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runnersc [2016/04/22 12:53] – [Submitting a Job] wsirunnersc [2022/07/21 06:59] (current) – external edit 127.0.0.1
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 +====== Running Jobs at NERSC ======
  
 +===== Logging on to NERSC =====
 +
 +  $ ssh simonw@cori.nersc.gov
 +  
 +Use the home directory to store data, but don't run codes here as space is limited.
 +See [[compilenersc|Compiling Codes at NERSC]]
 +
 +Use the scratch directory to compile and run codes, but don't use scratch as longterm storage.
 +
 +  $ cd $SCRATCH
 +  
 +There is a long-term storage solution called HPSS: http://www.nersc.gov/users/storage-and-file-systems/hpss/
 +
 +===== Sample Batch Scripts =====
 +Save a batch script as a separate file (e.g. mybatch ). Submit with
 +  $ sbatch mybatch
 +  
 +Before launching a multi-hour run, use a debug script to make sure you set everything up right. Only one debug run can be active at once, time-limit is 30 minutes.
 +
 +**Debug Script**
 +  #!/bin/bash -l
 +  
 +  #SBATCH -p debug     
 +  #SBATCH -N 64        
 +  #SBATCH -t 00:20:00  
 +  #SBATCH -J my_job    
 +  
 +  srun -n 2048 ./mycode.exe
 +
 +
 +**Regular batch script**
 +  #!/bin/bash -l
 +  
 +  #SBATCH -p regular 
 +  #SBATCH -N 2 
 +  #SBATCH -t 00:30:00
 +  
 +  cd $SLURM_SUBMIT_DIR   # optional, since this is the default behavior
 +  srun -n 64 ./my_executable
 +  
 +Use the account number m2560 (default acct) for runs. 
 +
 +===== Submitting a Job =====
 +
 +  sbatch mybatch_script
 +===== Checking Job Status =====
 +Check your job status
 +  $ sqs
 +
 +Cancel a job
 +  $ scancel jobid
 +
 +Alter options for currently queued job (does not work on running jobs)
 +  $ scontrol update jobid=jobid partition=new_partition timelimiit=timelimit qos=normal
 +===== More Information =====
 +http://www.nersc.gov/users/computational-systems/cori/running-jobs/