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Talk about Python and "Big Data" at Level39 in Canary Wharf in London on September 30, 2013.

Talk about Python and "Big Data" at Level39 in Canary Wharf in London on September 30, 2013.

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    London level39 London level39 Presentation Transcript

    • Python in the future of “Big Data” analytics Travis Oliphant, PhD Continuum Analytics, Inc September 30, 2013 London, UK
    • Beginnings AfterBefore ⇢0 (2⇡f) 2 Ui (a, f) = [Cijkl (a, f) Uk,l (a, f)],j
    • 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
    • A sample of users
    • Why Python License Community Readable Syntax Modern Constructs Batteries Included Free and Open Source, Permissive License • Broad and friendly community • Over 34,000 packages on PyPI • Commercial Support • Many conferences (PyData, SciPy, PyCons...) • Executable pseudo-code • Can understand and edit code a year later • Fun to develop • Use of Indentation IPython • Interactive prompt on steroids • Allows less working memory • Allows failing quickly for exploration • List comprehensions • Iterator protocol and generators • Meta-programming • Introspection • (JIT Compiler and Concurrency) • Internet (FTP, HTTP, SMTP, XMLRPC) • Compression and Databases • Logging, unit-tests • Glue for other languages • Distribution has much, much more....
    • Python supports a developer spectrum DeveloperOccasional Scientist Developer • Cut and paste • Modify a few variables • Call some functions • Typical Quant or Engineer who doesn’t become programmer • Extend frameworks • Builds new objects • Wraps code • Quant / Engineer with decent developer skill • Creates frameworks • Creates compilers • Typical CS grad • Knows multiple languages Unique aspect of Python
    • 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 in 2001. 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?? Gist XPLOT DISLIN Gnuplot Helping with f2py
    • 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
    • Community effort many, many others! • Chuck Harris • Pauli Virtanen • Nathaniel Smith • Warren Weckesser • Ralf Gommers • Robert Kern • David Cournapeau • Stefan van der Walt • Jake Vanderplas • Josef Perktold • Anne Archibald • Dag Sverre Seljebotn • Joe Harrington --- Documentation effort • Andrew Straw --- www.scipy.org
    •      About 2,000,000 users of NumPy!
    • Scientific Stack NumPy SciPy Pandas Matplotlib scikit-learnscikit-image statsmodels PyTables OpenCV Cython Numba SymPy NumExpr astropy BioPython GDALPySAL ... many many more ...
    • Now What? After watching NumPy and SciPy get used all over Science and Technology (including Finance) --- what would I do differently? Blaze Numba Conda (Anaconda)
    • Continuum began operations in January of 2012 Python Travis Oliphant Peter Wang
    • (Most of) Our Team Scientists Developers Business NumFOCUS
    • expertise Big Picture
    • We are big backers of NumFOCUS and organizers of PyData Spyder
    • How we pay the bills Enterprise Python Scientific Computing Data Processing Data Analysis Visualisation Scalable Computing • Products • Training • Support • Consulting
    • “Big Data” and the Hype Cycle
    • Advanced Analytics and HPC HPC Supercomputing HSC Fault Tolerance Erasure Coding Hadoop / Disco MPI Big-Compute Scalapack Trilinos PETSc GPUs ? Python
    • Python and Science Python is the “language of Science” (Lots of R users might disagree) IPython notebook is quickly becoming the way scientists communicate about their work Pandas has recently started converting even R users to Python
    • The problem of Hadoop Hadoop wants to be the OS for “big-data”. Advanced analytics and Hadoop don’t blend well. Many people (led by hype) use Hadoop when they don’t need to --- and it slows them down and costs them $$. Scale up first. Then, scale-out. http://www.chrisstucchio.com/blog/2013/hadoop_hatred.html “Don’t use Hadoop --- your data is not that big”
    • Options if you do need Hadoop • Give Disco a try • Try a non Java-specific emerging alternative to HDFS (OrangeFS, GlusterFS, CephFS, Swift) • Use Python wrapper to HDFS (snakebite, webHDFS) and interface to map-reduce (luigi, mrjob, MortarData CPython UDF etc.)
