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{{Prace-user-guide}}
<small>< [[Bem User Guide]] < Running Jobs on Supernova</small>

The [[Bem overview|Bem Cluster]] uses PBS Pro to schedule jobs. Writing a submission script is typically the most convenient way to submit your job to the batch system. Example submission scripts (with explanations) are provided below for a few job types.

== Qsub ==
To run a simple '''interactive job''' with default resources (1CPU, 2000MB RAM) use the <code>-I</code> option and the <code>-l walltime=6:00:00</code> parameter (to set a walltme limit):
  qsub -I -l walltime=6:00:00

Resources are requested by using <code>-l</code> option. The resources are assigned to chunks, and you may request different resources to every chunk. To request interactive job with 2 chunks with 2 CPUs and 300MB of memory plus 3 chunks with 1 CPU and 100MB of memory execute:
  qsub -I -l walltime=6:00:00 -l select=2:ncpus=2:mem=300mb+3:ncpus=1:mem=100mb

Qsub manual pages describes a lot of other interesting options (such as job dependencies, mail events etc). To see manual type:
  man qsub

== Job submission scripts ==

If you are using the same software many times you probably want to use some scripting.
Qsub allows you to run your application from a script with all options defined inside. The example script "test.sh" defines PBS options, loads prace module and executes some commands:
  #!/bin/bash
  #PBS -l walltime=24:00:00
  #PBS -l select=1:ncpus=1:mem=100MB
  #PBS -m be
  #PBS -N test-job
  
  module load prace
  cd $dir
  pwd
  date
To submit a job you just type:
  qsub test.sh
It submits your <code>test.sh</code> script as a 24 h job (<code>-l walltime=24:00:00</code>) with <code>job-name test-job</code> (<code>-N</code> parameter) requesting 1CPU and 100MB RAM in one chunk (<code>-l</code> option). PBS server will notice you on job beginning (<code>-m b</code>) and end (<code>-m e</code>).

After the end of the job it's output will be saved in a file "<code>test-job.o$JOBID</code>". <code>$JOBID</code> is the job number printed by qsub after successful job submission. File "<code>test-job.e$JOBID</code>" will contain <code>STDERR</code>. If your application's <code>STDOUT</code> will exceed 30MB please redirect it to a file in your home directory using standard bash redirection:
  app_exec_command > output_filename

We usually write scripts that prepare some environment and then run qsub. The simple sub-test script to change job execution directory to the one the job was submitted from:
  #!/bin/bash
  
  C=$PWD
 
  cat << EOF | qsub
  #!/bin/bash
  #PBS -l walltime=24:00:00
  #PBS -l select=1:ncpus=1:mem=100MB
  #PBS -m be
  #PBS -N test-job
  
  module load prace
  cd $C
  pwd
  EOF

== Checking status of jobs ==

To see all your waiting and running jobs type:
  qstat -u $USER

== Scratch directory ==

If your application is <code>I/O</code> intensive you may ask (please write to the prace-support@wcss.pl) for setting up your scratch directory for storing and accessing the data during computation:
  /lustre/scratch/$USER
This directory would be available only on worker nodes, so if you want to access its contents, please do it in an interactive job.

<small>< [[Bem User Guide]] < Running Jobs on Bem</small>
[[Kategoria:User Guide]]