Upload
pycontw
View
111
Download
3
Embed Size (px)
DESCRIPTION
Keynote for Day 1 of PyCon Taiwan 2012, by Travis Oliphant http://tw.pycon.org/2012/speaker/
Citation preview
Large-scale array-oriented computing with Python
PyCon Taiwan, June 9, 2012
Travis E. Oliphant
Friday, June 8, 12
My Roots
Friday, June 8, 12
My RootsImages from BYU Mers Lab
Friday, June 8, 12
Science led to Python
Raja Muthupillai
Armando Manduca
Richard Ehman1997
⇢0 (2⇡f)2 Ui (a, f) = [Cijkl (a, f)Uk,l (a, f)],j
Friday, June 8, 12
Finding derivatives of 5-d data⌅ = r⇥U
Friday, June 8, 12
Scientist at heart
Friday, June 8, 12
Python origins.Version Date
0.9.0 Feb. 1991
0.9.4 Dec. 1991
0.9.6 Apr. 1992
0.9.8 Jan. 1993
1.0.0 Jan. 1994
1.2 Apr. 1995
1.4 Oct. 1996
1.5.2 Apr. 1999
http://python-history.blogspot.com/2009/01/brief-timeline-of-python.html
Friday, June 8, 12
Python origins.Version Date
0.9.0 Feb. 1991
0.9.4 Dec. 1991
0.9.6 Apr. 1992
0.9.8 Jan. 1993
1.0.0 Jan. 1994
1.2 Apr. 1995
1.4 Oct. 1996
1.5.2 Apr. 1999
http://python-history.blogspot.com/2009/01/brief-timeline-of-python.html
Friday, June 8, 12
Brief History
Person Package Year
Jim Fulton Matrix Object in Python
1994
Jim Hugunin Numeric 1995
Perry Greenfield, Rick White, Todd Miller Numarray 2001
Travis Oliphant NumPy 2005
Friday, June 8, 12
1999 : Early SciPy emergesDiscussions on the matrix-sig from 1997 to 1999 wanting a complete data analysis
environment: Paul Barrett, Joe Harrington, Perry Greenfield, Paul Dubois, Konrad Hinsen, and others. Activity in 1998, led to increased interest in 1999.
In response on 15 Jan, 1999, I posted to matrix-sig a list of routines I felt needed to be present and began wrapping / writing in earnest. On 6 April 1999, I announced I would
be creating this uber-package which eventually became SciPy
Gaussian quadrature 5 Jan 1999
cephes 1.0 30 Jan 1999
sigtools 0.40 23 Feb 1999
Numeric docs March 1999
cephes 1.1 9 Mar 1999
multipack 0.3 13 Apr 1999
Helper routines 14 Apr 1999
multipack 0.6 (leastsq, ode, fsolve, quad)
29 Apr 1999
sparse plan described 30 May 1999
multipack 0.7 14 Jun 1999
SparsePy 0.1 5 Nov 1999
cephes 1.2 (vectorize) 29 Dec 1999
Plotting??
GistXPLOTDISLINGnuplot
Helping with f2py
Friday, June 8, 12
SciPy 2001
Founded in 2001 with Travis Vaught
Eric JonesweaveclusterGA*
Pearu Petersonlinalg
interpolatef2py
Travis Oliphantoptimizesparse
interpolateintegratespecialsignalstats
fftpackmisc
Friday, June 8, 12
Community effort• Chuck Harris• Pauli Virtanen• David Cournapeau• Stefan van der Walt• Dag Sverre Seljebotn• Robert Kern• Warren Weckesser• Ralf Gommers• Mark Wiebe• Nathaniel Smith
Friday, June 8, 12
Why Python for Technical Computing
• Syntax (it gets out of your way)• Over-loadable operators• Complex numbers built-in early• Just enough language support for arrays• “Occasional” programmers can grok it• Supports multiple programming styles• Expert programmers can also use it effectively• Has a simple, extensible implementation• General-purpose language --- can build a system• Critical mass
Friday, June 8, 12
What is wrong with Python?• Packaging is still not solved well (distribute, pip, and
distutils2 don’t cut it)• Missing anonymous blocks • The CPython run-time is aged and needs an overhaul
(GIL, global variables, lack of dynamic compilation support)• No approach to language extension except for
“import hooks” (lightweight DSL need)• The distraction of multiple run-times...• Array-oriented and NumPy not really understood by
most Python devs.
Friday, June 8, 12
Putting Science back in Comp Sci
• Much of the software stack is for systems programming --- C++, Java, .NET, ObjC, web- Complex numbers?- Vectorized primitives?
• Array-oriented programming has been supplanted by Object-oriented programming
• Software stack for scientists is not as helpful as it should be
• Fortran is still where many scientists end up
Friday, June 8, 12
Array-Oriented Computing
Example1: Fibonacci Numbers
fn = fn�1 + fn�2
f0 = 0f1 = 1
f = 0, 1, 1, 2, 3, 5, 8, 13, 21, 34, . . .
Friday, June 8, 12
Common Python approaches
Recursive Iterative
Algorithm matters!!
Friday, June 8, 12
Array-oriented approaches
Using LFilter
Using Formula
Friday, June 8, 12
Array-oriented approaches
Friday, June 8, 12
NumPy: an Array-Oriented Extension• Data: the array object
– slicing and shaping – data-type map to Bytes
• Fast Math: – vectorization – broadcasting– aggregations
Friday, June 8, 12
NumPy Array
shape
Friday, June 8, 12
Zen of NumPy
• strided is better than scattered• contiguous is better than strided• descriptive is better than imperative • array-oriented is better than object-oriented• broadcasting is a great idea • vectorized is better than an explicit loop• unless it’s too complicated --- then use Cython/Numba• think in higher dimensions
Friday, June 8, 12
More NumPy Demonstration
Friday, June 8, 12
Conway’s game of Life
• Dead cell with exactly 3 live neighbors will come to life
• A live cell with 2 or 3 neighbors will survive
• With too few or too many neighbors, the cell dies
Friday, June 8, 12
Interesting Patterns emerge
Friday, June 8, 12
APL : the first array-oriented language
• Appeared in 1964• Originated by Ken Iverson• Direct descendants (J, K, Matlab) are still
used heavily and people pay a lot of money for them
• NumPy is a descendent APL
J
K Matlab
NumericNumPy
Friday, June 8, 12
Conway’s Game of Life
APL
NumPyInitialization
Update Step
Friday, June 8, 12
Demo
Python Version
Array-oriented NumPy Version
Friday, June 8, 12
Memory using Object-oriented
Object
Attr1
Attr2
Attr3
Object
Attr1
Attr2
Attr3
Object
Attr1
Attr2
Attr3
Object
Attr1
Attr2
Attr3
Object
Attr1
Attr2
Attr3
Object
Attr1
Attr2
Attr3
Friday, June 8, 12
Array-oriented (Table) approach
Attr1 Attr2 Attr3
Object1
Object2
Object3
Object4
Object5
Object6
Friday, June 8, 12
Benefits of Array-oriented
• Many technical problems are naturally array-oriented (easy to vectorize)
• Algorithms can be expressed at a high-level• These algorithms can be parallelized more
simply (quite often much information is lost in the translation to typical “compiled” languages)
• Array-oriented algorithms map to modern hard-ware caches and pipelines.
Friday, June 8, 12
We need more focus on complied array-oriented languages with fast compilers!
Friday, June 8, 12
What is good about NumPy?• Array-oriented• Extensive Dtype System (including structures)• C-API• Simple to understand data-structure• Memory mapping• Syntax support from Python• Large community of users• Broadcasting• Easy to interface C/C++/Fortran code
Friday, June 8, 12
What is wrong with NumPy
• Dtype system is difficult to extend• Immediate mode creates huge temporaries
(spawning Numexpr)• “Almost” an in-memory data-base comparable
to SQL-lite (missing indexes)• Integration with sparse arrays • Lots of un-optimized parts• Minimal support for multi-core / GPU• Code-base is organic and hard to extend
Friday, June 8, 12
Improvements needed• NDArray improvements
• Indexes (esp. for Structured arrays)• SQL front-end• Multi-level, hierarchical labels• selection via mappings (labeled arrays)• Memory spaces (array made up of regions)• Distributed arrays (global array)• Compressed arrays• Standard distributed persistance• fancy indexing as view and optimizations• streaming arrays
Friday, June 8, 12
Improvements needed
• Dtype improvements• Enumerated types (including dynamic enumeration)• Derived fields• Specification as a class (or JSON)• Pointer dtype (i.e. C++ object, or varchar)• Finishing datetime• Missing data with bit-patterns• Parameterized field names
Friday, June 8, 12
Example of Object-defined Dtype
@np.dtypeclass Stock(np.DType): symbol = np.Str(4) open = np.Int(2) close = np.Int(2) high = np.Int(2) low = np.Int(2) @np.Int(2) def mid(self): return (self.high + self.low) / 2.0
Friday, June 8, 12
Improvements needed• Ufunc improvements
• Generalized ufuncs support more than just contiguous arrays
• Specification of ufuncs in Python• Move most dtype “array functions” to ufuncs• Unify error-handling for all computations• Allow lazy-evaluation and remote computation ---
streaming and generator data• Structured and string dtype ufuncs• Multi-core and GPU optimized ufuncs• Group-by reduction
Friday, June 8, 12
More Improvements needed• Miscellaneous improvements
• ABI-management• Eventual Move to library (NDLib)?• Integration with LLVM• Sparse dimensions• Remote computation• Fast I/O for CSV and Excel• Out-of-core calculations• Delayed-mode execution
Friday, June 8, 12
New Project
Blaze
NumPy
Next Generation NumPyOut-of-core
Distributed Tables
Friday, June 8, 12
Blaze Main Features• New ndarray with multiple memory segments• Distributed ndtable which can span the world• Fast, out-of-core algorithms for all functions• Delayed-mode execution: expressions build up
graph which gets executed where the data is• Built-in Indexes (beyond searchsorted)• Built-in labels (data-array)• Sparse dimensions (defined by attributes or
elements of another dimension)• Direct adapters to all data (move code to data)
Friday, June 8, 12
Delayed execution
Demo Code Only
Friday, June 8, 12
Dimensions defined by Attributes
Day Month Year High Low
15 3 2012 30 20
16 3 2012 35 25
20 3 2012 40 30
21 3 2012 41 29
dim1
Friday, June 8, 12
OutlineNDTable
NDArray
Bytes
GFunc DType
Domain
Friday, June 8, 12
NDTable (Example)
Proc0 Proc1 Proc2 Proc3
Proc0 Proc1 Proc2 Proc3
Proc0 Proc1 Proc2 Proc3
Proc4 Proc4 Proc4 Proc4
Each Partition:• Remote• Expression• NDArray
Friday, June 8, 12
Data URLs
• Variables in script are global addresses (DATA URLs). All the world’s data you can see via web can be in used as part of an algorithm by referencing it as a part of an array.• Dynamically interpret bytes as data-type• Scheduler will push code based on data-type
to the data instead of pulling data to the code.
Friday, June 8, 12
Overview
Main Script
Processing Node
Processing Node
Processing Node
Processing Node
Processing Node
Code
Code
Code
Code
Friday, June 8, 12
NDArray
• Local ndarray (NumPy++)• Multiple byte-buffers (streaming or random
access)• Variable-length arrays• All kinds of data-types (everything...)• Multiple patterns of memory access possible
(Z-order, Fortran-order, C-order)• Sparse dimensions
Friday, June 8, 12
GFunc
• Generalized Function• All NumPy functions• element-by-element• linear algebra• manipulation• Fourier Transform
• Iteration and Dispatch to low-level kernels• Kernels can be written in anything that builds a
C-like interface
Friday, June 8, 12
Early Timeline
Date Milestone
July 2012 Pre-alpha release
December 2012 Early Beta Release
June 2013 Version 1.0
Friday, June 8, 12
PyData
All computing modules known to work with Blaze will be placed under PyData umbrella of
projects over the coming years.
Friday, June 8, 12
Introducing Numba (lots of kernels to write)
Friday, June 8, 12
NumPy Users
• Want to be able to write Python to get fast code that works on arrays and scalars
• Need access to a boat-load of C-extensions (NumPy is just the beginning)
PyPy doesn’t cut it for us!
Friday, June 8, 12
Dynamic compilationPython
Function
NumPy Runtime
Ufu
ncs
Gen
eral
ized
U
Func
s
Func
tion-
base
d In
dexi
ng
Mem
ory
Filte
rs
Win
dow
K
erne
l Fu
ncs
I/O F
ilter
s
Red
uctio
n Fi
lters
Com
pute
d C
olum
ns
Dynamic Compilation
function pointer
Friday, June 8, 12
SciPy needs a Python compiler
integrateoptimize
odespecial
writing more of SciPy at high-level
Friday, June 8, 12
Numba -- a Python compiler
• Replays byte-code on a stack with simple type-inference
• Translates to LLVM (using LLVM-py)• Uses LLVM for code-gen• Resulting C-level function-pointer can be
inserted into NumPy run-time• Understands NumPy arrays• Is NumPy / SciPy aware
Friday, June 8, 12
NumPy + Mamba = Numba
LLVM 3.1
Intel Nvidia AppleAMD
OpenCLISPC CUDA CLANGOpenMP
LLVM-PY
Python Function Machine Code
Friday, June 8, 12
Examples
Friday, June 8, 12
Examples
Friday, June 8, 12
Software Stack Future?
LLVM
Python
COBJCFORTRAN
R
C++
Plateaus of Code re-use + DSLs
MatlabSQL
TDPL
Friday, June 8, 12
How to pay for all this?
Friday, June 8, 12
Dual strategy
Blaze
Friday, June 8, 12
NumFOCUS
Num(Py) Foundation for Open Code for Usable Science
Friday, June 8, 12
NumFOCUS
• Mission• To initiate and support educational programs
furthering the use of open source software in science.
• To promote the use of high-level languages and open source in science, engineering, and math research
• To encourage reproducible scientific research• To provide infrastructure and support for open
source projects for technical computing
Friday, June 8, 12
NumFOCUS
• Activites• Sponsor sprints and conferences• Provide scholarships and grants for people using
these tools• Pay for documentation development and basic
course development• Fund continuous integration and build systems• Work with domain-specific organizations• Raise funds from industries using Python and
NumPy
Friday, June 8, 12
NumFOCUS
Core Projects
Other Projects (seeking more --- need representatives)
NumPy SciPy IPython Matplotlib
Scikits Image
Friday, June 8, 12
NumFOCUS
• Directors• Perry Greenfield• John Hunter• Jarrod Millman• Travis Oliphant• Fernando Perez
• Members• Basically people who donate for now. In time, a
body that elects directors.
Friday, June 8, 12
• Large-scale data analysis products• Python and NumPy training• NumPy support and consulting• Rich-client or web user-interfaces• Blaze and PyData Development
Friday, June 8, 12