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Python, Part 2

The document discusses using Python for scientific programming. It covers MPI programming in Python, NumPy arrays, plotting in Python using bar charts and pie charts, and image processing. It provides code examples for computing Pi in parallel using MPI4Py, constructing and indexing NumPy arrays, and generating a bar chart from CSV data using Matplotlib.

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Gabe
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4 views

Python, Part 2

The document discusses using Python for scientific programming. It covers MPI programming in Python, NumPy arrays, plotting in Python using bar charts and pie charts, and image processing. It provides code examples for computing Pi in parallel using MPI4Py, constructing and indexing NumPy arrays, and generating a bar chart from CSV data using Matplotlib.

Uploaded by

Gabe
Copyright
© © All Rights Reserved
We take content rights seriously. If you suspect this is your content, claim it here.
Available Formats
Download as PDF, TXT or read online on Scribd
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Scientific Programming with

Python: part II
Advanced Research Computing
Outline
• MPI programming in Python
• NumPy (SciPy) arrays
• Plotting in Python:
– bar-charts, pie-charts, mesh-grids
• Plotting and image processing in Python
– image representation, conversion to array and
processing (interpolation)

Advanced Research Computing


2
About me
• Gabriel Mateescu
• I work in the Advanced Research Computing
Group
• Email: gabriel@vt.edu

Advanced Research Computing


3
USING MPI IN PYTHON

Advanced Research Computing 4


MPI multiprocessing
• MPI is a widely used API for inter-process
communication. It supports
– general send, receive, broadcast operations
– HPC-specific operations: all-to-all, reduce, all-
reduce, scatter, gather
– synchronization: barrier and left to right of
expressions
• There are many implementations of MPI
– I prefer Open MPI

Advanced Research Computing


MPI4Py
• MPI4Py is one of the Python modules for
providing access to MPI functions in Python
• The MPI4Py functions (send, receive reduce)
delegate the work to the underlying MPI
implementation
• An MPI4Py program is launched like any MPI
program
mpirun –np 4 python myprogram.py

Advanced Research Computing


Compute Pi in MPI4Py
from openmpi.mpi4py import MPI
import random
num_samples = 10e6
comm = MPI.COMM_WORLD
mpisize = comm.Get_size(); rank = comm.Get_rank()
nsamples = int (num_samples/mpisize)
random.seed(rank); inside = 0
for i in range(nsamples):
x = random.random(); y = random.random()
if (x*x) + (y*y) < 1: inside += 1
inside = comm.reduce(inside, op=MPI.SUM, root=0)
if rank == 0:
pi = (4.0 * inside)/num_samples; print ' pi =', pi
Advanced Research Computing
NUMPY ARRAYS

Advanced Research Computing 8


NumPy Arrays
• NumPy arrays, also called N-d arrays are
strongly typed, homogeneous arrays
– default type is float
• N-d arrays available in NumPy and SciPy
(which used the NumPy arrays)
• NumPy also defines operations on N-d arrays
• N-d arrays can be passed to Python functions
that expect a list

Advanced Research Computing


Anatomy of Nd-arrays (1)

Taken from
http://pages.physics.cornell.edu/~myers/teaching/ComputationalMethods/
python/arrays.html
Advanced Research Computing
Anatomy of Nd-arrays (2)

Taken from
http://pages.physics.cornell.edu/~myers/teaching/ComputationalMethods/
python/arrays.html
Advanced Research Computing
Constructing Arrays (1)

a = np.array([[1,2,3],[4,5,6]])
b = np.array([i*i for i in range(10) if i%2==1])
c = np.zeros(100) # array of float zeros
d = np.zeros((2,4), int) # 2x4array of int zeros
e = np.ones(10, int) # array of int ones
f = np.ones((5,5))
i = np.eye(10,10, int)

Advanced Research Computing


Constructing Arrays (2)
r = np.arange(0, 10, 2) # step =2

l = np.linspace(-1.0, 1.0, 20) # num points = 20

# 10x10 array of floats uniformly on [0., 1.)


r = np.random.random((10,10))

# 10 random ints uniform on [0, 5)


ri = np.random.randint(0,5 (10,))

Advanced Research Computing


Array Indexing (1)
last_elem = a[-1] # the last element of the array
i_ind = np.array([0,1,2,3]) # array of indices
j _inf= np.array([1,2,3,4]) # array of indices

# return array([a[0,1], a[1,2], a[2,3], a[1,4]])


a[i_ind,j_ind]

b = np.array([True, False, True, False])

# return array([a[0], a[2]])


a[b]

Advanced Research Computing


Array Indexing (2)

a[1:5, 3:7] # 4x4 sub-block starting at [1,3]


a[2, 3:] # until end of array
a[:15, :11] # from start of array

a[:, 1] # column 1
a[:, -8:] # a slab of width 8

Advanced Research Computing


Array Operations (1)
a = np.arange(0, 16).reshape(4,4)
b = np.transpose(a) ; bb = a.T

c=a+b # add a and b element-wise


d=a*b # multiply a and b element-wise
e = -a # negate every element of a

f = a > 0.0 # boolean array indicating


# which elements are > 0.0

Advanced Research Computing


PLOTTING IN PYTHON

Advanced Research Computing 17


Overview
• There are several Python packages for ploting
– The most widely used are Matplotlib and Pylab
• Pylab gathers Matplotlib and Numpy in one
namespace
• Plots, bar-charts, pie-charts are supported
• Matplotlib together with statistics packages
allows to represent probabilistic distributions

Advanced Research Computing


Before you start
• When using Matplotlib on Linux/Mac OS X,
your client machine must have an X11 server
running, and you must ssh into the machine
using X11 forwarding:
$ ssh –X matplotlib_host
• If connecting from Windows you need to
install an X11 server

Advanced Research Computing


Loading Data From a CSV File

$ more data.csv
"name","worth","age"
Donald Trump,30,65
Bill Gates,580,55
Tom Cruise,40,41
Mr Manager,10,41

Advanced Research Computing


Generate a bar-chart
$ more bar.py
import numpy as np
import matplotlib.pyplot as plt
data = np.recfromcsv('data.csv')
names = [ data[i][0] for i in range(len(data)) ]
worth = [ data[i][1] for i in range(len(data)) ]
ages = [ data[i][2] for i in range(len(data)) ]
N = len(data); ind = np.arange(N); width = 0.2

plt.bar(ind, worth, width, color='r', label='worth')


plt.ylabel('Worth')
plt.xticks(ind+width/2., names )
plt.legend()
plt.title('worth by person')
plt.show()

Advanced Research Computing


Thank you.

Questions?

Advanced Research Computing

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