Revision as of 02:34, 2 March 2012

This wiki page is about part II of SciNet's Scientific Computing course.
Information on part I can be found on the page Scientific Software Development Course
Information about part II can be found on the page Numerical Tools for Physical Scientists (course)

Syllabus

The third part of SciNet's for-credit Scientific Computing course (Phys 2109 modular course credit / Ast 3100 mini-course credit) will start on February 10 2012.

Whereas the first part of the course focused on the basics of best practice for writing maintainable, modular scientific programs, and the second part focused on common techniques and algorithms, such as floating point computations, validation+verification, visualization, ODEs, monte Carlo, linear algebra and fast fourier transforms, the third part focusses on high performance computing and parallel programming.

At the end of minicourse III, "High Performance Scientific Computing", students will leave with a basic understanding of distributed and shared memory parallel programming paradigms, and will be able apply these in their own code.

The course will require 4-6 hours each week spent on reading and homework.

Required Software

Each lecture will have a hands-on component; students are strongly encouraged to bring laptops. (Contact us if this will be a problem). Windows, Mac, or Linux laptops are all fine, but some software will have to be installed *before* the first lecture:

On windows laptops only, Cygwin (http://www.cygwin.com/) will have to be installed ; ensure that development tools (gcc/g++/gfortran, gdb), git, the X environment (Xorg), and ssh are installed.

Hands-on parts will be done on SciNet's GPC cluster. For those who don't have a SciNet account yet, the instructions can be found at https://wiki.scinet.utoronto.ca/wiki/index.php/Essentials#Accounts .

Course outline

The classes will cover the material as follows; homework will be due by email at Thursday noon on the day before the following class.

Lecture 9: Introduction to Parallel Programming and OpenMP

Lecture 10: MPI- part 1

Lecture 11: OpenMP - part 2

Lecture 12: MPI - part 2

Evaluation will be based entirely on the four home works, with equal weighting given to each.

Location and Dates

The location is the same as for part II, i.e.

Fridays 10:00am - 12:00am

Feb 10, 17, Mar 2, 9.

Bahen Centre for Information Technology

40 St. George Street

Room 1230

Office Hours

The instructors will have office hours on Monday and Wednesday afternoons, 3pm-4pm, starting the week of the first class.

Location: SciNet offices at 256 McCaul, 2nd Floor.

Mon, Feb 13, 3pm-4pm
Wed, Feb 15, 3pm-4pm
Mon, Feb 27, 3pm-4pm
Wed, Feb 29, 3pm-4pm
Mon, Mar 5, 3pm-4pm
Wed, Mar 7, 3pm-4pm
Mon, Mar 12, 3pm-4pm
Wed, Mar 14, 3pm-4pm

Materials from Lectures

Homeworks

Homework following lecture 1

Make sure you've got a SciNet account!
Read the SciNet User Tutorial (mostly as it pertains to the GPC, but do not skip the data management section).
Read the GPC Quickstart.
Get the first set of code as follows
- git clone /scinet/course/sc3/hw1
- cd hw1
- source setup
- make
- make testrun
This set contains the serial daxpy.
Make sure it compiles and runs on the GPC.
Create the openmp version as just discussed.
Run this version for all values of OMP_NUM_THREADS from 1 to 32 on a single node, using a batch script. (Make sure to time the duration of these runs.)
Submit git log, makefile, code, job script(s), and plots of the speedup and efficiency as a function of P.

Due: Thursday Feb 16 at noon. Email the files to rzon@scinet.utoronto.ca and ljdursi@scinet.utoronto.ca.

Homework following Lecture 2

Get the second set of code as follows
- git clone /scinet/course/sc3/hw2
- cd hw2
- source setup
- make
This set contains the serial version of a 1-d thermal diffusion code
Introduce MPI into this code:
- add standard MPI calls: init, ﬁnalize, comm_size, comm_rank
- Figure out how many points PE is responsible for (locpoints~totpoints/size)
- All totpoints -> locpoints
- adjust xleft,xright
- Figure out neighbors
- Start at 1, but end at locpoints
- At end of step, exchange guardcells; use sendrecv (once to send data rightwards and receive from the left, and once to send data leftwards and receive from the right)
- Get total error (allreduce)

Due: Thursday March 1 at noon. Email the files to rzon@scinet.utoronto.ca and ljdursi@scinet.utoronto.ca.

Answers

Links

Git

Git cheat sheet from Git Tower: http://www.git-tower.com/files/cheatsheet/Git_Cheat_Sheet_grey.pdf

Python

Enthought python distribution: http://www.enthought.com/products/edudownload.php
Intro to python from software carpentry: http://software-carpentry.org/4_0/python
Tutorial on matplotlib: http://conference.scipy.org/scipy2011/tutorials.php#jonathan

Top500

TOP500 Supercomputing Sites: http://top500.org

OpenMP

OpenMP (open multi-processing) application programming interface for shared memory programming: http://openmp.org

SciNet

Anything on this wiki, really, but specifically:

@@ Line 68: / Line 68: @@
 * [[Media:lecture9.pdf | Slides of lecture 1]]
 * [[Media:SC3-MPI.pdf | Slides of lecture 2]]
+* [[Media:SCLecture11.pdf | Slides of lecture 3]]
 =Homeworks=

Difference between revisions of "High Performance Scientific Computing"