School on numerical analysis and algorithms at the exascale: Classical N-body methods for complex systems on massively parallel architectures: CoS-1

The School on numerical analysis and algorithms at the exascale: Classical N-body methods for complex systems on massively parallel architectures is the third out of four training workshops organised by HPC-LEAP for the students enrolled on the programme. Successful completion of any one of the programmes will be worth 5 ECTS accreditation units.

 

Venue: RWTH Aachen

Dates: 5th - 22nd April 2016

Credit: 5 ECTS

Scientists-in-charge: Paolo Carloni

 

Description:

This school is the second part of CoS-1 and will provide an introduction to N-body methods such as molecular dynamics and Monte Carlo and will discuss different parallelisation strategies suited to these approaches. The lectures will focus on methods appropriate for both short- and long-range interactions and conclude with a review of spectral methods. Students will be required to implement a simple molecular dynamics code and test different parallelisation algorithms as well as analysis tools to understand the output of their simulations. The course will conclude with a discussion of hybrid methodologies applied to biological systems of pharmacological relevance.

 
Topic Lecture hours Laboratory hours
Introduction to statistical physics 5 3
Statistical methods and sampling 5 3
Modelling complex systems with short-range interactions 4 2  
Modelling complex systems with long-range interactions 4 3
Spectral methods for complex systems 4 2
  26 15

 

Components:

• Introduction to statistical physics: a review of the essentials of statistical physics will be presented, with applications to biological systems.

• Statistical methods and sampling: the essentials of the Monte Carlo method and the statistical techniques for understanding the output of these simulation will be described.

• Modelling short-range interactions: Efficient simulation of the molecular dynamics induced by short-ranged interactions will be discussed. Software techniques to maintain and update lists of nearby particles will be presented allowing students to develop code to model examples of these systems.

• Modelling long-range interactions: Techniques for studying the molecular dynamics of N- body systems with long-ranged interactions will be presented. The focus will be on resummation techniques based on the Ewald sum.

• Spectral methods for complex systems: Techniques for solving differential equations efficiently by analysing the system’s fourier modes will be introducted. Students will develop software to study examples in laboratory sessions.

• Hybrid techniques for biological systems: The School will conclude by describing techniqes for solving biological systems where a broad range of dynamical time-scales are important. Effectively addressing these problems requires a hybrid approach, dealing with each of the distinct dynamics separately. The implementation of these ideas will be presented in this component.

 

 Analytical Schedule

Tuesday 5th of April

Time Activity

08:30 - 09:00

Registration

09:00 - 10:00

T. Lippert - Overview of the HPC Applications

10:00 - 10:30

Coffee Break

10:30 - 12:30 G. Gompper - Introduction to Statistical Physics I
12:30 - 14:30 Lunch Break
14:30 - 16:30 G. Gompper - Introduction to Statistical Physics II

 

Wednesday 6th of April

Time Activity

09:00 - 10:30

G. Gompper - Phase Transitions and Critical Phenomena

10:30 - 11:00

Coffee Break

11:00 - 12:30 G. Gompper - Soft Matter Physics
12:30 - 14:30 Lunch Break
14:30 - 16:30 G. Gompper - Q&A Session

 

Thursday 7th of April

Time Activity

09:00 - 10:30

C. Dellago - Monte Carlo Simulation

10:30 - 11:00

Coffee Break

11:00 - 12:30 C. Dellago - Molecular Dynamics Simulation
12:30 - 14:30 Lunch Break
14:30 - 16:30 C. Dellago & C. Moritz - Tutorial/Hands-on

 

Friday 8th of April

Time Activity

09:00 - 10:30

C. Dellago - MC and MD simulations in various ensembles

10:30 - 11:00

Coffee Break

11:00 - 12:30 C. Dellago - Free Energy Calculations
12:30 - 14:30 Lunch Break
14:30 - 16:30 C. Dellago & C. Moritz - Tutorial/Hands-on

 

Monday 11th of April

Time Activity

09:00 - 10:30

M. Parrinello - Rare events

10:30 - 11:00

Coffee Break

11:00 - 12:30 M. Abraham - Short range interactions I
12:30 - 14:30 Lunch Break
14:30 - 16:30 M. Abraham - Short range interactions II