    • “Data Has Mass” http://blog.mccrory.me/2010/12/07/data-gravity-in-the-clouds/
    • Workflow Perspective
    • Workflow Perspective Data-centric Perspective
    • The largest data analysis gap is in this man-machine interface. How can we put the scientist back in control of his data? How can we build analysis tools that are intuitive and that augment the scientist’s intellect rather than adding to the intellectual burden with a forest of arcane user tools? The real challenge is building this smart notebook that unlocks the data and makes it easy to capture, organize, analyze, visualize, and publish. -- Jim Gray et al, 2005
    • Why Don’t Scientists Use DBs? • Do not support scientific data types, or access patterns particular to a scientific problem • Scientists can handle their existing data volumes using programming tools • Once data was loaded, could not manipulate it with standard/familiar programs • Poor visualization and plotting integration • Require an expensive guru to maintain
    • “If one takes the controversial view that HDF, NetCDF, FITS, and Root are nascent database systems that provide metadata and portability but lack non-procedural query analysis, automatic parallelism, and sophisticated indexing, then one can see a fairly clear path that integrates these communities.” Convergence
    • Key Question How do we move code to data, while avoiding data silos?
    • Continuum key OS technologies Conda Browser-based interactive visualization for Python users Cross-platform package manager (with environments) Array-oriented Python Compiler for CPUs and GPUs (speed target is Fortran)Numba Blaze Bokeh CDX NumPy and Pandas for out-of-core and distributed data (general data-base execution engine for data-flow subset of Python) Continuum Data Explorer Ashiba New web-app building with only Python and a little HTML
    • Our Emerging Platform Rapid App Platform for SMEs Wakari Anaconda Binstar
    • What is Conda • Full package management (like yum or apt-get) but cross-platform • Control over environments (using link farms) --- better than virtual-env. virtualenv today is like distutils and setuptools of several years ago (great at first but will end up hating it) • Architected to be able to manage any packages (R, Scala, Clojure, Haskell, Ruby, JS) • SAT solver to manage dependencies • User-definable repositories
    • Binstar
    • Packaging and Distribution Solved • conda and binstar solve most of the problems that we have seen people encounter in managing Python installations (especially in large-scale institutions). • They are supported solutions that can remove the technology pain of managing Python • Allow focus on software architecture and separation of components (not just whatever makes packaging convenient)
    • Anaconda Free enterprise-ready Python distribution of open- source tools for large-scale data processing, predictive analytics, and scientific computing
    • Anaconda Add-Ons (paid-for) •Revolutionary Python to GPU compiler •Extends Numba to take a subset of Python to the GPU (program CUDA in Python) •CUDA FFT / BLAS interfaces Fast, memory-efficient Python interface for SQL databases, NoSQL stores,Amazon S3, and large data files. NumPy, SciPy, scikit-learn, NumExpr compiled against Intel’s Math Kernel Library (MKL)
    • Launcher
    • Why Numba? •Python is too slow for loops •Most people are not learning C/C++/Fortran today •Cython is an improvment (but still verbose and needs C-compiler) •NVIDIA using LLVM for the GPU •Many people working with large typed-containers (NumPy arrays) •We want to take high-level, tarray-oriented expressions and compile it to fast code
    • NumPy + Mamba = Numba LLVM Library Intel Nvidia AppleAMD OpenCLISPC CUDA CLANGOpenMP LLVMPY Python Function Machine Code ARM
