Supercomputers play an important role in the field of computational science and are used in various fields like climate research, molecular modelling, biological macromolecules and physical simulations (such as nuclear detonation, aerodynamics, fluid dynamics etc).
These High-performance Computing (HPC) clusters are used for large scale data processing and data analysis, fine grained parallel calculations and simulations of ever increasing fidelity. This course material is meant to introduce learners to the core principles behind using a HPC cluster, how to connect to it, how to dispatch jobs and retrieve their results, and how to program applications that can harness the full power of this machinery. As using the Unix shell is a prerequisite, this workshop offers an introduction to the Unix shell as an optional module at the beginning.
The entire course will be held online with zoom. So if you want to participate, make sure that you have zoom installed and a stable internet connection as well as a microphone and speakers/headphones.
The course material will be delivered on two days only: July 14th and July 22, 2020. The course module introducing HPC (half day on July 22, 2020) is mandatory for the course.
The course is free of charge and provided as an in-kind contribution of FWCC.
Course Content
Introduction to the Unix Shell (full day on July 14, 2020)
This material will be delivered in an interactive fashion as a full day course. To participate, you need a Unix shell installed and able to run on your system. Setup instructions can be found here. This module is optional. Please indicate during your registration if you'd like to take part. Except for the software installed, there are no prerequisites for participating.
Note: The introduction to using an HPC system requires that you know the Unix terminal! So if you never worked with it or feel not confident doing so, please consider taking part.
Here the topics covered in the course:
- Navigating Files and Directories (listing file system content, changing directories)
- Working With Files and Directories (creating/removing folders, copying/moving files)
- Pipes and Filters (How can I combine existing commands to do new things? )
- Loops (How can I perform the same actions on many different files?)
- Shell Scripts (How can I save and re-use commands?)
- Finding Things
Introduction to HPC (half day in the morning of July 22, 2020)
This material will be delivered in an interactive fashion as a half day course. To participate, you need a ssh client installed and able to run on your system. Setup instructions can be found here. This module is mandatory, hence the name of this workshop. Except for the software installed, you will need an active cluster account. In case of doubt or if you need to apply for one, please contact cluster-admin@hzdr.de.
Note: The introduction to using an HPC system requires that you know the Unix terminal!
Here the topics covered in the course:
- Logging into a cluster (connecting to the cluster, transferring files to/fro)
- Submitting a job with slurm
- Monitoring jobs, cancelling jobs with slurm
- The file system hierarchy (where are things stored and where are they visible)
- Making software available (using the module system)
Introduction to Parallel Computing with Python (half day in the morning of July 22, 2020)
This material will be delivered in an interactive fashion as a half day course. To participate, you need a ssh client installed and able to run on your system. Setup instructions can be found here. This module is optional. Please indicate during your registration if you'd like to take part. Except for the software installed, you are expected to have a minimal understanding of writing programs in python. In addition, you will need an active cluster account. In case of doubt or if you need to apply for one, please contact cluster-admin@hzdr.de.
Here the topics covered in the course:
- Profiling a Compute Heavy Python program
- Parallelising a Python program to run on one computer
- Distributed Parallelisation of a Python program
Miscellaneous
We currently only have 15 seats available in the course, that are provided on a first-come-first-serve basis.
