Computational Physics
Lecture 10
Dr. Guy Tel-Zur
Agenda
•
•
•
•
•
•
Quantum Monte Carlo
Star HPC
Parallel Matlab
GPGPU Computing
Hybrid Parallel Computing (MPI + OpenMP)
OpenFoam
‫מנהלה‬
‫• השעור האחרון הוזז‪ .‬במקום יום ה'‪ ,‬ה‪, 6/1/11 -‬‬
‫השיעור יתקיים ביום א'‪ ,‬ה‪17:00- ,2/1/11 -‬‬
‫‪ ,20:00‬בבניין ‪ 90‬חדר ‪.141‬‬
‫• פרויקטי הגמר – כמה תלמידים טרם בחרו נושא או‬
‫לא כתבו אלי מייל עם הנושא‪.‬‬
‫*** דחוף להסדיר את הפרוייקטים***‬
News…
• AMD, 16 cores in 2011
– How can a scientist continue to program in the old
fashioned serial way???? Do you want to utilize
only 1/16 of the power of your computer????
Quantum Monte Carlo
• MHJ Chapter 11
Star-HPC
• http://web.mit.edu/star/hpc/index.html
• StarHPC provides an on-demand computing
cluster configured for parallel programming in
both OpenMP and OpenMPI technologies.
StarHPC uses Amazon's EC2 web service to
completely virtualize the entire parallel
programming experience allowing anyone to
quickly get started learning MPI and OpenMP
programming.
Username: mpiuser
Password: starhpc08
Parallel Matlab
Unfortunately Star-P is dead
MatlabMPI
http://www.ll.mit.edu/mission/isr/matlabmpi/matlabmpi.html#introduction
MatlabMPI Demo
Installed on the vdwarf machines
Add to Matlab path:
vdwarf2.ee.bgu.ac.il> cat startup.m
addpath /usr/local/PP/MatlabMPI/src
addpath /usr/local/PP/MatlabMPI/examples
Addpath ./MatMPI
xbasic
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Basic Matlab MPI script that
% prints out a rank.
%
% To run, start Matlab and type:
%
%
eval( MPI_Run('xbasic',2,{}) );
%
% Or, to run a different machine type:
%
%
eval( MPI_Run('xbasic',2,{'machine1' 'machine2'}) );
%
% Output will be piped into two files:
%
%
MatMPI/xbasic.0.out
%
MatMPI/xbasic.1.out
%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% MatlabMPI
% Dr. Jeremy Kepner
% MIT Lincoln Laboratory
% kepner@ll.mit.edu
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Initialize MPI.
MPI_Init;
% Create communicator.
comm = MPI_COMM_WORLD;
% Modify common directory from default for better
performance.
% comm = MatMPI_Comm_dir(comm,'/tmp');
% Get size and rank.
comm_size = MPI_Comm_size(comm);
my_rank = MPI_Comm_rank(comm);
% Print rank.
disp(['my_rank: ',num2str(my_rank)]);
% Wait momentarily.
pause(2.0);
% Finalize Matlab MPI.
MPI_Finalize;
disp('SUCCESS');
if (my_rank ~= MatMPI_Host_rank(comm))
exit;
end
Demo folder ~/matlab/, watch top at the other machine
GPGPU
An interesting new article
URL: http://www.computer.org/portal/c/document_library/get_file?uuid=2790298b-dbe4-4dc7-b550b030ae2ac7e1&groupId=808735
GPGPU and Matlab
http://www.accelereyes.com
GP-you.org
>> GPUstart
Copyright gp-you.org. GPUmat is distribuited as Freeware.
By using GPUmat, you accept all the terms and conditions
specified in the license.txt file.
Please send any suggestion or bug report to gp-you@gp-you.org.
Starting GPU
- GPUmat version: 0.270
- Required CUDA version: 3.2
There is 1 device supporting CUDA
CUDA Driver Version:
CUDA Runtime Version:
Device 0: "GeForce 310M"
CUDA Capability Major revision number:
CUDA Capability Minor revision number:
Total amount of global memory:
- CUDA compute capability 1.2
...done
- Loading module EXAMPLES_CODEOPT
- Loading module EXAMPLES_NUMERICS
-> numerics12.cubin
- Loading module NUMERICS
-> numerics12.cubin
- Loading module RAND
3.20
3.20
1
2
455475200 bytes
Let’s try this
A
B
C
D
=
=
=
=
rand(100, GPUsingle); % A is on GPU memory
rand(100, GPUsingle); % B is on GPU memory
A+B; % executed on GPU.
fft(C); % executed on GPU
Executed on GPU
A
B
C
D
=
=
=
=
single(rand(100));
double(rand(100));
A+B; % executed on
fft(C); % executed
Executed on CPU
% A is on CPU memory
% B is on CPU memory
CPU.
on CPU
GPGPU Demos
OpenCL demos are here:
C:\Users\telzur\AppData\Local\NVIDIA Corporation\NVIDIA GPU Computing
SDK\OpenCL\bin\Win64\Release
And
C:\Users\telzur\AppData\Local\NVIDIA Corporation\NVIDIA GPU Computing SDK\SDK
Browser
My laptop has Nvidia Geforce 310M with 16 cuda cores
oclParticles.exe
Hybrid MPI + OpenMP Demo
Machine File:
hobbit1
hobbit2
hobbit3
hobbit4
Each hobbit has 8 cores
MPI
mpicc -o mpi_out mpi_test.c -fopenmp
An Idea for a
final project!!!
cd ~/mpi program name: hybridpi.c
OpenMP
MPI is not installed yet on
the hobbits, in the
meanwhile:
vdwarf5
vdwarf6
vdwarf7
vdwarf8
top -u tel-zur -H -d 0.05
H – show threads, d – delay for refresh, u - user
Hybrid MPI+OpenMP continued
OpenFoam