Information about TACC for bioinformatics is sparse on the web; the BioITeam Wiki (search for it) has some info. TACC has user guides, and a very useful consulting system for users. You can also email me or anyone else at the Bioinformatics Consulting Group.
- User Guides
- Consulting Ticket System. I’ve been impressed with their speed in answering questions (even very basic ones!), and their willingness to help me with odd problems.
- $HOME (
- 5GB on Stampede, 5GB on Lonestar5
- $WORK (
- 1 TB across all TACC systems
- Not backed-up
- $SCRATCH (
- 8.5PB (8,500,000GB) on Stampede, 5.5PB on Lonestar5
- Not backed-up, files older than 10 days deleted with no warning
- Search for a module:
module spider <search_term>
- List current modules:
- Load a module:
module load <module_name>
- Swap modules:
module swap <old_module> <new_module>
normal: best for most job submissions.
- Stampede: 48 hour limit, 16 cores per node
- Lonestar5: 48 hour limit, 24 cores per node
largemem: when you need lots of memory, these have 1TB.
- Stampede: 48 hour limit, 32 cores per node
- Lonestar5: ? (Not clear from user guide)
development: good for quick, small tests.
- Stampede: 2 hour limit, 16 cores per node
- Lonestar5: 2 hour limit, 24 cores per node
I recommend using
launcher_creator.py. Information is available here:
(or you can search for “BioITeam wiki” and look under “Software”)
launcher_creator.py, you should probably add a line to your
.profile file (see last section).
Stampede and Lonestar5 both use SLURM as their job scheduling systems.
- Submit a job:
- Check status:
squeue -u <username>or
- Delete a job:
- Specific job:
- All your jobs:
scancel -u <username>
- Specific job:
Pre-rolled BioITeam Scripts
Not working on Stampede yet, but soon!
Add BioITeam To Your $PATH
One way to do it (but keep it on one line):
echo 'source /corral-repl/utexas/BioITeam/bin/profile_ngs_course.bash' >> ~/.profile_user