Jste zde

Productivity tools for High Performance Computing (PTC course)

Po, 27.11.2017 9:30 - Út, 28.11.2017 15:30
Uzávěrka registrace: 
Út, 21.11.2017 23:00
VŠB - Technical University Ostrava, IT4Innovations building, room 207
Branislav Jansík, David Hrbáč, Josef Hrabal, Lukáš Krupčík, Lubomír Prda, Roman Slíva (IT4Innovations)


This HPC training aims to expand skills and knowledge in using productivity tools and technologies, to quickly build up an efficient HPC user environment, from scratch, without admin rights. We shall demonstrate tools and procedures tailored to the Salomon or Anselm clusters, however they are rapidly replicable on any HPC system.

In particular, our “Swiss knife” course will cover the following tools:

  • Singularity, a novel technology for paravirtualization allowing for rapid deployment of highly customized environment,
  • EasyBuild, a software build and installation framework which allows management of (scientific) packages on HPC systems in an efficient way,
  • Lmod, a program to manage the user environment under Unix (Linux, Mac OS X, ...), a new implementation of environment modules,
  • GIT/GitLab, Continuous Integration, a version control system for tracking changes in computer files and coordinating work on those files among multiple users,
  • KVM (Kernel-based Virtual Machine), a virtualization infrastructure for the Linux kernel that turns it into a hypervisor.

Hands-on practical examples will be an integral part of the course.

Purpose of the course (benefits for the attendees)

The participants will broaden their range of techniques for efficient use of HPC by mastering modern technologies for code management and execution.

About the tutors

Branislav Jansik obtained his PhD in computational chemistry at the Royal Institute of Technology, Sweden in 2004. He took a postdoctoral position at IPCF, Consiglio Niazionale delle Ricerche, Italy,  to carry on development and applications of high performance computational methods for molecular optical properties. From 2006 he worked on  the development of highly parallel optimization methods in the domain of electronic structure theory at Aarhus University, Denmark. In 2012 he joined IT4Innovations, the Czech national supercomputing center, as the head of supercomputing services. He has published over 35 papers and co-authored the DALTON electronic structure theory code.

Josef Hrabal obtained his Master's Degree in Computer Science and Technology at VŠB - Technical University of Ostrava in 2014. From then he contributed to projects within the University, and in 2017 he joined IT4Innovations, the Czech national supercomputing center, as an HPC application specialist.

David Hrbáč obtained his Master's Degree in Measurement and Control Engineering at VŠB - Technical University of Ostrava in 1997. Since 1994 he has worked for many IT companies as a system architect and CIO. In 2013 he joined IT4Innovations.

Lukáš Krupčík obtained his Master's Degree in Computer Science and Technology at VŠB - Technical University of Ostrava in 2017. In 2016 he joined IT4Innovations, the Czech national supercomputing center, as an HPC systems specialist.

Lubomír Prda obtained his Master's Degree in Information and Communication Technologies at VŠB - Technical University of Ostrava in 2010. Before joining the IT4Innovations team as an HPC specialist in 2016, he worked at the Tieto Corporation as a network engineer, and later moved to identity and access management for the company's nordic and international customers. Lubomír's focus is to manage and maintain the centre's back-end IT infrastructure and services.

Roman Slíva obtained his Master's Degree in Computer Science at VŠB - Technical University of Ostrava in 1998. He worked as an IT system specialist and project leader in the areas of servers, high performance computing, and storage and backup. From 2007-2009 he led the IT Server Infrastructure group at VŠB - Technical University of Ostrava. In 2011 he joined IT4Innovations as an HPC system specialist and architect.

Preliminary agenda


Day 1
9:30 – 10:00


10:00 – 12:00


  • Computing environment at IT4Innovations

GIT (Prda, Hrbáč)

  • Introduction to Git
  • Hands-on session
13:00 – 14:30

Container and virtualization technology: Singularity (Krupčík, Hrabal)

  • Introduction to the Singularity Containers on the Salomon cluster
  • How to bootstrap a singularity image from docker
  • Hands-on session
15:00 – 16:30

Container and virtualization technology: KVM, VDE2 (Jansík)

  • Introduction to the QEMU and KVM
  • KVM networking and interconnect, VDE2
  • Hands-on session


Day 2 
9:00 – 10:00Lmod, software for management of environment modules (Krupčík, Hrabal)
  • Introduction to the Lmod environment
  • Tips and tricks
10:30 – 12:30

EasyBuild framework for user software installation (Krupčík, Hrabal)

  • Introduction to the EasyBuild tool
    • Meeting the EasyBuild tool for the first time
    • Short examples
  • Hands-on session
    •  Setting up /home for building
    •  Building your first software using easyconfigs
    •  Modification of an existing easyconfig (new software version, other toolchains, ...)
    •  Creating a new easyconfig from scratch
    •  Troubleshooting
    •  Tips and tricks
14:00 – 15:30

GitLab, Continuous Integration (Hrbáč)

  • Introduction
  • Software project workflow
  • Continuous integration


Basic knowledge of Linux and its command line. Own notebook with Linux, VNC viewer and root privileges. For other platforms, a training virtual machine will be distributed - install VirtualBox.


Obligatory registration via the PRACE Events Portal and its registration form.

Capacity and Fees

30 participants. The event is provided free of charge.


  • See the links below for how to get to the campus of VŠB - Technical University Ostrava, and to the IT4Innovations building.
  • Documentation for IT4Innovations' computer systems is available at https://docs.it4i.cz/.


This training is a PRACE Training Centre (PTC) course, co-funded by the Partnership of Advanced Computing in Europe (PRACE). The main web page of the course is located on the PRACE Events Portal.