PBS Information for the CGL compute Server

• Introduction
• Queue Structure
• How to Create a Command File
• How to Submit a Job
• How to Submit OpenMP Jobs
• How to Submit MPI Jobs
• How to Check Job Status
• How to Remove and Kill Jobs

Introduction

The Computational Genetics Laboratory compute server resources consist of cgls1 (16-CPU Sun Fire 6800 and 12 CPUs for pbs) and cs0 (8-CPU Sun Fire v890 and 7 CPUs for pbs).

PBS is a queueing system for submitting serial and parallel jobs. It matches job requirements with the machine's resources by use of a command file. It ensures that the machines are used fairly and to their full potential and that resources don't go unused.

Queue Structure

The following table gives a summary of the enforced limits on memory and number of processors.

Queue	Architecture	Max Wall Clock Time per Job	Max Number of CPUs per Job
sun		24 hrs	12 cpus

How to Create a Command File

  #PBS -l mem=2000mb,ncpus=1,walltime=24:00:00
  #PBS -m abe
  #PBS -M your_email@umn.edu
  
    cd /home/cgl/your_cgl_username/whatever_folder

    module load bioinformatics

    blastall -p blastn -d nt -a 1 -i test.seq -o test_nt.out
  

#PBS -M your_email@umn.edu

How to Submit a Job

You may use PBS to submit jobs from cgls1.

There are two major ways to submit jobs. One is by using the qsub command. The other is by using the xpbs graphical user interface to PBS.

• qsub

  The qsub command is used to submit a job to the queuing system. qsub takes a job submission script that contains PBS commands and the commands necessary to run your job.

  For example, if your submission script is "myscript," you could submit it as follows:

           module load pbs
           qsub myscript
  

• xpbs

  The xbps command allows you to select the resources you want by clicking on buttons and selecting options. One helpful hint is you can select all the resources you need and save the settings to a PBS submission text file that can be used with the qsub command.

How to Submit OpenMP Jobs

The following is a 4-processors OpenMP job. The wall time represents the amount of time the job takes to complete. So, if you specified 00:30:00, the job would need to finish in 30 minutes.

  #PBS -l ncpus=4,mem=1gb,walltime=00:30:00
  #PBS -m abe
  #PBS -M your_email@umn.edu

  cd /home/cgl/your_cgl_username/whatever_folder
  setenv OMP_NUM_THREADS 4

  ./a.out

  # end of example script

How to Submit MPI Jobs

  #PBS -l ncpus=4,mem=1gb,walltime=00:30:00
  #PBS -m abe
  #PBS -M your_email@umn.edu

    cd /home/cgl/your_cgl_username/whatever_folder

    mprun -np 4 ./a.out

  # end of example script
  

How to Check Job Status

You can check job status using the qstat command.

Alternatively, you can use the showq command. showq is provided with the Maui Scheduler, the job scheduler that we use in the CGL.

You can also use command: qstat -f job_number | grep walltime to figure out walltime of your job.

How to Remove and Kill Jobs