    • Example Numba
    • Numba @jit('void(f8[:,:],f8[:,:],f8[:,:])') def filter(image, filt, output): M, N = image.shape m, n = filt.shape for i in range(m//2, M-m//2): for j in range(n//2, N-n//2): result = 0.0 for k in range(m): for l in range(n): result += image[i+k-m//2,j+l-n//2]*filt[k, l] output[i,j] = result ~1500x speed-up
    • Numba changes the game! LLVM IR x86 C++ ARM PTX C Fortran Python Numba turns (a subset of) Python into a “compiled language” as fast as C (but much more flexible). You don’t have to reach for C/C++
    • Laplace Example @jit('void(double[:,:], double, double)') def numba_update(u, dx2, dy2): nx, ny = u.shape for i in xrange(1,nx-1): for j in xrange(1, ny-1): u[i,j] = ((u[i+1,j] + u[i-1,j]) * dy2 + (u[i,j+1] + u[i,j-1]) * dx2) / (2*(dx2+dy2)) Adapted from http://www.scipy.org/PerformancePython originally by Prabhu Ramachandran @jit('void(double[:,:], double, double)') def numbavec_update(u, dx2, dy2): u[1:-1,1:-1] = ((u[2:,1:-1]+u[:-2,1:-1])*dy2 + (u[1:-1,2:] + u[1:-1,:-2])*dx2) / (2*(dx2+dy2))
    • Results of Laplace example Version Time Speed Up NumPy 3.19 1.0 Numba 2.32 1.38 Vect. Numba 2.33 1.37 Cython 2.38 1.34 Weave 2.47 1.29 Numexpr 2.62 1.22 Fortran Loops 2.30 1.39 Vect. Fortran 1.50 2.13 https://github.com/teoliphant/speed.git
    • LLVMPy worth looking at LLVM (via LLVMPy) has done much heavy lifting LLVMPy = Compilers for everybody
    • New Project Blaze NumPy Out of Core, Distributed and Optimized NumPy
    • Blaze Objectives • Flexible descriptor for tabular and semi-structured data • Seamless handling of: • On-disk / Out of core • Streaming data • Distributed data • Uniform treatment of: • “arrays of structures” and “structures of arrays” • missing values • “ragged” shapes • categorical types • computed columns
    • Blaze Deferred Arrays +" A" *" B" C" A + B*C • Symbolic objects which build a graph • Represents deferred computation Usually what you have when you have a Blaze Array
    • DataShape Type System   • A data description language • A super-set of NumPy’s dtype • Provides more flexibility • Integration with PADS coming Shape DType DataShape
    • Blaze Database GPU Node Array Server NFS Array Server Array Server Blaze Client Synthesized Array/Table view array+sql:// array:// file:// array:// Python REPL, Scripts Viz Data Server C, C++, FORTRAN JVM languages
    • Progress • Basic calculations work out-of-core (via Numba and LLVM) • Hard dependency on dynd and dynd-python (a dynamic C++-only multi-dimensional library like NumPy but with many improvements) • Persistent arrays from BLZ • Basic array-server functionality for layering over CSV files • 0.2 release in 1-2 weeks. 0.3 within a month after that (first usable release)
    • Querying BLZ In [15]: from blaze import blz In [16]: t = blz.open("TWITTER_LOG_Wed_Oct_31_22COLON22COLON28_EDT_2012-lvl9.blz") In [17]: t['(latitude>7) & (latitude<10) & (longitude >-10 ) & (longitude < 10) '] # query Out[17]: array([ (263843037069848576L, u'Cossy set to release album:http://t.co/Nijbe9GgShared via Nigeria News for Android. @', datetime.datetime(2012, 11, 1, 3, 20, 56), 'moses_peleg', u'kaduna', 9.453095, 8.0125194, ''), ... dtype=[('tid', '<u8'), ('text', '<U140'), ('created_at', '<M8[us]'), ('userid', 'S16'), ('userloc', '<U64'), ('latitude', '<f8'), ('longitude', '<f8'), ('lang', 'S2')]) In [18]: t[1000:3000] # get a range of tweets Out[18]: array([ (263829044892692480L, u'boa noite? ;( ue058ue41d', datetime.datetime(2012, 11, 1, 2, 25, 20), 'maaribeiro_', u'', nan, nan, ''), (263829044875915265L, u"Nah but I'm writing a gym journal... Watch it last 2 days!", datetime.datetime(2012, 11, 1, 2, 25, 20), 'Ryan_Shizzle', u'Shizzlesville', nan, nan, ''), ...
    • Kiva:Array Server DataShape + Raw JSON = Web Service type KivaLoan = { id: int64; name: string; description: { languages: var, string(2); texts: json # map<string(2), string>; }; status: string; # LoanStatusType; funded_amount: float64; basket_amount: json; # Option(float64); paid_amount: json; # Option(float64); image: { id: int64; template_id: int64; }; video: json; activity: string; sector: string; use: string; delinquent: bool; location: { country_code: string(2); country: string; town: json; # Option(string); geo: { level: string; # GeoLevelType pairs: string; # latlong type: string; # GeoTypeType } }; .... {"id":200533,"name":"Miawand Group","description":{"languages": ["en"],"texts":{"en":"Ozer is a member of the Miawand Group. He lives in the 16th district of Kabul, Afghanistan. He lives in a family of eight members. He is single, but is a responsible boy who works hard and supports the whole family. He is a carpenter and is busy working in his shop seven days a week. He needs the loan to purchase wood and needed carpentry tools such as tape measures, rulers and so on.rn r nHe hopes to make progress through the loan and he is confident that will make his repayments on time and will join for another loan cycle as well. rnrn"}},"status":"paid","funded_amount": 925,"basket_amount":null,"paid_amount":925,"image":{"id": 539726,"template_id": 1},"video":null,"activity":"Carpentry","sector":"Construction","use":"He wants to buy tools for his carpentry shop","delinquent":null,"location": {"country_code":"AF","country":"Afghanistan","town":"Kabul Afghanistan","geo":{"level":"country","pairs":"33 65","type":"point"}},"partner_id": 34,"posted_date":"2010-05-13T20:30:03Z","planned_expiration_date": null,"loan_amount": 925,"currency_exchange_loss_amount":null,"borrowers": [{"first_name":"Ozer","last_name":"","gender":"M","pictured":true}, {"first_name":"Rohaniy","last_name":"","gender":"M","pictured":true}, {"first_name":"Samem","last_name":"","gender":"M","pictured":true}],"ter ms": {"disbursal_date":"2010-05-13T07:00:00Z","disbursal_currency":"AFN"," disbursal_amount":42000,"loan_amount":925,"local_payments": [{"due_date":"2010-06-13T07:00:00Z","amount":4200}, {"due_date":"2010-07-13T07:00:00Z","amount":4200}, {"due_date":"2010-08-13T07:00:00Z","amount":4200}, {"due_date":"2010-09-13T07:00:00Z","amount":4200}, {"due_date":"2010-10-13T07:00:00Z","amount":4200}, {"due_date":"2010-11-13T08:00:00Z","amount":4200}, {"due_date":"2010-12-13T08:00:00Z","amount":4200}, {"due_date":"2011-01-13T08:00:00Z","amount":4200}, {"due_date":"2011-02-13T08:00:00Z","amount":4200}, {"due_date":"2011-03-13T08:00:00Z","amount": 4200}],"scheduled_payments": ... 2.9gb of JSON => network-queryable array: ~5 minutes Kiva Array Server Demo
    • DARPA providing help DARPA-BAA-12-38: XDATA TA-1: Scalable analytics and data processing technology   TA-2: Visual user interface technology
    • Bokeh Plotting Library • Interactive graphics for the web • Designed for large datasets • Designed for streaming data • Native interface in Python • Fast JavaScript component • DARPA funded • v0.1 release imminent
    • Reasons for Bokeh 1. Plotting must happen near the data too 2. Quick iteration is essential => interactive visualization 3. Interactive visualization on remote-data => use the browser 4. Almost all web plotting libraries are either: 1. Designed for javascript programmers 2. Designed to output static graphs 5. We designed Bokeh to be dynamic graphing in the web for Python programmers 6. Will include “Abstract” or “synthetic” rendering (working on Hadoop and Spark compatibility)
    • Abstract Rendering Pixels'are'Bins…' and'always'have'been' 1 2 2 3 4 4 3 2 2 1 A' D' B' C' B' C' D' A' Counts' Z>View' Geometry' Pixels'
    • Hi-def Alpha
    • Abstract Rendering Basic AR can identify trouble spots in standard plots, and also offer automatic tone mapping, taking perception into account. 37 mil elements, showing adjacency between entities in Kiva dataset
    • Wakari • Browser-based data analysis and visualization platform • Wordpress /YouTube / Github for data analysis • Full Linux environment with Anaconda Python • Can be installed on internal clusters & servers
    • Why Wakari? • Data is too big to fit on your desktop • You need compute power but don’t have easy access to a large cluster (cloud is sitting there with lots of power) • Configuration of software on a new system stinks (especially a cluster). • Collaborative Data Analytics --- you want to build a complex technical workflow and then share it with others easily (without requiring they do painful configuration to see your results) • IPython Notebook is awesome --- let’s share it (but we also need the dependencies and data).
    • Wakari • Free account has 512 MB RAM / 2 GB disk and shared multi-core CPU • Easily spin-up map-reduce (Disco and Hadoop clusters) • Use IPython Parallel on many-nodes in the cloud • Develop GUI apps (possibly in Anaconda) and publish them easily to Wakari (based on full power of scientific python --- complex technical workflows (IPython notebook for now)
    • Basic Data Explorer
    • Continuum Data Explorer (CDX) • Open Source • Goal is interactivity • Combination of IPython REPL, Bokeh, and tables • Tight integration between GUI elements and REPL • Current features - Namespace viewer (mapped to IPython namespace) - DataTable widget with group-by, computed columns, advanced- filters - Interactive Plots connected to tables
    • CDX
    • Conclusion Projects circle around giving tools to experts (occasional programmers or domain experts) to enable them to move their expertise to the data to get insights --- keep data where it is and move high-level but performant code) Join us or ask how we can help you!