Sample PBS script for serial job
For most applications, you should only need to change items indicated in red. Items shown in amber may also warrant your attention.
#!/bin/sh -f
###############################################################
# #
# Bourne shell script for submitting a serial job to the #
# PBS queue using the qsub command. #
# #
###############################################################
# Remarks: A line beginning with # is a comment.
# A line beginning with #PBS is a PBS directive.
# PBS directives must come first; any directives
# after the first executable statement are ignored.
#
##########################
# #
# The PBS directives #
# #
##########################
# Set the name of the job (up to 15 characters,
# no blank spaces, start with alphanumeric character)
#PBS -N JobName
# By default, the standard output and error streams are sent
# to files in the current working directory with names:
# job_name.osequence_number <- output="" p=""># job_name.esequence_number <- error="" p=""># where job_name is the name of the job and sequence_number
# is the job number assigned when the job is submitted.
# Use the directives below to change the files to which the
# standard output and error streams are sent.
# #PBS -o stdout_file
# #PBS -e stderr_file
# The directive below directs that the standard output and
# error streams are to be merged, intermixed, as standard
# output.
#PBS -j oe
# Specify the maximum cpu and wall clock time. The wall
# clock time should take possible queue waiting time into
# account. Format: hhhh:mm:ss hours:minutes:seconds
# Be sure to specify a reasonable value here.
# If the job does not finish by the time reached,
# the job is terminated.
#PBS -l cput=6:00:00
#PBS -l walltime=6:00:00
# Specify the queue. The CMU cluster currently has three queues:
# "green", "blue", and "red". Jobs submitted to these queues
# will run in cpu-dedicated mode; if all cpu's assigned to the
# queue are occupied with a job, then new jobs are queued and will
# not run until a cpu is freed up. You should take this waiting
# time into account when setting "walltime".
#PBS -q green
# Specify the maximum amount of physical memory required.
# kb for kilobytes, mb for megabytes, gb for gigabytes.
# Take some care in setting this value. Setting it too large
# can result in your job waiting in the queue for sufficient
# resources to become available.
#PBS -l mem=512mb
# PBS can send informative email messages to you about the
# status of your job. Specify a string which consists of
# either the single character "n" (no mail), or one or more
# of the characters "a" (send mail when job is aborted),
# "b" (send mail when job begins), and "e" (send mail when
# job terminates). The default is "a" if not specified.
# You should also specify the email address to which the
# message should be send via the -M option.
# #PBS -m abe
# #PBS -m ae
#PBS -M user_email_address
# Declare the time after which the job is eligible for execution.
# If you wish the job to be immediately eligible for execution,
# comment out this directive. If you wish to run at some time in
# future, the date-time argument format is
# [DD]hhmm
# If the day DD is not specified, it will default to today if the
# time hhmm is in the future, otherwise, it defaults to tomorrow.
# If the day DD is specified as in the future, it defaults to the
# current month, otherwise, it defaults to next month.
# #PBS -a 2215 commented out
# Specify the priority for the job. The priority argument must be
# an integer between -1024 and +1023 inclusive. The default is 0.
# #PBS -p 0
# Specify the number of nodes requested and the
# number of processors per node.
#PBS -l nodes=1:ppn=1
# Define the interval at which the job will be checkpointed,
# if checkpointing is desired, in terms of an integer number
# of minutes of CPU time.
# #PBS -c c=2
##########################################
# #
# Output some useful job information. #
# #
##########################################
echo ------------------------------------------------------
echo -n 'Job is running on node '; cat $PBS_NODEFILE
echo ------------------------------------------------------
echo PBS: qsub is running on $PBS_O_HOST
echo PBS: originating queue is $PBS_O_QUEUE
echo PBS: executing queue is $PBS_QUEUE
echo PBS: working directory is $PBS_O_WORKDIR
echo PBS: execution mode is $PBS_ENVIRONMENT
echo PBS: job identifier is $PBS_JOBID
echo PBS: job name is $PBS_JOBNAME
echo PBS: node file is $PBS_NODEFILE
echo PBS: current home directory is $PBS_O_HOME
echo PBS: PATH = $PBS_O_PATH
echo ------------------------------------------------------
##############################################################
