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SNIC Training News Letter

No 84, 8 February 2019

– Published 8 February 2019

Topics of this issue:

  • New web page collating online training
  • Training course: “An introduction to parallel programming using Message Passing with MPI”, Gothenburg, 21 - 22 March 2019
  • Only a few spaces left: Training Course for PhD students: “CFD with OpenSource Software, 2019”, Gothenburg, starting 2 Sept 2019
  • Training course: Efficient MD simulations at HPC2N, HPC2N, Umeå University, 21 February 2019
  • Registration closing for training course: “Introduction to PDC" in Stockholm, 13 February 2018, 13:00-17:00
  • Training seminar: “Cluster architecture and job submission” in Lund, 14 February 2019, 12:30 - 14:00
  • Training seminar: “Transferring data to and from an HPC system” in Lund, 21 February 2019, 12:30 - 14:00
  • Training seminar: “Visualisation and interactivity in HPC - The LUNARC HPC Desktop” in Lund,  7 March 2019, 12:30 - 14:00
  • Training seminar: “C3SE Introductory Seminar” in Gothenburg, 26 March 2019, 15:15 - 17:00


Training opportunities in Sweden, recommended by SNIC:

  • CodeRefinery Training workshop: "Writing Reproducible and Sustainable Research Code", Stockholm, Sweden, 25-27 March 2019
  • Training courses in OpenFOAM at foundation and advanced level, Stockholm, 8 - 11 April, 2019


Attend training in the Nordics:

  • CSC Summer School in High-Performance Computing 2019 in Finland, 25 June 25 - 4 July 2019
  • NeIC Nordic Training Calendar


Training overview:

  • SNIC training webpage



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New web page collating online training


In collaboration with the SNIC application experts and the staff working at the SNIC centres, the SNIC training team has created a web page with publicly available online training materials.  The material is from various external sources and only a subset of this has been created within SNIC.  This is an ongoing effort and we hope to add more material in the future.


SNIC can not assume any responsibility for material created by external sources and hosted on external servers.


The URL for online training overview page is: http://docs.snic.se/wiki/Online_training_materials


If you aware of publicly available training material, which you expect of interest to the SNIC community, we like to hear from you.  Please email us on application-support@snic.se.


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Training course: “An introduction to parallel programming using Message Passing with MPI”, Gothenburg, 21 - 22 March 2019


Message Passing is presently the most widely deployed programming model in massively parallel high performance computing. Message passing is suitable for programming a wide range of current computer architectures, ranging from multi-core desk top equipment to the fastest HPC systems in the world, offering several hundred thousand processing elements. 


The course is at the beginners level and assumes no prior experience in parallel computing. The concepts behind message passing and distributed memory computing will be introduced and the syntax of the key MPI calls will be explained. The course will include point-to-point communications, non-blocking communication and the collective communications calls. Practical sessions to deepen the understanding of the lectures will be part of the course. At the end of the course participants should be able to write their own MPI programs at an intermediate level. The teaching language will be English. 


For more information and registration, please see https://www.c3se.chalmers.se/news/mpi-2019/



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Only a few spaces left: Training Course for PhD students: “CFD with OpenSource Software, 2019”, Gothenburg, starting 2 Sept 2019


This event is almost fully booked.  Students interested students should register directly!


The course gives an introduction to the use of OpenSource software for CFD applications. It has a strong focus on how to efficiently use the Linux operating system and different softwares that are useful for CFD (to the largest extent OpenFOAM), rather than having a focus on teaching the basics of CFD or fluid dynamics. A major project work in OpenFOAM forms a large part of the course. The project may be defined according to the student's special interests. The result of the project should be a detailed tutorial for a specific application or library of OpenFOAM (Docendo discimus – Latin: “by teaching, we learn”). The tutorials will be peer-reviewed by the students, and the tutorials thus form a part of the course. The tutorials will be made available, as a contribution to the OpenFOAM community. To pass the course the student must do the project and peer-review a tutorial from another project. There are also some compulsory assignments.


Organisation: Preparation and introduction at distance, three two-day occasions on-campus, project work at distance. Oral and written presentations, and a review process.


