NHR Graduate School Course Week 2022
Topic outline
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This course week, organized by the NHR Alliance and the NHR centers at Berlin, Darmstadt, and Erlangen, aims to convey essential HPC software development skills to the PhD students of the NHR Graduate School. Date: June 13-17, 2022
Place: Seminarraum (room number 2006) at Zuse Institute Berlin (ZIB), Takustr. 7, 14195 Berlin (View on map)
The lectures are broadcasted within a zoom session. Each day the broadcast opens some minutes before the lecture starts. All participants receive the session data in separated email.
This Moodle page provides all necessary information to the attendees, including lecture slides, example code, and miscellaneous material.
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15:00-17:00 welcome event
location: Zuse-Institute Berlin (ZIB)- foyer or seminar room
- short speech Prof. Christof Schütte (president of ZIB and chairman of the NHR association board)
- the fellows introduce themselves and their research plans (10 min. each)
from 17:00 Get-togetherlocation: ZIB (foyer and exterior)
There will be beverages, pretzels and other small snacks.
- short speech Prof. Christof Schütte (president of ZIB and chairman of the NHR association board)
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Agenda:
Lectures on Day 2 are about node-level computer architecture and performance engineering.
Lecturers: Dr. G. Hager, Dr. M Wittmann09:00-09:30 General intro, computer architecture
09:30-10:00 Affinity and performance tools
10:00-10:30 Roofline model: introduction
10:30-10:45 Break
10:45-11:30 Roofline model: case studies
11:30-12:15 Special topics (NUMA, SIMD, SMT)
12:15-13:15 Lunch
13:15-16:00 Guided Hands-OnIn order to work with the exercises on the cluster at ZIB, you need to have an SSH client installed on your laptop (for Windows we recommend MobaXterm Home Edition). We assume that you are familiar with working on the command line in a Linux environment.This day provides a condensed version of our popular three-day tutorial "Node-Level Performance Engineering" (link points to most recent version from December 2021).16:30 - 18:00 guided Dahlem-tour
theme: Im Götterhimmel der Wissenschaft - The realm of gods of science / Nobel Prize winners
language: English
guide: Ms Schmidt-Graute
start and end: Harnack-Haus, Ihnestr. 16-20. It´s a 15-20 minute walk from ZIB.participants: fellows, Ms Diederich.
Additional participants are welcome.------------------------------------------------------
Please find below lecture slides and exercises:
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Lecturers: Dr.-Ing. Tomislav Maric, Dr. Alexander Hück, Moritz Schwarzmeier, M.Sc.
09:00-10:30 Introduction to Continuous Integration for Research Software
Links:
10:30-10:45 Break
10:45-11:00 Hands-on: repository preparation
11:00-12:15 Hands-on: Docker images
12:15-13:15 Lunch
13:15-14:30 Hands-on: Continuous Integration pipelines
14:30-14:40 Break
14:40-16:00 Teamwork: enabling CI for the OpenFOAM HPC example from June 14.- Slides: "Continuous" Integration of Scientific Software (in Computational Science and Engineering)
- Minimal example repository: https://gitlab.com/tmaric/minimal-cse-ci-examples
- NHR OpenFOAM Conjugate Gradient example repository: https://gitlab.com/tmaric/nhr-rse-lecture
Homework:
- Basic git version control commands (add, commit, push, pull, checkout, merge)
- On your laptops, install Docker and sudo rights (or Podman), git, python (pandas, matplotlib), Jupyter, a C++ compiler (gcc), CMake.
- Register an account at gitlab.com and https://hub.docker.com/
from 16:30 Free time at your disposal
- Slides: "Continuous" Integration of Scientific Software (in Computational Science and Engineering)
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Lecturer: PD Dr. Marcus Weber, Dominik Ernst, Dr. Christian Tuma
09:00-10:30 Introduction to the methodology of of combining molecular simulation and AI
10:30-10:45 Break
10:45-12:00 Introduction to performance analysis on GPUs
12:00-12:15 Introduction of the ML benchmark
12:15-13:15 Lunch
13:15-14:30 Hands-on Session I: Performance analysis on a CPU node
14:30-14:40 Break
14:40-16:00 Hands-on Session II: Performance analysis on a GPU node18:40 - 21:10 Evening cruise on the river Spree
- start and end point Friedrichstrasse/Reichstagufer, next to the station "Friedrichstrasse" (20 minutes with S-Bahn S1 from your hotel/Rathaus Steglitz)
- WE MEET at 18:20 AT THE POINT OF DEPARTURE - Stern und Kreisschiffahrt GmbH
- possibility to buy food and beverages on board
- accompanied by Mr Hück, Mr Schwarzmeier, Yvonne, Britta
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Lecturer: Nora Benariba & Dennis Kirschbaum
09:00 - 11:30 Workshop
11:30 - 12:00 Break
12:00 - 14:00 Workshop