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2012.06.28 Range Maps
2012.06.28 Range Maps
June 28, 2012 Parametric launcher
Participants
John Donoghue, Edwin Skidmore, Martha Narro
Agenda
Edwin teaching John how to submit a job to TACC using the parametric launcher
General Info
- Module launcher
- Login to longhorn
- A module is a command that loads programs to be used
File systems
- In HPC, there are three work locations (file systems):
- Home dir <cd or cd $HOME>
- Work dir
- Scratch dir <cds or cd $SCRATCH>
- Longhorn directly exposes home and scratch, but not work
- There’s no quota on scratch, but those files will get deleted fairly often, as often as weekly.
- Depends on last time files were accessed.
- If you need to keep some files for a while, log in daily and touch all the files.
- For example in scratch directory:
- cds
- touch
- find . --exe touch {} \:
- John needs to write to scratch since his scripts generate lots of output files.
- Put all files in the iPlant Data Store.
- Use iget to move them to Longhorn.
- Since the total size of input files is small, they could go in the home directory.
- If it was large, would need to put them in scratch.
- John (and Martha) need to read the Longhorn user guide (http://www.tacc.utexas.edu/user-services/user-guides/longhorn-user-guide).
launcher1
- Launcher1 is the submit script
- Read the batch queue info at http://www.tacc.utexas.edu/user-services/user-guides/longhorn-user-guide . (see “Running your Applications)
- For the first large scale range model run, Edwin used the normal queue
- There is a priority for long queue jobs.
- There’s a limit to the number of jobs a user can run at a time.
- The others are held in queue
- The # alone indicates a comment.
- If # is followed by $ or @ it indicates parameters.
- # comment
- #$, #@ are parameters
- job – one or more tasks
- -pe 8way queues 8 jobs at once
- Edwin had to submit another job with tasks that didn’t finish.
- module load launcher - sets up the environment
- qsub - sumits job to the queue
- qstat – tells you if job is running, where, how long, etc.
- Parameters in launcher1 are defined in longhorn documentation (user guide)
- Edwin suggested John run a hello world version of submitting a job. Use the development node (queue).
- Use 8way 8
paramlist
- Lists all the tasks for a given job.
- >& pipes the output
genparam
- generates the paramlist
- change paramlist1 to whatever number
paramlist-tar
- tar
- tar as if in output dir compress dir boundingbox
- Test runs
- run 8-16 on a paramlist on development queue to see it runs
- run RSCRIPT command (no interactive shell)
- log into longhorn
- ssh xsedeusrname@longhorn.tacc.texas.edu
- xsede.org
- user portal
- my xsede
- tg-login.longhorn.tacc.teragrid.org
- Note the help and helpdesk
- can login using ssh client