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Batch Queuing Systems

Batch Queuing Systems. The Portable Batch System (PBS) and the Load Sharing Facility (LSF) queuing systems share much common functionality in running batch jobs. However, they differ in their implementation of the batch environment and their user commands.

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Batch Queuing Systems

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  1. Batch Queuing Systems The Portable Batch System (PBS) and the Load Sharing Facility (LSF) queuing systems share much common functionality in running batch jobs. However, they differ in their implementation of the batch environment and their user commands. Table 1 below provides a comparative list of command options to help users migrating from LSF (used on halem) to PBS (used on palm and discover).

  2. Table 1: Syntax for frequently used options

  3. Batch Job Management The following table compares commonly-used LSF and PBS commands to control and monitor the jobs. Table 2: Frequently used job management commands (checkman pages of each command for more information)

  4. Environment Variables Both LSF and PBS provide support for special environment variables, which simplify scripting and configuration of the batch jobs. Table 3: Useful environmental variables

  5. Example Batch Scripts The following simple LSF and PBS submission scripts compare how the batch systems request comparable resources and run the same parallel executable: LSF example: #!/bin/csh #BSUB -n 4 #BSUB -W 6:00 #BSUB -q special_b #BSUB -J myJobName #BSUB -o out.o%J #BSUB -u my_email@gsfc.nasa.gov #BSUB -P k1234 echo "Master Host: `hostname` " echo "Node List: $LSB_HOSTS " cd $LS_SUBCWD prun -n 16 ./mpihello To submit job, type: bsub < script_name PBS example: #!/bin/csh #PBS -l select=4:ncpus=4 <--- on discover or… #PBS -l ncpus=16 <--- on palm #PBS -l walltime=6:00:00 #PBS -q general #PBS -N myJobName #PBS -j oe #PBS -me -M my_email@gsfc.nasa.gov #PBS -W group_list=k1234 echo "Master Host: $PBS_O_HOST" echo "Nodes:"; cat -n $PBS_NODEFILE cd $PBS_O_WORKDIR mpirun -np 16 ./mpihello To submit job, type: qsub script_name

  6. Interactive Batch Both queuing systems can enter an interactive batch mode, commonly used for debugging, by using the -Is (LSF) or -I (PBS) option. Other options are the same as previously shown, but will be entered all on one line. Commands for the two different queuing systems are compared below: LSF example (halem): % bsub -Is -Pk1234 -qspecial_b -W6:00 -n4 /usr/dlocal/bin/tcsh When the requested processors are available, the interactive prompt will appear: bsub> cd $LS_SUBCWD bsub> prun -n 16 ./mpihello bsub> exit PBS example (discover or palm): on discover: % qsub -I -W group_list=k1234 -q general -l walltime=06:00:00,select=4:ncpus=4or on palm: % qsub -I -W group_list=k1234 -q general -l walltime=06:00:00,ncpus=16 When the requested processors are available, the interactive prompt will appear: % cd $PBS_O_WORKDIR % mpirun -np 16 ./mpihello % exit

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