Computational Physics

Dr. Guy Tel-Zur2011A

Sunny Yellow Flower. Picture by Sharee Basinger, publicdomainpictures.net

About me...

1988 1991 1996 1996+

2001+ 2003-2004

2005+

Survey• Please answer the survey at:http://spreadsheets.google.com/gform?key=t3TcOcxehKAzYyhm6WukzeA#invite

The Course Vision

“The crucial need for today's students and readers is to move forward from the

older "formula-based" emphasis toward a solution-based course. Solving problems

is the heart of modern engineering mathematics and scientific computing. “ – Gilbert Strang – Computational Science and Engineering, page 7, SIAM (2007).

What is Computational Physics

Reference: Resource Letter CP-2: Computational PhysicsRubin H. Landau, Am. J. Phys. 76 4&5, April/May 2008

A broader view – Computational Science

X

MathCS

Computational X

X=Physics, Biology, Chemistry, …

Reference: Resource Letter CP-2: Computational PhysicsRubin H. Landau, Am. J. Phys. 76 4&5, April/May 2008

3 Pillars

TheoryComputational

Physics Experiment

4 Pillars?

TheoryComputational

Physics Data Mining Experiment

2 Computational Pillars

See next slide, from Communications of the ACM, http://cacm.acm.org/magazines/2010/9/98038-science-has-only-two-legs/fulltext

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NVIDIA CEO at the GTC2010, Sept. 2010

The 3rd Pillar of Science is HPC !!!

HPC = High – Performance Computing

What is Computational Physics?

Computational Physics combines physics, computer science and applied mathematics in order to provide scientific solutions to realistic and often complex problems. Areas of application include the nature of elementary particles, the study and design of materials, the study of complex structures (like proteins) in biological physics, environmental modeling, and medical imaging. A computational physicist understands not only the workings of computers and the relevant science and mathematics, but also how computer algorithms and simulations connect the two.

Source: http://www.sru.edu/academics/colleges/ches/physics/Pages/ComputationalPhysics%28BS%29.aspx

Computational Physics is an active field

Journals and Magazines…

APS, EPS, IPS…

No CP division

Scientific Papers On-line at arXiv.org

http://arxiv.org/list/physics.comp-ph/recent

Career Opportunities for Computational Physicists

• A graduate degree in physics in areas such as biophysics, condensed matter physics, particle physics, astrophysics to name a few.

• A career in High-performance and scientific computing, in the energy and aerospace sectors, with chemical and pharmaceutical companies, with environmental management agencies.

• Employment in firms that develop scientific software, as well as computer games.

• A research career in an academic, industrial, or national laboratory• A teaching career in physics • A job in Wall Street. Even Wall Street employers are interested in people

with a background in computational physics.

Source: http://www.sru.edu/academics/colleges/ches/physics/Pages/ComputationalPhysics%28BS%29.aspx

Physics Engine in Computer Games

Course Building Blocks

Tools Methods

Case Studies

Practice

Parallel and distributed computing

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Scheme on previous slide refers to at least 2 quarters (20 weeks) course

Scientific Discovery through Advanced Computing (SciDAC)

DOE Office of Sciencehttp://www.scidac.gov/

When will be such a national initiative in Israel…?

Source: http://www.princeton.edu/as/LNL/presentations/spring2010/LnL031010TangFusionSimulation.pdf

What V&V Means?

The problem of quantifying uncertainty:Validation "Solving the right equations"Verification "Solving the equations right"

Tools

• Programming Languages– C/C++– Fortran– Python

• Numerical Tools– CERN paw/root/Matlab/Octave/Scilab

• Visualization– VTK - grace - Paraview -VisIt -Mayavi– Vpython - GNUplot -DX

• Workflow– Kepler(?)

