BOOTCAMP_2010_VT
OpenMP and Parallel MATLAB

Lecture Notes:

The slides used during the presentations are available online:

1. http://people.sc.fsu.edu/~jburkardt/presentations/vt_2010_openmp.pdf, Parallel Programming with OpenMP;
2. http://people.sc.fsu.edu/~jburkardt/presentations/vt_2010_matlab.pdf, Parallel Programming with MATLAB;

Documents:

The following are two reference cards, which briefly list the OpenMP directives, the associated clauses, and their meanings.

1. http://people.sc.fsu.edu/~jburkardt/pdf/OpenMP3.0-FortranCard.pdf, OpenMP FORTRAN Reference Card
2. http://people.sc.fsu.edu/~jburkardt/pdf/OpenMP3.0-SummarySpec.pdf, OpenMP C/C++ Reference Card

Tuesday, 10 August, 9:00am-4:00pm

9:00-10:30	OpenMP I
10:30-10:45	Break
10:45-12:00	OpenMP II
12:00-1:00	Lunch
1:00-2:30	Parallel Matlab
2:30-2:45	Break
2:45-4:00	Exercises

Local Programs for the OpenMP Exercises:

If you are using the PC interface on one of the lab machines, then you should go to the All Programs menu in order to use the following:

• jEdit, an editor with which you can view and modify the exercise files and create new ones;
• WinSCP3, a "secure copy" program that uses a visual interface. It allows you to log into a remote machine (such as Ithaca), and then transfer files back and forth by dragging their images.
• PuTTY, includes a secure shell terminal program PuTTY that allows you to log into a remote system, and a secure file transfer program PSFTP that allows you to transfer files back and forth.

If you are using the Macintosh interface on one of the lab machines, then programs you will need include:

• TextEdit, an editor with which you can view and modify the exercise files and create new ones, available in the Applications folder;
• Terminal, which opens a Unix command interface, available in the Applications/Utilities folder;
• ssh which is a secure shell terminal program that allows you to log into a remote system. Invoke it from the Terminal program by

  ssh my_id@ithaca2.arc.vt.edu

• sftp which is a secure file transfer program that allows you to move files to and from a remote system. Invoke it from the Terminal program by

  sftp my_id@ithaca2.arc.vt.edu

Remote Programs for the OpenMP Exercises:

Remember, to compile your program with OpenMP, you use one of the following GNU compilers:

• gcc -fopenmp myprog.c
• g++ -fopenmp myprog.C
• gfortran -fopenmp myprog.f
• gfortran -fopenmp myprog.f90

• icc -openmp -parallel myprog.c
• icpc -openmp -parallel myprog.C
• ifort -openmp -parallel myprog.f
• ifort -openmp -parallel myprog.f90

To set the number of OpenMP threads, use a command like:

export OMP_NUM_THREADS=4

Compilation creates an executable program called a.out. To run it interactively, simply type

./a.out

Interactive execution is OK for small programs and small numbers of processors. However, regular users put their jobs into shell scripts and submit them. For the exercises below, when a shell script is recommended, an example file is supplied. However, to run the shell script, you will need to replace the account information with the account you have been assigned. This is the line that reads

#PBS -A hpcb0001

The OpenMP Exercises:

Each of these exercises studies a particular program, and asks you to carry out several steps, to study a particular aspect of OpenMP programming. The exercises are listed in order of difficulty.

1. The Hello Exercise
2. The Quadrature Exercise
3. The Heated Plate Exercise
4. The Schedule Exercise

OpenMP Exercise Solutions:

If you get stuck on an exercise, or want to compare your solution with mine, the solutions are discussed here. I did NOT run my solutions on Ithaca, so my timings and your timings will probably differ.

1. Solutions for The Hello Exercise
2. Solutions for The Quadrature Exercise
3. Solutions for The Heated Plate Exercise
4. Solutions for The Schedule Exercise

Parallel MATLAB Exercises:

Using parallel MATLAB on the Ithaca cluster requires some initial setup that we can't easily do in the lab. However, you can certainly try out parallel MATLAB on your own machine, if you have a multicore machine and are using Virginia Tech's network-licensed version of MATLAB.

The examples discussed in class are available online, and include:

• QUAD_PARFOR
• MD_PARFOR
• PRIME_PARFOR
• ODE_SWEEP_PARFOR
• QUAD_SPMD
• DIJKSTRA_SPMD
• CONTRAST_SPMD
• CONTRAST2_SPMD

You can go up one level to the main web page.