Categorized list of topics

(Česká verze)

Metacentrum wiki is deprecated after March 2023 Dear users, due to integration of Metacentrum into https://www.e-infra.cz/en (e-INFRA CZ service), the documentation for users will change format and site. The current wiki pages won't be updated after end of March 2023. They will, however, be kept for a few months for backwards reference. The new documentation resides at https://docs.metacentrum.cz.

Basic tutorials

• PBS Pro Quick Start [PDF] – PBS and batch script commands reference card (.pdf)
• Beginners guide – detailed guide for users new to MetaCentrum and grid computing
• Working with data – basic information about data copying, backup and archiving on MetaCentrum machines
• Applications – list of installed software

Advanced topics

Accessing machines

• How to ssh from Linux – guide on how to access MetaCentrum machines from computer with Linux
• How to ssh from Windows – guide on how to access MetaCentrum machines from computer with Windows
• Usage of PuTTY – tutorial on PuTTY, an SSH client for Windows
• Usage of Bitvise SSH Client – tutorial on Bitvise, an SSH client for Windows
• Usage of WinSCP – tutorial on WinSCP, an FTP, SCP, FTPS and FTP client for Windows
• Kerberos authentication system – general info on Kerberos, a single sign-on system used between MetaCentrum machines
• Kerberos on Linux – how to use Kerberos from Linux
• Kerberos on Windows – how to use Kerberos from Windows

Jobs

• About scheduling system – PBS Pro options detailed page
• Trap command usage – how to tune the batch script using trap command
• Fairshare – how the jobs are prioritized based on the past resource use
• Video on job tracking – youtube tutorial on job tracking
• Parallelization – how to run parallelized jobs
• Email notifications – how the emails about jobs are aggregated
• Prolong walltime – how to prolong walltime for your job in case of need

Data

• Mounting data storages on local station – advanced tutorial on how to mount remote NFS4 servers locally
• Sharing data in group – how to share data within a group of users
• Sharing data through filesender – method to pass data to someone without Metacentrum account
• Access Control Lists on NFSv4 – how to share data within a group of users using AC
• Quotas – user disk quotas description

Applications and software

• Available applications – list of installed software (sorted alphabetically)
• MetaCentrum Application List – list of installed software (sorted by field of interest)
• Docker in Podman – How to run Docker image
• Application modules – tutorial on modules
• How to install an application – how to install your own software
• Running an application on Java platform – a few notes on running jobs on Java platform
• Debian compatibility – what to do in case your application misses some library due to Debian version incompatibility

Graphical output for GUI applications

• OnDemand – how to access GUI applications through internet browser
• Remote desktop – how to access GUI applications through VNC client
• X-Window – how to access GUI applications in a low-level way through SSH connection

GPU computing & deep learning

• GPU clusters – clusters allowing submission of GPU jobs
• Cluster Adan – cluster for machine learning, deep learning, AI
• NVidia deep learning frameworks

Infrastructure

• Grids and supercomputers – more on grids, supercomputers and clusters
• Scratch storage – types of scratch storages and their properties
• Frontend – list of available frontend machines
• Oven node – special oven node for submitting master jobs
• Xeon Phi – massively parallel cluster
• ScaleMP – software layer to aggregate resources into one virtual machine

Presentations & downloads

• How to bring down Metacentrum in 10 steps [PDF] – About most common user mistakes, presentation slides
• Going graphical [PDF] – How to run applications with GUI in Metacentrum, presentation slides
  • Matlab on X-Window video – example 1: Matlab via X-Window
  • Matlab on Remote desktop video – example 2: Matlab via Remote desktop
  • Matlab in OnDemand as a direct link – example 3: Matlab via OnDemand as a direct link
  • Matlab in OnDemand from interactive desktop – example 4: Matlab via OnDemand from interactive desktop
• Containers at Metacentrum [PDF] – About usage of containers at Metacentrum, presentation slides
• NVidia GPU cloud at Metacentrum [PDF] – How to use NVidia GPU cloud packages at Metacentrum, presentation slides

Troubleshooting, FAQs and user support

NVidia_GPU

• FAQ/Grid computing
• Troubleshooting – what to check in case of problems
• User support