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razor_usage [2017/09/11 23:10]
wlfarris
razor_usage [2017/09/12 22:31]
wlfarris
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 The main production queues, with 6 and 72 hour walltime limits respectively,​ are ''​tiny12core''​ and ''​med12core''​ on Razor I and ''​tiny16core''​ and ''​med16core''​ or Razor II. Both systems also have quick-turnaround non-production 30-minute limit ''​debug12core''​ and ''​debug16core''​. On Razor I only there is a ''​serial12core''​ queue for single-core jobs of 2GB or less memory, which runs up to twelve jobs on a single node.  There are a number of special-purpose and [[condo_computing|condo]] queues documented in [[queues]]. The main production queues, with 6 and 72 hour walltime limits respectively,​ are ''​tiny12core''​ and ''​med12core''​ on Razor I and ''​tiny16core''​ and ''​med16core''​ or Razor II. Both systems also have quick-turnaround non-production 30-minute limit ''​debug12core''​ and ''​debug16core''​. On Razor I only there is a ''​serial12core''​ queue for single-core jobs of 2GB or less memory, which runs up to twelve jobs on a single node.  There are a number of special-purpose and [[condo_computing|condo]] queues documented in [[queues]].
  
-A sample Maui/Torque job script follows. ​ This requests two 12-core nodes for 6 hours in the tiny12core queue. The job starts and runs in the submit directory ($PBS_O_WORKDIR) and uses every core available in the requested nodes for MPI ''​NP=$(wc -l < $PBS_NODEFILE)'',​ or nodes*ppn=24 cores in this case.  The MPI executable was previously compiled with Intel compiler version 14.0.3 and Intel MPI version 5.1.1 (see [[modules]]).+A sample Maui/Torque job script follows. ​ This requests two 12-core nodes for 6 hours (The format is walltime=DD:​HH:​MM:​SS) ​in the tiny12core queue. The job starts and runs in the submit directory ($PBS_O_WORKDIR) and uses every core available in the requested nodes for MPI ''​NP=$(wc -l < $PBS_NODEFILE)'',​ or nodes*ppn=24 cores in this case.  The MPI executable was previously compiled with Intel compiler version 14.0.3 and Intel MPI version 5.1.1 (see [[modules]]).
 <​code>​ <​code>​
 #PBS -N example1 #PBS -N example1
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 mpirun -np $NP -machinefile $PBS_NODEFILE ​ ./​mympiexecutable mpirun -np $NP -machinefile $PBS_NODEFILE ​ ./​mympiexecutable
 </​code>​ </​code>​
 +
 +Lines beginning with ''#​PBS''​ are meaningful only to the scheduler, and lines that don't begin ''#​PBS''​ are commands to the compute node operating system.
 +
 +In PBS scripts, the ''​ppn''​ parameter is very important. If the requested value of ''​ppn''​ is larger than the number of cores per node present on the hardware, the job will never run and will stay queued until deleted. In practice, you should almost always use ''​ppn''​=8 on 8core queues, ''​ppn''​=12 on 12core queues, and so on. If ''​ppn''​ is smaller than the correct value for the queue, the job will run, but will not use all the cores, if you are calculating the number of mpirun threads as in the example script above.
 +
 +==== Submitting and Checking on Your Job ====
 +
 +The completed job script can be submitted to the scheduler with the ''​qsub''​ command. The name and extension of the script are arbitrary. If the script is called MPI-test-script.pbs,​ you will run ''​qsub MPI-test-script.pbs''​. To check the status of jobs, use the interactive commands ''​showq''​ or ''​checkjob''​. The ''​showq''​ command will print general information about the state of the job queue.
 +
 +=== Cancelling a Job ===
 +If a job that has been submitted to the scheduler needs to be cancelled, use the ''​qdel''​ command
 +
razor_usage.txt · Last modified: 2017/09/12 22:31 by wlfarris