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Logging In

ssh <username>@login.hpc.uams.edu

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You are now on the HPC login node. From here you can stage your data and jobs to be submitted to the computational nodes in the cluster. You can view the current load of the overall system from the login node with the showq command.

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SRun SRun

Submit a Simple Job

While the login node is a relatively powerful server, it should not be used to do any actual work, as that could impede others ability to use the system. We use Slurm to manage jobs and resources on the cluster. The srun and sbatch programs will be your primary interface for submitting jobs to the cluster. In its simplest form you can feed it a command on standard input and it will schedule and run a job. Here we will schedule a single command lscpu to run using all of the defaults

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 The output from this job will print to directly to your terminal. This can be useful for very simple commands or testing, however normally you will submit more complex jobs as a batch file.

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SBatch SBatch

Submit a Scripted Job

The sbatch program takes many arguments to control where the job will be scheduled and can be fed a script of commands and arguments to be run instead of just feeding them in through a pipe. We will now create a script which will both contain the arguments and actual commands to be run.

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sbatch --constraint=xeon cpuinfo.script

Monitoring Jobs

Jobs so far have been quick to run, often though you will want to monitor longer running jobs. Remember that the showq program will display the state of the entire cluster. There are many other programs which can help you monitor your own state and jobs.

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pdsh -w <nodename> free -h
pdsh -w <nodename> uptime
pdsh -w <nodename> top -b -n1

Installing Software

The HPC has some software packages already installed, however they will need to be activated using Lmod. You can browse available modules or search for them and see descriptions with these commands.

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