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- | **Getting Started** | + | =====Getting Started |
This section shows how to login to the the system and submit a basic job on the cluster. If you do no have an account already, please apply for one by following the link [[applying_for_an_account|]] | This section shows how to login to the the system and submit a basic job on the cluster. If you do no have an account already, please apply for one by following the link [[applying_for_an_account|]] | ||
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- | **Submitting | + | **Submitting |
- | The cluster uses [[http:// | + | [[http:// |
- | **sinfo** reports | + | In order to use the HPC compute |
+ | **Creating a PBS Script** | ||
- | **squeue** reports | + | To set the parameters for your job, you can create |
+ | Here is a sample PBS file, named myjobs.pbs, followed by an explanation of each line of the file. | ||
- | **srun** is used to submit a job for execution or initiate job steps in real time. srun has a wide variety of options to specify resource requirements, | + | < |
+ | # | ||
+ | #PBS -l nodes=1:ppn=2 | ||
+ | #PBS -l walltime=00: | ||
+ | cd / | ||
+ | | ||
+ | sas my.sas | ||
+ | </ | ||
+ | The first line in the file identifies which shell will be used for the job. In this example, bash is used. | ||
+ | The second line specifies the number of nodes and processors desired for this job. In this example, one node with two processors is being requested. | ||
+ | The third line in the PBS file states how much wall-clock time is being requested. In this example 59 seconds of wall time have been requested. | ||
+ | The fourth line tells the HPC cluster to access the directory where the data is located for this job. In this example, the cluster is instructed to change the directory to the / | ||
+ | The fifth line tells the cluster which program you would like to use to analyze your data. In this example, the cluster sources the environment for SAS. | ||
+ | The sixth line tells the cluster to run the program. In this example, it runs SAS, specifying my.sas as the argument in the current directory, / | ||
+ | To submit your job without requesting additional resources, issue the command | ||
+ | **qsub myjob.pbs** | ||
- | **sbatch** is used to submit | + | If you have the myjob.pbs set up as explained in the example above and you want to override the default options in the myjob.pbs file, then you can use the -l parameter on the qsub command line to override the option specified in the file. |
+ | |||
+ | Below are some examples of these overrides. | ||
+ | |||
+ | **Requesting Additional Wall Time** | ||
+ | |||
+ | If you need to request more or less wall time after you have already created your PBS script, you can do this by using the qsub command. | ||
+ | |||
+ | In the example script above, we have requested 59 seconds of wall time. If you realize later that your job actually requires five minutes to complete, the command | ||
+ | |||
+ | **qsub -l walltime=0: | ||
+ | will ask PBS for a limit of five minutes of wall time. If your job does not finish within the specified time, it will be terminated. | ||
+ | |||
+ | **Requesting Nodes and Processors** | ||
+ | |||
+ | You may also alter the number of nodes and processors requested | ||
+ | |||
+ | If you later decide that you need four HPC nodes for your job but you are going to use only one of the dual-processors on each node, then use the following command: | ||
+ | **qsub -l walltime=0: | ||
+ | |||
+ | If you want to use both processors on each HPC node, you should use the following command: | ||
+ | **qsub -l walltime=0: | ||
+ | |||
+ | **Requesting a Specific Network** | ||
+ | |||
+ | To run your job on the infiniband network, add the IB feature to your PBS script. | ||
+ | |||
+ | **#PBS -l nodes=1: | ||
+ | |||
+ | MPI jobs using OpenMPI 1.6.4 or later can run on the Infiniband network. | ||
+ | |||
+ | NOTE: Only one network should be specified for each job. If no network is specified. the job will be scheduled to run on whichever network is available. | ||
+ | |||
+ | **Checking Job Status** | ||
+ | |||
+ | To check on the status of your job, you will use the qstat command. The command | ||
+ | **qstat –u [your username]** | ||
+ | will show you the current status of all your submitted jobs. | ||
+ | |||
+ | More information can be obtained from the [[http:// | ||
- | **scancel** is used to cancel a pending or running job or job step. It can also be used to send an arbitrary signal to all processes associated with a running job or job step. | ||
- | More information can be obtained from [[https:// |