Credits: 7.5 hec


For more information visit the website:  http://www.tfd.chalmers.se/~hani/kurser/OS_CFD/#YEAR_2019


Registration: Notification of interest by mail to hakan.nilsson@chalmers.se.  Interested participants are entered into a mailing list for future communication.  Final registration will be done later.  SNIC PhD students should mention that they are SNIC users.  There is a maximum number of attendees - register your interest as soon as possible.



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Training course: Efficient MD simulations at HPC2N, HPC2N, Umeå University, 21 February 2019


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
  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-2019  



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Registration closing for training course:  “Introduction to PDC" in Stockholm, 13 February 2018, 13:00-17:00


This is an afternoon 4-hour hands-on course centered on how to use the systems that PDC is providing, and is a good starting point for people that want to get started with high performance computing (HPC) using PDC clusters.


The course will focus on basic and advanced methods for using PDC systems. It will cover some background, what clusters are available, applying for PDC resources, how to login to PDC, running software on different nodes, storing data on different file systems, compiling code, etc... 


Location: room 304, Teknikringen 14.

Time: 13 February 2019, 13:00-17:00

Further information and registration:


Note that if you wish to participate in the course, you need to have a PDC account. If you do not yet have a PDC account, please request an account at least one week before the course starts according to the instructions at 



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Training seminar: “Cluster architecture and job submission” in Lund, 14 February 2019, 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, 21 February 2019, 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 seminar: “Visualisation and interactivity in HPC - The LUNARC HPC Desktop” in Lund,  7 March 2019, 12:30 - 14:00


The LUNARC HPC Desktop provides LUNARC and SNIC users with a solution for hardware accelerated remote visualization that will provide a new scalable approach to HPC and scientific data visualization. The desktop introduces a convenient way to work with our clusters using not only multiple terminal windows but also file browsers, editors, graphical tools such as queue status and debuggers, 2D and 3D applications, etc. 


This seminar will give a short introduction on how to get started with the LUNARC HPC Desktop and the applications available. We will also present LUNARC HPC Desktop On-Demand, which enables users to request time on dedicated servers for running graphical user interfaces with hardware accelerated graphics. 




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Training seminar: “C3SE Introductory Seminar” in Gothenburg, 26 March 2019, 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. 


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



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Training opportunities in Sweden, recommended by SNIC


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CodeRefinery Training workshop: "Writing Reproducible and Sustainable Research Code", Stockholm, Sweden, 25-27 March 2019


A three-day CodeRefinery workshop on best practices for writing research code will be held in Stockholm on 25-27 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:


There is a limited number of seats available for the workshop, so make sure to register early!



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Training courses in OpenFOAM at foundation and advanced level, Stockholm, 8 - 11 April, 2019


As part of an industry collaboration with the ESI-Group, PDC is offering two training courses on OpenFOAM.  One is at foundation level, the other is at an advanced level.  


For information on the course and possibly discounted course fees, consult the following pages.




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Attend training in the Nordics:


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CSC Summer School in High-Performance Computing 2019 in Finland, 25 June 25 - 4 July 2019


Registration for the CSC Summer School in HPC is now open! Ten days of coding, sport activities and good company right in the middle of beautiful Finnish nature just 30km from Helsinki. https://www.youtube.com/watch?v=fZVwJgfhl-4


CSC Summer School celebrates its 10th anniversary by bringing together undergraduate and graduate students and postdoctoral researchers in different disciplines of scientific computing. The school consists of lectures and hands-on training on parallel programming, code optimization and other essential skills in development of scientific software. During the school you can build up your HPC expertise from almost zero up to an intermediate / semi-advanced level.


The aim of the school is to give you the skill set necessary to start writing high-performance scientific software! ... and to have a great time while doing it!




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NeIC Nordic Training Calendar:


The NeIC Nordic Training Calendar gives an overview on eScience related training throughout the Nordics.  Have a look at https://neic.no/training/#neic-training-calendar for an overview on training in Nordic partner countries that is typically accessible to Swedish academic research.  The page also provides direct links to training portals of the national e-Science provides in the Nordics.



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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.