General Usage of Hydra

• Login

  ssh hydra  
  

• Example of job.pbs file

  ### AUTOMATICALLY GENERATED BATCH FILE
  
  # ### name of job
  #PBS -N [name_of_job]
  
  # ### mail for end/abort
  #PBS -m ea
  #PBS -M [email_address]
  
  # ### maximum wall time
  #PBS -l walltime=[dd:hh:mm:ss]
  
  # ### maximum physical memory required (use 'kb', 'mb', or 'gb')
  #PBS -l mem=512mb
  
  # ### number of nodes and processors per node
  #PBS -l nodes=1:ppn=1
  
  # ### queue
  #PBS -q [queue_name]
  
  # ### indicates that job should not rerun if it fails
  #PBS -r n
  
  # ### stdout and stderr merged as stderr
  #PBS -j eo
  
  # ### write stderr to file
  #PBS -e log.err
  
  # ### the shell that interprets the job script
  #PBS -S /bin/bash
  
  cd /home/[job_location]
  time /opt/lammps/lmp2013 < input.dat
  
  if [ $? -eq 0 ] ; then
  touch COMPLETED
  fi
  

  [name_of_job] This is the name of the job that will be showed in the queue.

  [email_address] This is the email address you used to receive the system notice when job begins, aborted or ended.

  [dd:hh:mm:ss] This is the maximum allowed running time for your job. dd: days; hh: hours; mm: minutes; ss: seconds.

  [queue_name] There are two options for queue name: fast or default.

  [job_location] This is the address of the folder where your input file is located.

• Submit jobs

  qsub job.pbs
  

• Check job status

  qstat
  

  show status of all jobs.

  qstat -u [username]
  

  where [username] is your own username. This command will show the status of your own jobs.