#!/bin/bash
###############################################################
# #
# Bourne shell script for submitting a parallel MVAPICH2 #
# 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;
# Assume (upper/lower) case to be sensitive;
# PBS directives must come first; any directives
# after the first executable statement are ignored.
#
# Use: submit job with command
# qsub pbs_mvapich2.pbs
#
##########################
# #
# The PBS directives #
# #
##########################
# Set the name of the job (up to 15 characters,
# no blank spaces, start with alphanumeric character)
# Default is name of pbs script file
#PBS -N JobName
# Specify the number of nodes requested and the
# number of processors per node.
# For tdgrocks and hpcsim, the number of processors per node=2
# For sciblade, the number of processors per node=8
# In this example request of 8 compute nodes, with 2 processors on each.
#PBS -l nodes=8:ppn=2
# By default, the standard output and error streams are sent
# to files in the current working directory with names:
# JobName.oJobid <- output stream
# JobName.eJobid <- error stream
# where JobName is the name of the job and Jobid
# 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. Otherwise you get them in separate files.
#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 name. 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".
# The default queue "default" , need not be specified.
#
#PBS -q default
# Specify the maximum amount of physical memory required per process.
# 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 pmem=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.
# e.g. send me mail when job aborts (with an error) or job end
# #PBS -m ae
# if you want more than one message, you can group flags as follows:
# #PBS -m abe
#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
# [MMDD]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.
# e.g July 11, 22:15
# #PBS -a 07112215 commented out
# Do not rerun this job if it fails
#PBS -r n
##########################################
# #
# PBS Environment Variables #
# #
##########################################
# When a batch job starts execution, a number of environment variables
# predefined, which include:
#
# The following reflect the environment where the user ran qsub:
# PBS_O_HOST The host where you ran the qsub command.
# PBS_O_LOGNAME Your user ID where you ran qsub.
# PBS_O_HOME Your home directory where you ran qsub.
# PBS_O_WORKDIR The working directory where you ran qsub.
#
# These reflect the environment where the job is executing:
# PBS_ENVIRONMENT Set to PBS_BATCH to indicate the job is a batch job, or
# to PBS_INTERACTIVE to indicate the job is a PBS interactive job.
# PBS_O_QUEUE The original queue you submitted to.
# PBS_QUEUE The queue the job is executing from.
# PBS_JOBID The job's PBS identifier.
# PBS_JOBNAME The job's name.
#
##########################################
# #
# Output some useful job information. #
# #
##########################################
NCPU=`wc -l < $PBS_NODEFILE`
NNODES=`uniq $PBS_NODEFILE | wc -l`
echo ------------------------------------------------------
echo ' This job is allocated on '${NCPU}' cpu(s)'
echo 'Job is running on node(s): '
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: number of nodes is $NNODES
echo PBS: current home directory is $PBS_O_HOME
echo PBS: PATH = $PBS_O_PATH
echo ------------------------------------------------------
###########################################################
# #
# To avoid CPU affinity problem #
# #
###########################################################
VIADEV_USE_AFFINITY=0
###########################################################
# #
# Set MPIPATH #
# #
###########################################################
MPIPATH=/u1/local/mvapich2/bin
###########################################################
# #
# Execute the run. Do not run in the background. #
# #
###########################################################
${MPIPATH}/mpirun_rsh -np ${NCPU} -hostfile ${PBS_NODEFILE} program_executable input_file
|
TDGC Website