 | Tutorial This page is part of a tutorial that explains how to |
Run a Test Job
Running serial (non-MPI) jobs on HPC is not much different than running parallel jobs. There are only two major differences. The first is that you replace the mpirun command with whatever serial job you want to run. The second is in your qsub script's PBS -l nodes=... line. As an example, let's create the following qsub script test.qsub which will run the serial program echo. This script will use the testing queue, intended for short-lived, single-machine test jobs for debugging purposes. We will use the low_priority queue later:
#!/bin/bash : The above line tells Linux to use the shell /bin/bash to execute : this script. That must be the first line in the script. : You must have no lines beginning with # before these : PBS lines other than the /bin/bash line #PBS -N 'hello_parallel' #PBS -o 'qsub.out' #PBS -e 'qsub.err' #PBS -W umask=007 #PBS -q testing #PBS -l nodes=1:ppn=1 #PBS -m bea : Change our current working directory to the directory from which you ran qsub: cd $PBS_O_WORKDIR echo HELLO WORLD
Note that we are using nodes=1:ppn=1 – that requests a single processor core. As before, the #! /bin/bash line tells Linux to use the shell /bin/bash to run your script. Lines beginning with a ":" are comments, and the #PBS lines are used by PBS to decide what resources to give your job. Look at this page for more information those lines: HPC Parallel Job Submission. The cd $PBS_O_WORKDIR line changes to the directory in which you ran qsub. The echo HELLO WORLD command will run echo with HELLO WORLD as its arguments. The program echo is built in to bash and simply prints its arguments.
If you run:
qsub test.qsub
then eventually, your job will run and create qsub.out and qsub.err files. (You can use qstat to monitor your job while it is queued or running, or qdel to delete misconfigured or accidental jobs.) If everything went according to plan, the qsub.err file should be empty and the qsub.out job should contain "HELLO WORLD".
Real (Non-Test) Job
Once you have finished debugging your hello world program, you can resubmit it into the low_priority queue using this script:
#!/bin/bash : The above line tells Linux to use the shell /bin/bash to execute : this script. That must be the first line in the script. : You must have no lines beginning with # before these : PBS lines other than the /bin/bash line #PBS -N 'hello_parallel' #PBS -o 'qsub.out' #PBS -e 'qsub.err' #PBS -W umask=007 #PBS -q low_priority #PBS -l nodes=1:ppn=1 #PBS -m bea : Change our current working directory to the directory from which you ran qsub: cd $PBS_O_WORKDIR echo HELLO WORLD
If you have access to the high_priority queue, you can use that queue instead by replacing PBS -q low_priority with PBS -q high_priority. Note that we are using nodes=1:ppn=1 now – that requests that you get a single processor core somewhere on the cluster. If your job does not require large amounts of memory or multiple processors, please use nodes=1:ppn=1. If you need multiple processor cores, fast Infiniband I/O or more than three gigabytes of RAM, you should use nodes=1:ppn=4 instead to ensure that you get one machine all to yourself.
More Useful Serial Jobs
While printing simple text messages to an output file is enough for some people, you might need to do more. You can, of course, replace that "echo" line with a line that executes your own serial program. If you want to use IDL, Matlab, R or SAS, you have to do a few extra things:
Running IDL on HPC
Running Matlab on HPC
Running SAS on HPC
Running R on HPC
