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Introduction to HPC
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High Performance Computing (HPC) typically involves connecting remotely to a cluster of computers.
HPCs can be used to do work that would either be impossible or much slower in a Desktop environment.
Typical HPC workflows involve submitting “jobs” to a scheduler which queues/priortises the “jobs” of all users.
The standard method of interacting with HPC’s is via a Linux-based Command Line Interface called “The Shell”.
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Connect to the HPC
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We connect to remote servers using the terminal
SSH is a secure protocol for connecting to remote servers
To connect to a server, you need it’s address, an open port (usually 22 for ssh), and your user ID
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Basic UNIX Commands
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scp (The Secure Copy Program) is a standard way to securely transfer data to remote HPC systems.
File ownership is an important component of a shared computing space and can be controlled with chmod.
Scripts are mostly just lists of commands from the command line in the order they are to be performed.
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Using a cluster: Introduction
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A cluster is a set of networked machines.
Clusters typically provide a login node and a set of worker nodes.
Files saved on one node are available everywhere.
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Using a cluster: Scheduling jobs
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The scheduler handles how compute resources are shared between users.
Everything you do should be run through the scheduler.
A job is just a shell script.
If in doubt, request more resources than you will need.
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Using a cluster: Accessing software
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Load software with module load softwareName
The module system handles software versioning and package conflicts for you automatically.
You can edit your .bashrc file to automatically load a software package.
When using software on any HPC system, check the software documents for details on how to use it effectively.
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Using a cluster: Using resources effectively
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The smaller your job, the faster it will schedule.
Don’t run stuff on the login node.
Again, don’t run stuff on the login node.
Don’t be a bad person and run stuff on the login node.
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