Welcome

• This workshop is on-site (SYKE,LUKE) + online
• Schedule
  -> `https://ssl.eventilla.com/event/pEb7a
• Q&A: HedgeDoc
  -> https://siili.rahtiapp.fi/spatialCSC22
• Reminder about hands-on session; link to survey:
  https://link.webropolsurveys.com/S/C4755A51FB4A6DFC
• Greetings from the organizers

Code of conduct

We strive to follow the Code of Conduct developed by The Carpentries organisation to foster a welcoming environment for everyone. In short:

• Use welcoming and inclusive language
• Be respectful of different viewpoints and experiences
• Gracefully accept constructive criticism
• Focus on what is best for the community
• Show courtesy and respect towards other community members

Goals

In the end you hopefully know more about…

• What kind of services are offered by CSC and Geoportti
• How these services might benefit your work
• The supercomputer and how to start using it
• What spatial data and data services are available

CSC Account

https://link.webropolsurveys.com/S/C4755A51FB4A6DFC

Introduction to CSC services for new users

• What services are available?
• How can I get access?
• What skills do I need?
• Getting started with Puhti supercomputer

Why use CSC services?

• “Outsource” heavy/specialized computations
• Free of charge for open science Finnish universities and research institutes
• CSC specialist support

CSC services

research.csc.fi/en/service-catalog

Why use CSC supercomputers?

When own computer is not enough:

• Resource needs (time, memory, storage, GPU)
• Prebuilt environments
• Run many experiments at same time
• Data availability
• Collaboration possibility

Allas

• Object storage
• Up to 200TB for free
• Connection to CSC computing services and own computer
• Project lifetime data storage
• Within CSC project data sharing
• Some tools support direct read from Allas
• NOT a file system, data management environment, backup service!

Get access

Working at Finnish University / Univeristy of applied Sciences / state research institute? -> Free of charge

1. Create a personal user account
2. Find a senior researcher / PI to create a CSC project and add needed services
3. Ask above person to add you to the project and add needed services
4. Read the documentation: https://docs.csc.fi

MyCSC

• Manage your account
• Manage your projects/services
• Estimate billing units
• Change password
• …

https://my.csc.fi

Skills needed

“You can’t learn everything you need all at once. Instead, continually learn and know when to ask for help.”
- Aalto Scientific Computing

• Using CSC computing resources: general Linux commands
• Supercomputer
  • serial & ‘embarassingly parallel’ tasks: general Linux commands, basic HPCterminology
  • parallel work: High Performance Computing (HPC), scientific coding
• Virtual Machines (VM): Linux administration

Training

• ‘CSC computing environment’ self-study course
• ‘Research data management’ self-study course
• CodeRefinery workshop March 2023
• CSC geoinformatics training materials

-> follow our training calendar

How we can help

• ‘Z is not working as expected’
• ‘My code gives error Y’
• ‘Can A be installed to Puhti?’
• ‘Any advice how to do X?’
• Training/example wishes

-> servicedesk@csc.fi
-> Weekly user support coffe break

Speed up your request

Supercomputer

Main differences to using own computer:

• Not faster, but bigger
• For speed up: parallelism
• More resources available (Memory, CPU, GPU) - application needs to make use of this!
• Non-interactive for heavy computations
• Resource management

Possibilities

• Use more memory / CPU / GPU than your own computer has available
  
  -> analyse large files, machine learning model training
  
• Speed up so-called embarrassingly parallel analyses (large number of identical independent tasks)
  
  -> doing same thing to multiple map tiles/ data chunks

Applications

Modules

Applications in Puhti are provided in modules. Use

module load <modulename>

before every application use to make application available.

Check https://docs.csc.fi/apps for module names and versions.

Puhti basics

Directories

• HOME – most important (small) files, personal access only
• PROJAPPL – project specific / your installations/ shared binaries
• SCRATCH – main working area, can be used to share with project members

Jobs and queueing

• Batch jobs
  • resource request
  • computing step(s)
• Queue for resource management system to grant resources
• All heavy computing must be done via batch jobs!

Example batch script

-> File simple_serial.bash
-> Submit for computation with sbatch simple_serial.bash

Puhti web interface

-> Check your data, testing, code development, file management, quotas, graphical applications

puhti.csc.fi

Take-home message

• Manage your CSC services via our CSC customer portal at MyCSC
• Resources are free for open science research (academic use)
• Participate in CSC trainings, read materials and watch webinars
• Take advantage of CSC docs pages
• Contact our helpdesk for support and guidance

How you can help

“The authors wish to thank CSC - IT Center for Science, Finland (urn:nbn:fi:research-infras-2016072531) and the Open Geospatial Information Infrastructure for Research (Geoportti, urn:nbn:fi:research-infras-2016072513) for computational resources and support”.

Feedback

Please give us feedback via the HedgeDoc! :)