Spring School 2017: HPC for Life Sciences Welcome Stockholm, April - - PowerPoint PPT Presentation

Spring School 2017: HPC for Life Sciences

Welcome

Stockholm, April 2017 Michaela Barth PRACE Sweden

Spring School 2017: HPC for Life Sciences

jointly organized by PRACE & BioExcel Center of Excellence

65 students

from 19 different countries

4 main speakers 5 tutors

4 full days

Spring School 2017: HPC for Life Sciences

08:30-09:00 Registration

E3

09:00-09:15 Welcome Michaela Barth

E3

09:15-10:00 BioExcel Center of Excellence – Training Programme Vera Matser

E3

10:00-10:30 Coffee break 10:30-12:00 Molecular visualisations with VMD John Stone

E3

12:00-13:00 Lunch 13:00-13:45 How to use the PDC Supercomputing systems Henric Zazzi

E3

13:45-15:00 Hands-on VMD

Red / Orange

15:00-15:30 Coffee break 15:30-17:30 Hands-on VMD

Red / Orange

17:30 Welcome Dinner

Syster o Bror

Monday

Welcome Dinner

• @ Syster o Bror
• 1 Glas of Beer, Wine or equivalent for free
• Menu (everything will be marked):

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Kyckling med örter och vitlök

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Sallad på varmröktlax

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Ört och vitlöks-marinerade champinjoner

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Paj på spenat och rödlök

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Vegetarisk lasagne

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Hummus

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Tzatziki

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Marinerade oliver

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Bakade rödbetor serveras med creme på chevré

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Hembakat lantbröd med vispat smör

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Kaffe med liten chokladbit

Spring School 2017: HPC for Life Sciences

Tuesday

09:30 – 10:30 HPC Simulations with NAMD Jim Phillips

E3

10:30 – 11:00 Group Picture and Coffee Break Campus 11:00 – 12:00 HPC Simulations with NAMD

E3

12:00 – 13:00 Lunch 13:00 – 14:30 Hands-on NAMD

Red / Orange

14:30 – 15:00 Coffee Break 15:00 – 17:00 Hands-on NAMD

Red / Orange

Spring School 2017: HPC for Life Sciences

Wednesday

09:30 – 10:30 HPC Simulations with GROMACS Erik Lindahl

E3

10:30 – 11:00 Coffee Break 11:00 – 12:00 HPC Simulations with GROMACS

E3

12:00 – 13:00 Lunch 13:00 – 14:30 Hands-on GROMACS

Red / Orange

14:30 – 15:00 Coffee Break 15:00 – 17:00 Hands-on GROMACS

Red / Orange

18:00 Guided Tour and Dinner

Vasa Museum

Visiting the Vasa Museum

Starting with a Guided Tour through the Museum Dinner at the Restaurant

• White asparagus from Germany with ramson Hollandaise, toasted almonds

and spring leafs

• Corvers Kauter Terra 50, Riesling, Rheingau, Germany, organic
• Pike-perch with green pea puree, Champagne sauce, chives, trout roe,

crispy cress and farmers beans

• Vegetarian alternative: New seasonal vegetable risotto with truffle and

parmesan cheese crisp

• Pouilly-Fumée "Villa Paulus" 2014, Masson-Blondelet, Loire, Frankrike
• Swedish variation of tiramisu with sponge cake, apple compote and rum

raisins

• Coffee

Guests with special requests will be taken care of separately

Spring School 2017: HPC for Life Sciences

Thursday

09:30 – 10:30 HPC Simulations with AMBER Tom Cheatham

E3

10:30 – 11:00 Coffee Break 11:00 – 12:00 HPC Simulations with AMBER

E3

12:00 – 13:00 Lunch 13:00 – 14:30 Hands-on AMBER

Red / Orange

14:30 – 15:00 Coffee Break 15:00 – 15:20 Course Feedback Vera Matser

Red / Orange

15:20 – 17:00 Hands-on AMBER

Red / Orange

Food

• Will be served in front of E3 (also in the afternoons!)
• Vegan, gluten free and allergy optimized food will be marked with names
• Vegetarian food will be served along side with the rest of the food
• Thursday no meat will be served since Friday is Long Friday

Logistics

Spring School 2017: HPC for Life Sciences

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Monday - Thursday 12:00 - 18:00

Partnership for Advanced Computing in Europe

PRACE Research Infrastructure

• 24 member countries
• access to computing and data

management resources

• access to services for large-scale

scientific and engineering applications

• at the highest performance level.

Partnership for Advanced Computing in Europe

PRACE Training Activities

PRACE Training Offerings

PRACE-PP

2 Seasonal Schools

PRACE-1IP 4 Seasonal Schools

2 Workshops 1 EU-US Summer School PATCs (conception) Training Portal (establishment)

PRACE-2IP 4 Seasonal Schools

2 Workshops 2 International Summer School 6 PATCs (establishment) Training Portal (content) Training Surveys

PRACE-3IP

3 Seasonal Schools 1 International Summer School 6 PATCs (sustainability, industry) Training Portal (industry)

PRACE-4IP 6 Seasonal Schools

2 International Summer School 6 PATCs (assessment) Training Portal InDiCo On-demand Events MOOCs CodeVault

PRACE-5IP

Seasonal Schools

• Have been running since 2008
• Offering top-quality face-to-face training events
• Organised around / all over Europe
• Topics range from generic intermediate to advanced
• From programming techniques to more specialised topical schools

PRACE Advanced Training Centres (PATCs)

• Six PRACE members sites in Spain, Italy, Finland, UK, Germany and France

are the current PATCs.

• PATC Programme 2016-2017 (until July)

–79 courses, 215 training days

• New courses on forward-looking topics

–New hardware and programming paradigms –Data science

• Collaboration with CoEs on several courses

Training and Events Portal

• www.training.prace-ri.eu
• Single hub for the PRACE

training events, training material and tutorials

• Number of page views

increased by 25% and number of users by 45% since 2014

CodeVault and More

• Repository of Open Source code samples

–https://gitlab.com/PRACE-4IP/CodeVault –Examples and model solutions of common HPC programming tasks

• Possible to utilise in training and as building blocks of

real-world applications

–Anonymous read access

• Best Practice Guides

–http://www.prace-ri.eu/best-practice-guides/

• White Papers

–http://www.prace-ri.eu/white-papers/

New/Upcoming Training Activities

• On-demand events addressing the needs of the CoEs

−Needs for basic, intermediate, and advanced training

• Launch of Massive Open Online Courses (MOOCs)

−First two held in March 2017

• PRACE Training Centres (PTCs)

−Cover basic and advanced needs across Europe

Goal: To inspire the next generation of software engineering, system administrators, and general users of HPC

PRACE Summer of HPC (SoHPC)

PRACE Summer of HPC (SoHPC)

Training week + 2 months internship SoHPC 2015

• 9 Partners/Sites
• 20 (of 80) Students chosen
• Training week in Barcelona

SoHPC 2016

• 10 Partners/sites
• 21 (of 110) students chosen
• Training week in Juelich

SoHPC 2017

• Registration was in January / February
• Training week will be in in Ostrava, (CZ)

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Thank You! Questions? Enjoy the School!