Computational Physics

Dr. Guy Tel-Zur

Version 09-12-2010.12:40

Agenda• Administration• MHJ Chapter 10: MC methods in Statistical Physics• More on VisIt:

– The Silo file format– A demo program– Creating a movie

• More HPC stuff• DLA• Demo: AWS – HPC Instance for Parallel Computing and Cellular

Automata / NKS demo on the cloud

• Home assignment #3

Final Projects

• Please hurry to choose a topic

Visualization: The Silo file format

• References:– Download:

https://wci.llnl.gov/codes/silo/release_notes.html(BSD License)– http://www.e-science.le.ac.uk/format/silo.shtml– http://www.e-science.le.ac.uk/format/silocode.sht

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Visualization: A demo program

• Use VirtualBox Ubuntu Install Silo and VisIt

• Installation was not smooth on Ubuntu 10.4, I had to install libstdc++5 manually (an older version)

• Let’s look at “wave.c”– Open DevC++ with: C:\Users\telzur\Documents\My Talks\MIL_OSS\

silo\silo-4.8-bsd\tests\wave.c

Silo

• Discuss in class the wave.c program• Run the program on the Virtual Machine• Make plot using VisIt• Make a mpeg movie!

wave.c silo file

Mini Course: Performance Tuning

• Intel Parallel Studio (commercial)• Vampir (commercial, only a free viewer)• TAU – Paraprof (free)• Scalasca (free)• Marmot (free, not in this course, perhaps in

CP2012A ?)

TAU –pprof, paraprofcd to: workshop-point/ring

HPC – Performance Optimization Cycle

Source: Scalasca user guide

Scalasca

Step1: scalasca –instrument mpicc –o jacobi ./main.c ./jacobi.c

Step 2: scalasca –analyze mpirun –np 4 ./jacobi

Step 3: scalasca –examine epick_<title>

Users guide: http://www.fz-juelich.de/jsc/datapool/scalasca/UserGuide.pdf

BTW: Virtual Box file sharing: as root:mount –t vboxsf guytmp ./guytmp

HPC Cloud Computing Demo

Goal:Install Condor on the HPC cloud machine

Run many Cellular Automata jobs

Check graphical output

How to install Condor on Debian:http://www.cs.wisc.edu/condor/debian/

AWS - CloudWatch

8 cores !

NKS

Reference: http://telzur.blogspot.com/2008/01/mysteries-of-cellular-automata.html