Tag Archive for: HPC

UNIX command line


UNIX command line

This course introduces the UNIX command line on a Linux or Mac.
It serves as a foundation of our Bash scripting
and CBE HPC cluster introduction courses.
The Regular expressions course also
builds on UNIX command line knowledge.

Instructor: András Aszódi.

Topics

  • UNIX overview: general principles.
  • Working with files and directories.
  • Users, groups, permissions, environment variables.
  • Command pipelines, job control.

Out of scope

This course focuses on the basics of using the UNIX command line.
We will not learn about how to run programs on the HPC cluster!
That knowledge is covered by the CBE HPC cluster introduction course.

Prerequisites

Programming experience is not required but desirable.
The ability to type with a low error rate is necessary, because this is a hands-on training.

Practical information

Number of participants: minimum 5, maximum 10.

Length: The course takes a half day,
usually from 09:00 to 13:00.

CBE HPC cluster introduction


CBE HPC cluster introduction

The CBE cluster at the VBC

This course provides an introduction to the CBE (“CLIP Batch Environment”)
high-performance computing cluster which is part of the
Vienna Biocenter Cloud Infrastructure Project.

Instructor: András Aszódi.

Topics

  • Introduction to the cluster: architecture, storage layout, access.
  • Environment modules.
  • Batch mode: SLURM queuing system, job scripts. Job arrays, task arrays, MPI jobs.
  • Interactive use: Jupyter, XPRA desktop, RStudio.

Prerequisites

You may attend this course only if you
already have an account on the CBE cluster or plan to use the cluster
in the near future
. You can request an account either by
emailing the cluster administrators or
at the VBC IT portal by clicking on the
“HPC Support Ticket” link and selecting the
“Get HPC access” option.

The cluster services are reachable only from the VBC internal network.
If the course is held over the Internet “remotely” then you’ll need
VPN access.

Because the cluster is mainly used through the command line, familiarity with basic
UNIX commands
such as ls, cd, cp, pwd is required.
The UNIX command line course provides a good introduction.

This is a hands-on course. Participants must bring a laptop with them. Under
Windows, they must have a remote login utility installed, such as:

UNIX operating systems such as Linux or MacOS already have the necessary
tools to connect to the cluster, so no extra software installation is
necessary.

Practical information

Length: The course takes four hours with two short breaks.

Number of participants: minimum 5, maximum 10.