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The BioITeam maintains a set of such scripts in the /workwork2/projects/BioITeam/common/script directory. Take a look at some of them after you feel more comfortable with initial NGS processing steps. They can be executed by anyone with a TACC account.
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idev -p developmentnormal -m 20 -A UT-2015-05-18 -N 1 -n 68 --reservation=BIO_DATA_week_1 |
Notes:
- -p developmentnormal requests nodes on the development normal queue
- -m 20 asks for a 20-minute session (120 minutes is the maximum for development)
- -A UT-2015-05-18 specifies the TACC allocation/project to use
- -N 1 asks for 1 node and -n 68 requests access to all 68 cores
- --reservation=BIO_DATA_week_1 gives us priority access to TACC nodes for the class. You normally won't use this argument.
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-> Checking on the status of development queue. OK -> Defaults file : ~/.idevrc -> System : stampede2 -> Queue : developmentnormal (cmd line: -p ) -> Nodes : 1 (cmd line: -N ) -> Total tasks : 68 (cmd line: -n ) -> Time (minutes) : 20 (cmd line: -m ) -> Project : UT-2015-05-18 (cmd line: -A ) ----------------------------------------------------------------- Welcome to the Stampede2 Supercomputer ----------------------------------------------------------------- --> Verifying valid submit host (login3)...OK --> Verifying valid jobname...OK --> Enforcing max jobs per user...OK --> Verifying availability of your home dir (/home1/01063/abattenh)...OK --> Verifying availability of your work2 dir (/work2/01063/abattenh/stampede2)...OK --> Verifying availability of your scratch dir (/scratch/01063/abattenh)...OK --> Verifying valid ssh keys...OK --> Verifying access to desired queue (development)...OK --> Verifying job request is within current queue limits...OK --> Checking available allocation (UT-2015-05-18)...OK --> Verifying that quota for filesystem /home1/01063/abattenh is at 0.00% allocated...OK --> Verifying that quota for filesystem /work2/01063/abattenh/stampede2 is at 16.51% allo cated...OK Submitted batch job 7829779 -> After your idev job begins to run, a command prompt will appear, -> and you can begin your interactive development session. -> We will report the job status every 4 seconds: (PD=pending, R=running). -> job status: PD -> job status: R -> Job is now running on masternode= c455-083...OK -> Sleeping for 7 seconds...OK -> Sleeping for 7 seconds...OK -> Sleeping for 7 seconds...OK -> Sleeping for 7 seconds...OK -> Checking to make sure your job has initialized an env for you....OK -> Creating interactive terminal session (login) on master node c455-083. TACC Stampede2 System Provisioned on 24-May-2017 at 11:47 |
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