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.escience.le.ac.uk/format/silocode.shtml
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
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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
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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, paraprof
cd 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