers connected to three file servers, each with unique characteristics.

You need to understand the file servers to know how to use them.

	$HOME	$WORK	$SCRATCH

	$HOME	$WORK	$SCRATCH
Purged?	No	No	Files can be purged if not accessed for 10 days.
Backed Up?	Yes	No	No
Capacity	5GB	1TB	Basically infinite. 8.5 PB
Command to Access	cdh cd $HOME	cdw cd $WORK	cds cd $SCRATCH
Purpose	Store Executables	Store Files	Run Jobs

Executables that aren't available on TACC through the "module" command should be stored in $HOME.

If you plan to be using a set of files frequently or would like to save the results of a job, they should be stored in $WORK.

Actual job activity, reading and writing to disk, should be offloaded to your resource's $SCRATCH file system. You can start a job from anywhere but the actual work of the job should occur only on the $SCRATCH partition.

If you're going to run a job, it's a good idea to keep your input files in a directory in $WORK and copy them to a directory in $SCRATCH where you plan to run your job.

This example command might help a bit:

 cp $WORK/my_fastq_data/*fastq $SCRATCH/my_project/

TACC File System Usage Recommendations (From TACC documentation)

File System	Recommended Use	Notes

File System	Recommended Use	Notes
`$HOME`	cron jobs, scripts and templates, environment settings, compilations	each user's `$HOME` directory is backed up
`$WORK`	software installations, original datasets that can't be reproduced.	The Stockyard file system is NOT backed up. Ensure that your important data is backed up to Ranch long-term storage.
`$SCRATCH` ¹	Reproducible datasets, I/O files: temporary files, checkpoint/restart files, job output files	Not backed up. All `$SCRATCH` file systems are subject to purge if access time ² is more than 10 days old.

Now let's go on to look at how jobs are run on Lonestar6.