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workshops:hpcprac2 [2017/07/04 17:07]
kevin
workshops:hpcprac2 [2017/07/05 09:27] (current)
kevin
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-=====Practical 2: Using CHPC=====+=====Practical 2: OpenMP & Using CHPC=====
  
 **Aim:** to launch a parallel job on the CHPC cluster //Lengau//. **Aim:** to launch a parallel job on the CHPC cluster //Lengau//.
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 Most of the prac can be done in an interactive session. Most of the prac can be done in an interactive session.
- 
-To execute longer running jobs you will need to submit a job script to the scheduler. ​ There is an example PBSPro job script on the school00 home directory called //​example.sh//​ and which can be copied to your current directory in the usual way: 
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-  cp ~/​../​student00/​example.sh . 
- 
- 
-**example.sh**:​ 
-<code lang=bash>​ 
-#!/bin/bash 
-#PBS -N example01 
-#PBS -l select=1:​ncpus=24:​mpiprocs=24 
-#PBS -P Wchpc 
-#PBS -q R522145 
-#PBS -W group_list=training 
-#PBS -l walltime=4:​00:​00 
- 
-CWD=/​mnt/​lustre/​users/​$USER/​example 
- 
- 
- 
-cd $CWD 
-echo "​Working directory is $CWD" 
-nproc=`cat $PBS_NODEFILE | wc -l` 
-echo "nproc is $nproc"​ 
-echo "Nodes used by this job:" 
-cat $PBS_NODEFILE 
- 
-echo "​Starting run..."​ 
-# Insert command to run here: 
- 
-echo "... done." 
-</​code>​ 
- 
-Note that the options passed to the **qsub** command appear as shell comment lines that start with ''#​PBS''​. 
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-**Note: the script uses //​example///​ as the working directory.** Create this before you run the script: 
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-  mkdir ~/​lustre/​example 
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-or edit the script file to point to the prac directory. 
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-**NOTE: your script will fail if you don't use the Lustre file system.** 
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-In the example file the command to actually run your code is missing. ​ Depending on which part of the prac you are attempting, this will differ. ​ Insert the command in the indicated place. 
- 
- 
-To then submit the job script to the scheduler you simply use 
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-  qsub example.sh 
-  ​ 
-The **qsub** command will read all its option parameters from the file. 
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- 
-====Job Control==== 
- 
- 
-To check the status of your jobs in the Winter School queue: 
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-  qstat | grep R522145 
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-This command lists all the jobs in the **R522145** queue. ​ Running jobs will have a ''​R''​ in the status column, a ''​Q''​ if the job is queued and waiting.  ​ 
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-Use the **qdel** command to remove a queue job from the queue. ​ The synatx is 
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-  qdel jobid 
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-where //jobid// is replaced by the number of the job (looks like ''​557809.sched01''​). 
- 
  
/var/www/wiki/data/pages/workshops/hpcprac2.txt · Last modified: 2017/07/05 09:27 by kevin