General Usage of Hydra

• Login

  ssh hydra  
  

• Example of job.pbs file

   ### AUTOMATICALLY GENERATED BATCH FILE
  
  # ### name of job
  #PBS -N [name_]
  
  # ### mail for begin/end/abort
  #PBS -m ea
  #PBS -M zonghuiroot@gmail.com
  
  # ### maximum cpu time
  ####PBS -l cput=5000:00:00
  #PBS -l walltime=30:00:00:00
  
  # ### number of nodes and processors per node
  #PBS -l nodes=1:ppn=1
  
  # # ### queue
  ###PBS -q fast
  
  # ### 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/zonghui/Scratch/Multi_chain/Double_length_DNA_experiment/ppa12.peg5_cr_5_double_ka_4/ppa.cat12.pegcat2.peg5
  #mpirun -np 2 /opt/lammps/lmp2013_mpi -in input.dat
  
  time /opt/lammps/lmp2013 < input.dat
  
  #/home/wei/Install/lammps/current/src/lmp_suse_linux < input.dat
  
  if [ $? -eq 0 ] ; then
  touch COMPLETED
  fi
  

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

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

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

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

• Submit jobs

  msb job.mbs
  

• Check job status

  showq
  

  show all jobs

  qstat
  

  show your own jobs