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SNIC Training News Letter

No 106, 6 February 2020

– Published 6 February 2020

Welcome to another edition of the SNIC training newsletter.  This week we newly advertise training on MD simulation codes in Umeå and on the NEC SX-Aurora TSUBASA architecture.


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


Training on specific HPC hardware architectures

  • Training webinar: NEC SX-Aurora TSUBASA, 14 February 2020
  • Training workshop: Arm HPC Hands-on Workshop, 18 February 2020, 09.00-17.00


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:

  1. Performance analysis of different versions of the packages (AMBER, NAMD, GROMACS, LAMMPS)   
  2. Performance analysis on different architectures (CPU, GPU, KNL)
  3. 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: “C3SE Introductory Seminar” in Gothenburg, 18 February 2020, 15:15 - 17:00


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 10 April and 15 May.


For more information and registration see: https://www.c3se.chalmers.se/



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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. 




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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. 



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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.  



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Training on specific HPC hardware architectures


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Training webinar: NEC SX-Aurora TSUBASA, 14 February 2020


In cooperation with NEC, PDC cordially invites you to join the NEC SX-Aurora TSUBASA Webinar on Friday, 14 February 2020, 9:30-13:00 CET.


In this 3.5-hour webinar NEC will present their newest generation Vector Engine (https://www.nec.com/en/global/solutions/hpc/sx/vector_engine.html) with emphasis on the impact

on potential application programmers and users.  


The webinar will take up:


- An overview of the SX-Aurora TSUBASA hardware and software ecosystem.

- Illustrated teaser examples of programming, optimization and tuning of application software and online demonstrations.

- An interactive questions and answers session.


Please register you interest at: https://www.kth.se/form/pdc-nec-webinar-feb2020 

Once registered, you will receive information on how to join the webinar.


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Arm HPC Hands-on Workshop, 18 February 2020, 09.00-17.00


This one day hands-on workshop will introduce the Arm HPC hardware and software ecosystem.


The workshop will be a mixture of presentations (to introduce topics) and hands-on tutorials (to explore those topics).


In addition to giving you a general overview of the ARM ecosystem, the workshop will provide training both for current generation hardware and instruction sets (Marvell ThunderX2 and NEON) and future generation (A64FX and SVE).


Through a set of pre-prepared tutorial examples, participants will be guided through an introduction to the compiler and maths libraries, and on to the compilation and emulation of SVE vector instructions. Additionally we invite participants to bring, and use, their own code examples to evaluate the hardware and HPC software stack.


For further information and registration, please visit https://www.pdc.kth.se/about/events/arm-hpc-hands-on-workshop-1.953884 



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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.