# #
# The prologue script automatically makes a directory #
# on the local disks for you. The name of this directory #
# depends on the job id, but you need only refer to it #
# using ${WORKDIR}. #
# #
##############################################################
SERVER=$PBS_O_HOST
WORKDIR=/scratch/PBS_$PBS_JOBID
SCP=/usr/bin/scp
SSH=/usr/bin/ssh
######################################################################
# #
# To minimize communications traffic, it is best for your job #
# to work with files on the local disk of the compute node. #
# Hence, one needs to transfer files from your permanent home #
# directory tree to the directory ${WORKDIR} automatically #
# created by PBS on the local disk before program execution, #
# and to transfer any important output files from the local #
# disk back to the permanent home directory tree after program #
# execution is completed. #
# #
# There are essentially two ways to achieve this: (1) to use the #
# PBS stagein and stageout utilities, or (2) to manually copy the #
# files by commands in this script. The stagein and stageout #
# features of OpenPBS are somewhat awkward, especially since #
# wildcards and macros in the file lists cannot be used. This #
# method also has some timing issues. Hence, we ask you to use #
# the second method, and to use secure copy (scp) to do the file #
# transfers to avoid NSF bottlenecks. #
# #
######################################################################
#####################################################
# #
# Specify the permanent directory(ies) on the #
# server host. Note that when the job begins #
# execution, the current working directory at #
# the time the qsub command was issued becomes #
# the current working directory of the job. #
# #
#####################################################
PERMDIR=${HOME}/work
SERVPERMDIR=${PBS_O_HOST}:${PERMDIR}
echo server is $SERVER
echo workdir is $WORKDIR
echo permdir is $PERMDIR
echo servpermdir is $SERVPERMDIR
echo ------------------------------------------------------
echo -n 'Job is running on node '; cat $PBS_NODEFILE
echo ------------------------------------------------------
echo ' '
echo ' '
###############################################################
# #
# Transfer files from server to local disk. #
# #
###############################################################
stagein()
{
echo ' '
echo Transferring files from server to compute node
echo Writing files in node directory ${WORKDIR}
cd ${WORKDIR}
${SCP} ${SERVPERMDIR}/input_file .
${SCP} ${SERVPERMDIR}/program_executable .
echo Files in node work directory are as follows:
ls -l
}
############################################################
# #
# Execute the run. Do not run in the background. #
# #
############################################################
runprogram()
{
program_executable < input_file > output_file
}
###########################################################
# #
# Copy necessary files back to permanent directory. #
# #
###########################################################
stageout()
{
echo ' '
echo Transferring files from compute nodes to server
echo Writing files in permanent directory ${PERMDIR}
cd ${WORKDIR}
${SCP} output_file ${SERVPERMDIR}
echo Final files in permanent data directory:
${SSH} ${SERVER} "cd ${PERMDIR}; ls -l"
}
#####################################################################
# #
# The "qdel" command is used to kill a running job. It first #
# sends a SIGTERM signal, then after a delay (specified by the #
# "kill_delay" queue attribute (set to 60 seconds), unless #
# overridden by the -W option of "qdel"), it sends a SIGKILL #
# signal which eradicates the job. During the time between the #
# SIGTERM and SIGKILL signals, the "cleanup" function below is #
# run. You should include in this function commands to copy files #
# from the local disk back to your home directory. Note: if you #
# need to transfer very large files which make take longer than #
# 60 seconds, be sure to use the -W option of qdel. #
# #
#####################################################################
early()
{
echo ' '
echo ' ############ WARNING: EARLY TERMINATION #############'
echo ' '
}
trap 'early; stageout' 2 9 15
##################################################
# #
# Staging in, running the job, and staging out #
# were specified above as functions. Now #
# call these functions to perform the actual #
# file transfers and program execution. #
# #
##################################################
stagein
runprogram
stageout
###############################################################
# #
# The epilogue script automatically deletes the directory #
# created on the local disk (including all files contained #
# therein. #
# #
###############################################################
exit
Ref:
http://qcd.phys.cmu.edu/QCDcluster/pbs/run_serial.html
No comments:
Post a Comment