Py tables

Large Data Analyzewith PyTables

Personal Profile:

● Ali Hallaji

● Parallel Processing and Large Data Analyze

● Senior Python Developer at innfinision Cloud Solutions

● [email protected]

● Innfinision.net

innfinision Cloud Solutions:

● Providing Cloud, Virtualization and Data Center Solutions

● Developing Software for Cloud Environments

● Providing Services to Telecom, Education, Broadcasting & Health Fields

● Supporting OpenStack Foundation as the First Iranian Company

● First Supporter of IRAN OpenStack Community

Large Data Analyze with PyTables innfinision.net

● Outline

● What is PyTables ?

● Numexpr & