Session 5:Extreme Python

An introduction to scientific programming with

Outline

•  Managing your environment

•  Efficiently handling large datasets

•  Optimising your code

•  Squeezing out extra speed

•  Writing neat and robust code

•  Graphical interfaces

Managing your environment

Managing your environment

•  Some good things about Python

•  lots of modules from many sources

•  ongoing development of Python and modules

•  Some bad things about Python

•  lots of modules from many sources

•  ongoing development of Python and modules

•  A solution

•  Maintain (or have option to create) separate environments (or manifests) for different projects

Managing your environment

•  virtualenv

•  general Python solution – http://virtualenv.pypa.io

•  modules are installed with pip – https://pip.pypa.io

$ pip install virtualenv # install virtualenv

$ virtualenv ENV1 # create a new environment ENV1

$ source ENV/bin/activate # set PATH to our environment

(ENV1)$ pip install emcee # install modules into ENV1

(ENV1)$ pip install numpy==1.8.2 # install specific version

(ENV1)$ python # use our custom environment

(ENV1)$ deactivate # return our PATH to normal

Managing your environment

•  virtualenv

•  can record current state of modules to a 'requirements' file

•  using that file can always recreate the same environment

(ENV1)$ pip freeze > requirements.txt

$ cat requirements.txt

emcee==2.1.0

numpy==1.8.2

$ deactivate

$ virtualenv ENV2

$ sourceENV2/bin/activate

(ENV2)$ pip install -r requirements.txt

Managing your environment

•  conda – http://conda.pydata.org

•  specific to the Anaconda Python distribution

•  similar to 'pip', but can install binaries (not just python)

•  avoid using pip within conda environment (unless you need to)

$ conda create -n ENV1 # create a new environment ENV1

$ source activate ENV1 # set PATH to our environment

$ conda install numpy # install modules into ENV1

$ conda install -c thebamf emcee # install from channel

$ source deactivate # return our PATH to normal

$ conda list –n ENV1 -e > requirements.txt # clone ENV1

$ conda create -n ENV2 --file requirements.txt # to ENV2

Managing your environment

•  Updating packages

$ conda update --all

$ conda update scipy emcee

OR

$ pip install --upgrade

$ pip install --upgrade scipy emcee

Efficiently handling large datasets

Databases

•  Python has tools for accessing most (all?) databases

•  e.g. MySQL, SQLite, MongoDB, Postgres, …

•  Allow one to work with huge datasets

•  Data can be at remote locations

•  However, most databases are designed for webserver use

•  Not optimised for data analysis

PyTables

•  http://pytables.github.io

•  For creating, storing and analysing datasets

•  from simple, small tables to complex, huge datasets

•  standard HDF5 file format

•  incredibly fast – even faster with indexing

•  uses on the fly block compression

•  designed for modern systems

•  fast multi-code CPU; large, slow memory

•  "in-kernel" – data and algorithm are sent to CPU in optimal way

•  "out-of-core" – avoids loading whole dataset into memory

PyTables

>>> from tables import *

>>> h5file = openFile("test.h5", mode = "w") >>> x = h5file.createArray("/", "x", arange(1000))

>>> y = h5file.createArray("/", "y", sqrt(arange(1000)))

>>> h5file.close()

•  Can store many things in one HDF5 file (like FITS)

•  Tree structure

•  Everything in a group (starting with root group, '/')

•  Data stored in leaves

•  Arrays (e.g. n-dimensional images)

PyTables

>>> class MyTable(IsDescription): z = Float32Col()

>>> table = h5file.createTable("/", "mytable", MyTable) >>> row = table.row

>>> for i in xrange(1000):

row["z"] = i**(3.0/2.0) row.append()

>>> table.flush() >>> z = table.cols.z

•  Tables (columns with different formats)

•  described by a class

•  accessed by a row iterator

PyTables Expr

>>> r = h5file.createArray("/", "r", np.zeros(1000)) >>> xyz = Expr("x*y*z")

>>> xyz.setOutput(r) >>> xyz.eval()

/r (Array(1000,)) ''

atom := Float64Atom(shape=(), dflt=0.0) maindim := 0

flavor := 'numpy' byteorder := 'little'

chunkshape := None

>>> r.read(0, 10) array([ 0. , 1. , 7.99999986, 26.9999989 ,

64. , 124.99999917, 216.00000085, 343.00001259,

511.99999124, 729. ])

•  Expr enables in-kernel & out-of-core operations

PyTables Expr

>>> r_bigish = [ row['z'] for row in table.where('(z > 1000) & (z <= 2000)' ]

>>> for big in table.where('z > 10000;'):

... print('A big z is {}'.format(big['z'])

•  where enables in-kernel selections

•  There is also a where in Expr

•  Python Data Analysis Library•  http://pandas.pydata.org

•  Easy-to-use data structures•  DataFrame (more friendly recarray)•  Handles missing data (more friendly masked array)•  read and write various data formats•  data-alignment

•  tries to be helpful, though not always intuitive•  Easy to combine data tables•  Surprisingly fast!

•  Also see Statsmodels•  http://statsmodels.sourceforge.net

Pandas

>>> import pandas as pd

>>> t = np.arange(0.0, 1.0, 0.1)

>>> s = pd.Series(t)

>>> x = t + np.random.normal(scale=0.1, size=t.shape)

>>> y = x**2 + np.random.normal(scale=0.5, size=t.shape)

>>> df1 = pd.DataFrame({ 'x' : x, 'y' : y}, index = t)

>>> df1.plot()

>>> df1.plot('x', 'y', kind='scatter')

•  1D Series, 2D DataFrame, 3D Panel

•  Various ways of creating these structures

Pandas

>>> t2 = t[::2]

>>> z = t2**3 + np.random.normal(scale=1.0, size=t2.shape)

>>> df2 = pd.DataFrame({ 'z' : z, 'z2' : z**2}, index = t2)

>>> df3 = df1.join(df2)

>>> df3.sort('y')

•  Always indexed

•  Indices used when joining tables

•  Handling data fairly intuitive, similar to numpy slices

•  Powerful and flexible

•  Good documentation

Pandas

data = pyfits.getdata('myfunkydata.fits')

df = pd.DataFrame(data)

# store DataFrame to HDF5

store = pd.HDFStore('myfunkydata.h5', mode='w', complib='blosc', complevel=5)

store['funkydata'] = df

# some time later…

store = pd.HDFStore('myfunkydata.h5', mode='r')

df = store['funkydata']

•  DataFrame can be created directly from a recarray

•  Pandas data structures can be efficiently stored on disk

•  based on PyTables

Graphical interfaces

GUIs

Several modules to construct GUIs in Python

wxpython is one of the most popular

http://www.wxpython.org

e.g., https://github.com/bamford/control/

Python web frameworks

Django

a high-level Python Web framework that encourages rapid development and clean, pragmatic design.

and many others, e.g. Zope (massive), web2py (light), …

•  Give your scientific code a friendly face!•  easy configuration•  monitor progress•  particularly for public code, cloud computing, HPC

•  An (unscientific) example, followed by another one

Optimising your code

Testing performance

timeit – use in interpreter, script or command line

Options:

-s S, --setup=S

statement to be executed once initially (default pass)

-n N, --number=N

how many times to execute 'statement' (default: take ~0.2 sec total)

-r N, --repeat=N

how many times to repeat the timer (default 3)

iPython magic version

python -m timeit [-n N] [-r N] [-s S] [statement ...]

%timeit # one line %%timeit # whole notebook cell

Testing performance

# fastest way to calculate x**5?

$ python -m timeit -s 'from math import pow; x = 1.23' 'x*x*x*x*x'

10000000 loops, best of 3: 0.161 usec per loop

$ python -m timeit -s 'from math import pow; x = 1.23' 'x**5'

10000000 loops, best of 3: 0.111 usec per loop

$ python -m timeit -s 'from math import pow; x = 1.23' 'pow(x, 5)'

1000000 loops, best of 3: 0.184 usec per loop

Profiling

•  Understand which parts of your code limit its execution time

•  print summary to screen, or save file for detailed analysis

From shell

From iPython

Lots of functionality… see docs

$ python -m cProfile –o program.prof my_program.py

%prun -D program.prof my_function()

%%prun # profile an entire notebook cell

Profiling

Nice visualisation with snakeviz – http://jiffyclub.github.io/snakeviz/

In iPython:

$ conda install snakeviz

OR

$ pip install snakeviz

%load_ext snakeviz

%snakeviz my_function()

%%snakeviz # profile entire cell

Extremely neat Python

Coding Guidlines

•  PEP8

•  https://www.python.org/dev/peps/pep-0008/

•  several tools to test compliance – search ‘pep8’

•  4 spaces for indentation

•  79 characters maximum line length (72 for docstrings)

•  use blank lines sparingly, but always around functions, etc.

•  whitespace

•  one space around operators (except = in function args)

•  after commas

•  ClassNames and function_names

Writing robust code

Tests

•  Unit tests

•  test individual units of code

•  specific units

•  e.g. a single function or interaction between functions

•  tested as generally as possible

•  Functional tests

•  test the whole programme under a variety of inputs

•  Regression tests

•  check for inconsistent behaviour between consecutive versions

•  detect new bugs, ensure old bugs do not reoccur

Tests

•  Several testing frameworks

•  unittest is the main Python module

•  doctest enables tests in documentation strings

•  nose is a third-party module that nicely automates testing

•  pytest is preferred by astropy

•  but generally all interoperable

•  Review docs, but basically just name any tests test_*

•  astropy has detailed testing guidelines:

•  http://docs.astropy.org/en/stable/development/testguide.html

Tests

•  Online testing (continuous integration) services

•  Integrate with GitHub

•  Free for public open source projects

•  Travis CI: https://travis-ci.org

•  Test coverage reports

•  Coveralls: https://coveralls.io

•  astropy affiliated package template

•  guides you through setup of these services

•  https://github.com/astropy/package-template

Squeezing out extra speed

Multiprocessing

•  Python includes modules for writing "parallel" programs:

•  threaded – limited by the Global Interpreter Lock

•  multiprocessing – generally more useful

from multiprocessing import Pool def f(x): return x*x

pool = Pool(processes=4) # start 4 worker processes z = range(10) print pool.map(f, z) # apply f to each element of z in parallel

Multiprocessing

from multiprocessing import Process from time import sleep def f(name): print('Hello {}, I am going to sleep now'.format(name)) sleep(3) print('OK, finished sleeping') if __name__ == '__main__': p = Process(target=f, args=(lock, 'Steven')) p.start() # start additional process sleep(1) # carry on doing stuff print 'Wow, how lazy is that function!' p.join() # wait for process to complete

$ python thinking.py Hello Steven, I am going to sleep now Wow, how lazy is that function! OK, finished sleeping

(Really, should use a lock to avoid writing output to screen at same time)

Mixing Python and C – fast and flexible

Cython is used for compiling Python-like code to machine-code•  supports a big subset of the Python language•  conditions and loops run 2-8x faster, overall 30% faster for plain Python

code•  add types for speedups (hundreds of times)•  easily use native libraries (C/C++/Fortran) directly

•  Cython code is turned into C code•  uses the CPython API and runtime

•  Coding in Cython is like coding in Python and C at the same time!

Some material borrowed from Dag Sverre Seljebotn (University of Oslo) EuroSciPy 2010 presentation

Cython

Use cases:

•  Performance-critical code•  which does not translate to array-based approach (numpy / pytables)•  existing Python code à optimise critical parts

•  Wrapping existing C/C++ libraries•  particularly higher-level Pythonised wrapper•  for one-to-one wrapping other tools might be better suited

Cython

Cython code must be compiled.

Two stages:

•  A .pyx file is compiled by Cython to a .c file, containing the code of a Python extension module

•  The .c file is compiled by a C compiler•  Generated C code can be built without Cython installed•  Cython is a developer dependency, not a build-time dependency•  Generated C code works with Python 2.3+•  The result is a .so file (or .pyd on Windows) which can be imported

directly into a Python session

Cython

Ways of building Cython code:

•  Run cython command-line utility and compile the resulting C file•  use favourite build tool•  for cross-system operation you need to query Python for the C build

options to use

•  Use pyximport to importing Cython .pyx files as if they were .py files; building on the fly (recommended to start).•  things get complicated if you must link to native libraries•  larger projects tend to need a build phase anyway

•  Write a distutils setup.py•  standard way of distributing, building and installing Python modules

Cython

•  Cython supports most of normal Python

•  Most standard Python code can be used directly with Cython•  typical speedups of (very roughly) a factor of two•  should not ever slow down code – safe to try•  name file .pyx or use pyimport = True

>>> import pyximport >>> pyximport.install()

>>> import mypyxmodule # converts and compiles on the fly

>>> pyximport.install(pyimport = True)

>>> import mypymodule # converts and compiles on the fly # should fall back to Python if fails

Cython

•  Big speedup from defining types of key variables

•  Use native C-types (int, double, char *, etc.)

•  Use Python C-types (Py_int_t, Py_float_t, etc.)

•  Use cdef to declare variable types

•  Also use cdef to declare C-only functions (with return type)•  can also use cpdef to declare functions which are automatically treated

as C or Python depending on usage

•  Don't forget function arguments (but note cdef not used here)

Cython – primes example

•  Efficient algorithm to find first N prime numbers

def primes(kmax): p = [] k = 0 n = 2 while k < kmax: i = 0 while i < k and n % p[i] != 0: i = i + 1 if i == k: k = k + 1 p.append(n) n = n + 1 return p

$ python -m timeit -s 'import primes as p' 'p.primes(100)' 1000 loops, best of 3: 1.35 msec per loop

primes.py

Cython – primes example

$ python -m timeit -s 'import pyximport; pyximport.install(); import cprimes as p' 'p.primes(100)'

1000 loops, best of 3: 731 usec per loop 1.8x speedup

def primes(kmax): p = [] k = 0 n = 2 while k < kmax: i = 0 while i < k and n % p[i] != 0: i = i + 1 if i == k: k = k + 1 p.append(n) n = n + 1 return p

cprimes.pyx

Cython – primes example

def primes(int kmax): # declare types of parameters cdef int n, k, i # declare types of variables cdef int p[1000] # including arrays result = [] # can still use normal Python types if kmax > 1000: # in this case need to hardcode limit kmax = 1000 k = 0 n = 2 while k < kmax: i = 0 while i < k and n % p[i] != 0: i = i + 1 if i == k: p[k] = n k = k + 1 result.append(n) n = n + 1 return result # return Python object

xprimes.pyx

40.8 usec per loop

33x speedup

contains only C-code

Cython and Numpy

•  Cython provides a way to quickly access Numpy arrays with specified types and dimensionality

à for implementing fast specific algorithms

•  Also provides way to create generalized Ufuncs

•  Can be useful, but often using functions provided by numpy, scipy, numexpr or pytables will be easier and faster

Numba

•  JIT: just in time compilation of Python functions

•  Compilation for both CPU and GPU hardware

from numba import jit @jit def sum2d(arr): M, N = arr.shape result = 0.0 for i in range(M): for j in range(N): result += arr[i,j] return result

a = np.arange(10000).reshape(1000,10) %timeit sum2d(a) 1000 loops, best of 3: 334 µs per loop %timeit sum2d(a) # without @jit 1 loops, best of 3: 2.15 µs per loop

Numba

•  JIT: just in time compilation of Python functions

•  Compilation for both CPU and GPU hardware

from numbapro import vectorize, float32 # MULTITHREADED UFUNC @vectorize([float32(float32, float32)], target=’parallel’) def sum(a, b): return a + b # CUDA ACCELERATED UFUNC @vectorize([float32(float32, float32)], target=’gpu’) def sum(a, b): return a + b

Anaconda Accelerate and IOPro

•  Accelerate•  Optimised versions of numpy, numexpr, scipy, scikit-learn, etc.•  NumbaPro: extends and speeds up Numba

•  IOPro•  loads very large NumPy arrays (and Pandas DataFrames) efficiently•  from files, SQL databases, and NoSQL stores•  drop-in replacement for NumPy loadtxt() and genfromtxt()

•  Free for academics:•  https://www.continuum.io/anaconda-academic-subscriptions-available

The End

An introduction to scientific programming with