General Usage

• Login

  ssh [netid]@quest.it.northwestern.edu    
  

  where [netid] is your NETID. The first time you login, it will ask you to enter file in which to save the key and then to enter passphrase twice. Just press "enter" for these three questions and you should be able to login successfully.

  Our group folder is located in /projects/b1011/luijten-group

• Example of job.mbs file

  # ### AUTOMATICALLY GENERATED BATCH FILE
  #MOAB -q [queue_name]
  #MOAB -l advres=grail
  #MOAB -A b1011
  #MOAB -l walltime=[dd:hh:mm:ss]
  
  # ###name of job
  #MOAB -N [name_of_job]
  
  # ### mail for begin/end/abort
  #MOAB -m ea
  #MOAB -M [email_address]                                                                                                      
  
  # ### number of nodes and processors per node
  #MOAB -l nodes=2:ppn=6
  
  # ### indicates that job should not rerun if it fails
  #MOAB -r n
  
  # ### stdout and stderr merged as stderr
  #MOAB -j eo
  
  # ### write stderr to file
  #MOAB -e log.err
  
  # ### the shell that interprets the job script
  #MOAB -S /bin/bash
  
  cd /projects/b1011/luijten-group/[job_location]
  time mpirun -np 12  ~/lammps-30Aug12_standard/src/lmp2013_mpi -in input.dat
  
  if [ $? -eq 0 ] ; then
  touch COMPLETED
  fi   
  

  [queue_name] There are two options for queue name: collab or collab-preempt. Both of them have startup priority of 5000. Collab has maximum cores of 262 and maximum walltime of 7 days. There is no resource restrictions for collab-preempt, but note that queues ending in ‘-preempt’ contain jobs that can be interrupted and re-queued by jobs from a higher priority queue.

  [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