+OpenMP +MPI +Condor

Full Scientific Research Study – “Workflow”

Raw Data Number Crunching/Data

AnalysisReduced Data

Visualization

“Batch”

“Data Base”Specific Format ,

e.g. NetCDF

Interactive mode

Prototyping (Matlab)

Parallelism

AMD – 6 cores microprocessor

My Goal: Introducing Parallelism whenever possible is going to be my own “twist” to the course

Power7: IBM’s Next-Generation Server Processor with 8 cores.The chip is 567 mm2 and contains 1.2 billion transistorsRecommended Reading: http://www.computer.org/cms/Computer.org/ComputingNow/homepage/2010/0710/W_MI_Power7.pdf

NVIDIA CEO at GTC2010GPGPU increase presence at the Top500 Supercomputers

Serial vs. Parallel - demoExecute: C:\FlexPDE5student\samples_student\steady_state\fluids\swirl

Low cpu utilization Uses only one core

Some highlights of the course – Next slides

We will have:

1. Standard “Classical” text PLUS2. Several “Mini-Courses” – My add-ons

1. Parallel Computing – MPI, OpenMP

2. Batch/Grid Computing – Condor3. Visualization (next slide)4. Cluster Computing

Parallel Visualization

A visit to the parallel visualization lab at the Mechanical Engineering building

How to build a parallel computing cluster – hands on demo

A report from SC10The Latest Innovations

Course Web Sitehttp://physics.bgu.ac.il/~gtelzur/teaching/comphy/2011A/

וציונים הקורס חובות

כל • הגשת חובת - 4קיימת ב ) יעשה התעוד הבית תרגיליLaTeX - כ .PDFויוגש " למרצה ל הדוא באמצעות

סוף ) • עד ציון עליהם ויינתן תרגילים יבדקו מדגמי באופןמכל אחת עבודה הפחות לכל תיבדק הסמסטר

: משקל( – 20%סטודנט• - ידי – על מאמר בפורמט יסוכם שיעור כל השיעור סיכומי

- . - ב יעשה הסיכום ציון כך על ויינתן אחר . LaTeXסטודנטהסטודנטים)*( - 10%משקל: במספר תלוי סופי לא

• : . חלקים – שני לפרויקט גמר פרויקטי הסמסטר בסוףמסכם ודוח .70%מצגת בהמשך– נוספים פרטים ראו

בקורס הצפוי העומס לגבי נשאלתי

Keys to success Right motivation, working diligently, effectively and efficiently is the key to success.If you work regularly and allocate enough time each day to practice and completethe assignments on time and keep up with the course, you will get the most out ofthe course both intellectually and grade-wise.You should invest about 6-9 hours per week outside of class to succeed in thiscourse. This is consistent with university guidelines (i.e. two to three hours ofoutside preparation time for every credit hour). Students with little or noprogramming experience (or those who love the subject and wish to do extremelywell in it) may want to put in more hours. Please, let me know as soon as possibleif you have difficulties and may need extra help.You are recommended to start you assignments well before the last night whenyour assignments are due. It is a general experience that a computer programusually does not work correctly (if works at all) at the beginning. A search for aproblem, or a computer bug, may take more time that you expect.

The following is from: Old Dominion University Physics 420/520 Spring 2010

: נוספות - הערות " המרצה ידי על פ בע

הבית תרגילי• Approximately 4 sets of homework problems will be assigned. • The students will write computer programs based on computational algorithms discussed in

class. • These assignments constitute a very important part of the course, since the thinking involved

in scientific programming can only be developed through practical work. • The assignments must be returned by their stated due dates, unless an extension is granted

by the instructor. For late return of assignments, a 10% point deduction will be applied for each late day.

• Programs should be written in Fortran 90/95 or in C/C++ or in Python.• The programs as well as a short report discussing the results should be handed in to the

instructor by the stated due date. The solution programs should be sent as an attachment in an e-mail to the address gtelzur@bgu.ac.il. The report (hardcopy required) should be handed to the instructor in class before the deadline.

• Every student is expected to work independently on the assignments. However, discussions with fellow students are allowed, indeed encouraged, as long as they are kept on a general level and do not amount to direct copying of ideas or programming solutions.

• Although discussions and some degree of cooperation between students is allowed, The material turned in must be independently written.

