UserPreferences

Examples

1. Example scripts for using PBS

1.1. Parallel jobs

A PBS parallel job (using the gigabit ethernet based MPI in this particular case)

1.1.1. script file example.csh

#!/bin/csh
# invoking mpirun on ITRDA Linux cluster
#
# All PBS options start as "#PBS " and can be specified on the command line
# after qsub instead of being embedded in the script file.
 
#----------------------------------------------
# o Queue name
# -q queue
# Queues available on itrda are:
# four (2hours,16nodes),four-twelve (12hours,26nodes),long (168hours,64nodes)
 
#PBS -q four
 
#----------------------------------------------
# o Job name instead of the PBS script filename
# -N Job name (use a distinguishing name)
 
#PBS -N Halo
 
#----------------------------------------------
# o Resource lists
# -l resource lists, separated by a ","
# To ask for N nodes use "nodes=N"
# To ask for 2 processor per node use ":ppn=2", otherwise ":ppn=1"
# after the nodes=N. Preferably use ppn=2 and ask for less nodes.
# To ask for Myrinet use ":myrinet", for Gigabit Ethernet use ":gigabit"
# after the nodes=N:ppn=M
# To specify total wallclock time use "walltime=hh:mm:ss"
 
#PBS -l nodes=16:ppn=1,walltime=00:10:00
 
#----------------------------------------------
# o stderr/out combination
# -j {eo|oe}
# Causes the standard error and standard output to be combined in one file.
# For standard output to be added to standard error use "eo"
# For standard error to be added to standard output  use "oe"
#
# o stderr/out (specify them instead if getting script.[oe]$PBS_JOBID
# -e standard error file
# -o standard output file
# You can append ${PBS_JOBID} to ensure distict filenames
 
#PBS -e surf.gigabit.stderr
#PBS -o surf.gigabit.stdout
 
#----------------------------------------------
# o Starting time
# -a time
# Declares the time after which the job is eligible for execution.
 
#----------------------------------------------
# o User notification
# -m {a|b|e}
# Send mail to the user when:
# job aborts: "a", job begins running: "b", job ends: "e"
 
#PBS -m ae
 
#----------------------------------------------
# o Exporting of environment
# -V export all my environment var's
 
#PBS -V
 
#----------------------------------------------
                                                                                
# Begin execution
 
#
# Check the environment variables
#
#printenv
 
#
# get PBS node info
#
echo $PBS_NODEFILE
cat  $PBS_NODEFILE
 
#----------------------------------------------
# cd to the working directory from which the job was submitted
#
 
cd $PBS_O_WORKDIR
#
# Run the MPI code
#
 
# Using Myrinet and the Intel compilers (not working yet)
#/usr/local/pkg/mpich-gm/mpich-1.2.6..13-gm/ifc/bin/mpirun -v -machinefile $PBS_NODEFILE -np 16 ./Halo.ifc8-myri
# Using Myrinet and the GNU compilers
#/usr/local/pkg/mpich-gm/mpich-1.2.6..13-gm/g77/bin/mpirun -machinefile $PBS_NODEFILE -np 16 ./Halo.g77-myri
# Using Gigabit Ethernet and the Intel compilers
#/usr/local/pkg/mpich/mpich-1.2.6/ifc/bin/mpirun -machinefile $PBS_NODEFILE -np
16 ./Halo.ifc8-gige
# Using Gigabit Ethernet and the GNU compilers
/usr/local/pkg/mpich/mpich-1.2.6/g77/bin/mpirun -machinefile $PBS_NODEFILE -np 16 ./Halo.g77-gige
 
#
# Exit (not strictly necessary)
#
exit

1.1.2. Submission

-bash-2.05b$ qsub example.csh
160.itrda
-bash-2.05b$ qstat
Job id           Name             User             Time Use S Queue
---------------- ---------------- ---------------- -------- - -----
81.itrda         STDIN            cnh                     0 T four
160.itrda        Halo             ce107                   0 Q four

1.1.3. Current Issues