SNIC Training News Letter
No 107, 20 February 2020
– Published 20 February 2020
Welcome to another addition of the SNIC training newsletter. This week we newly advertise the PDC Café and a CodeRefinery Training workshop in Copenhagen. We also remind on a number of training events advertised before.
Training for users of molecular dynamics applications
- Training course: Efficient MD simulations at HPC2N, HPC2N, Umeå University, 28 February 2020
Training suitable for new users of SNIC:
- Training seminar: “C3SE Introductory Seminar” in Gothenburg, 18 February 2020, 15:15 - 17:00
- Training seminar: “An introduction to UNIX/LINUX” in Lund, 26 February 2020, 12:30 - 14:00
- Training seminar: “Cluster architecture and job submission” in Lund, 11 March 2020, 12:30 - 14:00
- Training seminar: “Transferring data to and from an HPC system” in Lund, 18 March 2020, 12:30 - 14:00
Interactive user support session:
- PDC Cafe, Wednesday 27 February, 10-12:00, SeRC room, 5th floor Teknikringen 14
Training in the nordics
- CodeRefinery Training workshop: "Writing Reproducible and Sustainable Research Code”, Copenhagen, Denmark, 17-19 March 2020
Training overview:
- SNIC training webpage
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Training for users of molecular dynamics applications
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Training course: Efficient MD simulations at HPC2N, HPC2N, Umeå University, 28 February 2020
The aim of the course is to provide MD users with a set of best practices to improve the performance of their simulations. This will be accomplished by tuning the appropriate SLURM switches and flags proper to the MD packages.
Topics to be covered are:
- Performance analysis of different versions of the packages (AMBER, NAMD, GROMACS, LAMMPS)
- Performance analysis on different architectures (CPU, GPU, KNL)
- General recommendations when using plugins.
Please bring your laptop for the hands-on.
For more information and registration, please go to the course website: https://www.hpc2n.umu.se/events/courses/md-course-spring-2020
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Training suitable for new users of SNIC:
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Training seminar: “An introduction to UNIX/LINUX” in Lund, 26 February 2020, 12:30 - 14:00
This training seminar provides a first introduction to the UNIX/LINUX environment. It is aimed at new users of UNIX and will discuss UNIX skills required to work on a typical HPC cluster. Topics include manipulating files and directories, editing file contents and the development of simple scripts, such as required for job submission.
The event is organised as an informal lunchtime seminar – you are welcome to bring your lunch along. It addresses users who have recently started using HPC systems and prospective users considering using an HPC system in the near future.
For more information and registration visit: http://www.lunarc.lu.se/training/an-introduction-to-unixlinux-26-february-2020/
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Training seminar: “Cluster architecture and job submission” in Lund, 11 March 2020, 12:30 - 14:00
This event explains key features of a contemporary HPC cluster, with a focus on the systems deployed at Lunarc. It will explain the principles behind the job scheduler and how the scheduler can be used to accomplish your computational work in an efficient manner.
The event is organised as an informal lunchtime seminar – you are welcome to bring your lunch along. It addresses users who have recently started using HPC systems and prospective users considering using an HPC system in the near future.
For more information and registration visit: http://www.lunarc.lu.se/training/cluster-architecture-and-job-submission-11-march-2020/
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Training seminar: “Transferring data to and from an HPC system” in Lund, 18 March 2020, 12:30 - 14:00
Transferring data to and from an HPC system to another computer system is a common task for anyone utilising an HPC system for their work. The seminar will describe the storage available to users and how to transfer data from systems under Windows, macOS, UNIX and Linux to an HPC cluster. The event will further discuss the SNIC national storage system.
The event is organised as an informal lunchtime seminar – you are welcome to bring your lunch along. It addresses users who have recently started using HPC systems and prospective users considering using an HPC system in the near future.
For more information and registration visit: http://www.lunarc.lu.se/training/transferring-data-to-and-from-an-hpc-system-18-march-2020/
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Training seminar: “C3SE Introductory Seminar” in Gothenburg, 18 February 2020, 13:15 - 15:00
The seminar describes how to work on the systems and introduces the provided toolset. Work management and best practices are also discussed. The event is intended for all new users, to get a comprehensive overview on the systems and how to get started with using them.
This seminar will also be offered on 15 May.
For more information and registration see: https://www.c3se.chalmers.se/
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Interactive user support session:
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PDC Cafe, Wednesday 27 February, 10-12:00, SeRC room, 5th floor Teknikringen 14
PDC welcomes users to an informal "PDC Cafe". You can drop by, have fika, meet HPC experts, discuss problems and get useful advice. If there's anything that you think could be improved either in your own scripts, workflows or codes, or in the services that PDC provides, please drop by and discuss it with us, we would love to help! This is the place to get stuff done, so bring a laptop.
Suggestions for issues you can discuss:
• How to improve your run scripts
• Help with scripting
• Help with programming and software management
• Help with project organization and data management
• Help with Linux stuff
• How to improve performance of your calculations
• “Papercuts”: things that annoy you and how we can fix that
• How to improve services
• Project ideas
• Learn about cool services that you may not know yet
Please register if you wish to attend: https://www.pdc.kth.se/about/events/pdc-cafe-on-27-february-1.957146
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Training in the Nordics:
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CodeRefinery Training workshop: "Writing Reproducible and Sustainable Research Code”, Copenhagen, Denmark, 17-19 March 2020
A three-day CodeRefinery workshop on best practices for writing research code will be held at the Technical University of Denmark (DTU) in Kongens Lyngby, just north of Copenhagen, on 17-19 March. The workshop is for students and researchers who write code in any programming or scripting language, at any level of complexity, but it does not teach specific languages nor how to use the Linux/Unix terminal shell. Instead the focus is on using modern tools and workflows to make coding easier and more structured, reproducible and collaborative.
Further information and registration details can be found on the course website:
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SNIC training webpage
In addition to these news letters we also provide a SNIC training webpage: http://docs.snic.se/wiki/Training
This webpage currently gives an overview on all courses currently planed. It provides links to more information and the actual registration. The webpage also includes training which is expected to be mostly of interest to individual SNIC centres. Information will be added to this page as it becomes available.