 

Tuesday 12th of April

Time Activity

09:00 - 13:00

M. Parrinello - Enhanced sampling

10:30 - 11:00

Coffee Break

11:00 - 12:30 M. Abraham - Short range interactions III
12:30 - 14:30 Lunch Break
14:30 - 16:30 M. Abraham - Tutorial/Hands-on

 

Wednesday 13th of April

Day Off

 

Thursday 14th of April

Time Activity

09:00 - 10:30

G. Sutmann - Fast methods for electrostatics I

10:30 - 11:00

Coffee Break

11:00 - 12:30 G. Sutmann - Fast methods for electrostatics II
12:30 - 14:30 Lunch Break
14:30 - 16:30 M. Abraham - Projects assignments

 

Friday 15th of April

Time Activity

09:00 - 10:30

G. Sutmann - Fast methods for electrostatics III

10:30 - 11:00

Coffee Break

11:00 - 12:30 G. Sutmann - Fast methods for electrostatics IV
12:30 - 14:30 Lunch Break
14:30 - 16:30 M. Abraham - Project session

 

Monday 18th of April

Time Activity

09:00 - 10:30

M. Tuckerman - Liouville operators and nuerical integration algorithms in molecular dynamics

10:30 - 11:00

Coffee Break

11:00 - 12:30 M. Tuckerman - Multiple time-step integrators: Advantages and limitations due to resonances
12:30 - 14:30 Lunch Break
14:30 - 16:30 M. Tuckerman - Q&A Session

 

Tuesday 19th of April

Time Activity

09:00 - 10:30

M. Tuckerman - Resonance-free multiple time-steps integrators I: The isokinetic ensemble

10:30 - 11:00

Coffee Break

11:00 - 12:30 M. Tuckerman - Resonance-free multiple time-steps integrators II: Colored-noise methods
12:30 - 14:30 Lunch Break
14:30 - 16:30 Special Session - M. Modesto - Multiscale simulation of DNA

 

Wednesday 20th of April

Day Off

 

Wednesday 21st of April

Day Off

 

Tuesday 19th of April

Time Activity

09:00 - 10:30

Exam Session I

10:30 - 11:00

Coffee Break

11:00 - 12:30 Exam Session II

 

Assessment:

 Students will be assessed by a method common to all HPC-LEAP workshops. Over the course of each School, students will be required to develop software to solve a small number of substantial numerical problems. At the end of the three weeks, students will be required to submit their software, along with a report detailing the design, algorithm, testing methodology, results and performance of their projects. They will be expected then to give a 15 minute presentation to the examiners and their classmates, summarising their findings.

 

Additional Information:

Registration Information will follow.

HPC-LEAP in a nutshell

Progress in computers and algorithms in the last years has made numerical simulation and modelling a key research methodology in both academia and industry, which in turn drives exascale computing in order to maintain excellence in research and innovation. A disruptive evolution in computer technologies is required for attaining exascale performances in the coming years bringing challenges that urgently need to be addressed across science and engineering fields. Therefore, new interdisciplinary strategies are required in order to educate the next generation of scientists to address such challenges enabling them to be at the forefront of their respective research fields. Instead of the traditional domain-specific training, integrated approaches are needed that can be best implemented by collaborative networks of universities, research institutes and industrial partners. HPC-LEAP is a highly interdisciplinary joint doctorate program realized by bringing together world-leading experts in applied mathematics, high performance computing technologies, particle and nuclear physics, fluid dynamics and life sciences to appropriately train researchers in Europe to exploit high performance computing, advance science and promote innovation. Students will be trained in mathematical and computational concepts underpinning current and future numerical simulations in turbulent flows, computational biology and lattice Quantum Chromodynamics. The research projects are designed to enhance collaborations and interactions across these disciplines, integrating non-academic partners, and to develop methodologies that efficiently use large-scale numerical simulations on future high performance computer systems. Students who complete this training program will be versatile to undertake highly interdisciplinary projects, well positioned to embark on a successful career in academia or the industrial sector.

Consortium Institutions

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