Inspired from: http://physics.bu.edu/~py502/syllabus.pdf

הגמר פרויקטי

•. הקורס על בציון הארי החלק את מהווים•. רבה חשיבות להם מייחסהפרוייקט • נושא את הכיתה בפני יציג סטודנט כל

שלומטעמי • נושאים רשימת בהמשך אפרסם אני• . משלכם נושאים להציע מוזמנים אתם• : הבא בקישור רעיונות לקבל אפשר

:// . .http physics usc edu/~/516/ .shaas projects html

הגמר פרויקטי

• . לתאר – יש הכיתה בפני יוצג הפרויקט מצגת , והדרך החישובי האתגר העבודה נושא את . נדרשת לא הזה בשלב לאתגר מענה למתן

משקל – מחשב תכנית מהציון 10%כתיבתהסופי

• : לרבות הפרויקט כל את יסכם מסכם דוח . יצורף עבורו שתכתב המחשב ותכנית המצגתהעבודה ) – מבנה פרוט ומסקנות מלא תיעוד

: משקל(. הסופי 60%בהמשך מהציון

הגמר פרויקטי של המצגות

נושא • יציג סטודנט כלPPT, PDF, HTMLפורמט •הקורס • של האחרונים השיעורים בשני תתקיימנה המצגות•.) / ( / שקפים: דיבור אנגלית עברית שפהעד • המרצה אל המצגת את המייל באמצעות לשלוח יש

למחשב תועלה שהמצגת כך השיעור שלפני הלילה חצותמהתקנים התקנות של זמן בזבוז יהיה ולא המרצה

השיעור בזמן למקרן מחשבים חיבור או חיצוניים• : לכתובת לשלוח יש המצגות gtelzur@gmail.comאת

הגמר פרויקט של המסכם הדוח

הקורס • לאתר בהמשך תועלנה העבודות כל או חלק• , ,) ,. . , ( : תמצית כותרת ז ת שם שער העבודה מבנה

, , , סימוכין, רשימת מסקנות העבודה גוף מבואנספחים.

• , , להמחשת טבלאות תרשימים גראפים לכלול מומלץהתוצאות

פורמט • בהמשך – LaTeXמומלץ ראו• : לכתובת בלבד אלקטרונית הגשה

gtelzur@gmail.com

More tips about the Final Projects

• Consult these links:1. http://www.odu.edu/~

agodunov/teaching/phys420_10/organize_comp_proj.pdf

2. http://www.odu.edu/~agodunov/teaching/phys420_10/Sample_Project.pdf

3. http://www.odu.edu/~agodunov/teaching/notes/Intr02_projects.pdf

Programming Languages

• C/C++• Fortran 90/95• Python• More discussion on that in the next

presentation!

המחשה - Visualization Toolsכלי

• Gnuplot – included in Python(x,y)• Xmgrace – 2D, Linux only• vPython – included in Python(x,y)• Qtiplot – Free for Linux OS (Origin clone)

http://soft.proindependent.com/qtiplot.html

• Excel• CERN’s PAW/Root (if time will permit)

LaTeX

• Learn LaTex, here are a few links to tutorials:– http://

www.cs.cornell.edu/Info/Misc/LaTeX-Tutorial/LaTeX-Home.html

– http://www.pages.drexel.edu/~pyo22/students/latexRelated/latexTutorial.html

– Getting Started With LaTex: http://www.maths.tcd.ie/~dwilkins/LaTeXPrimer/GSWLaTeX.pdf

LaTeX Recommended Environment

(install it on your laptops)• MikTeX: http://www.miktex.org/• LaTeX Editor: Led -http://

www.latexeditor.org/index.html• Optional: LyX - http://www.lyx.org/(less recommended)• Online check your LaTeX equations with Texify:

http://www.texify.com/links.php

Linux Background

Check: http://www.physics.udel.edu/~bnikolic/teaching/phys660/RUTE/rute/index.html

? עוד מה

•! יפות ולהדגמות למשחקים זמן למצוא נשתדל• Open Source Physics -

http://www.compadre.org/osp/• ? רלוונטי קישור מעניין במאמר נתקלתם

זה – מידע תשלחו אם לכם אודה באינטרנטאלי

קשר על שמירה

• : במייל אלי לפנות יכולים אתם.gtelzur@gmail com

הקורס • של האינטרנט אתר אחרי לעקוב נאשוטף באופן מתעדכן אשר

•Mailing lists – ?בגוגל להקים אפשר•?... בפייסבוק קבוצה

Let’s get started!