Login to your account by ssh; Remote file transfer should also be done by ssh. An SSH client software is available at http://www.utmem.edu/ssh
Compile your code, create the wrapper PBS Batch script as in the example below;
Submit the PBS batch script by %qsub scriptname
Note: You are in the headnode by default after login, where you are only supposed to do Source
Code
Editing, Compilation and Job Submission through PBS. We want the headnode to act just as the control
console. Lengthy jobs in the headnode will be killed.
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Example batch scripts:
For serial jobs:
#PBS -N jobname
#PBS -M name@abc.com
#PBS -m ae
#PBS -q queueName
#PBS -l walltime=hh:mm:ss
cd $HOME/your_directory
./your_executable_file
For parallel jobs:
#PBS -N jobname
#PBS -M name@abc.com
#PBS -m ae
#PBS -q queueName
#PBS -l nodes=your_request_number_of_nodes:ppn=2
#PBS -l walltime=hh:mm:ss
MPIDIR=/usr/local/mpich/mpich-1.2.5_intel
PATH=$PATH:$MPIDIR/bin
cd $HOME/your_directory
NP=$(wc -l $PBS_NODEFILE | awk '{print $1}')
mpirun -np $NP -machinefile $PBS_NODEFILE your_executable_file
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Available queues for your job:
short: for jobs estimated to run 20 minutes, high priority
medium: for jobs estimated to run 24 hours, medium priority
long: for jobs estimated to run 72 hours, low priority
verylong: no time limit, lowest priority
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Useful Commands:
Show the status of all the nodes in the cluster: %pbsnodes -a
Display a relevant listing of both active and idle jobs: %showq
Check the Status of a PBS Batch Job: %qstat
Cancel a PBS Batch Job: %qdel jobid
Check the detail of the job: %checkjob jobid
Display the earliest possible start and completion times for a specified job: %showstart jobid
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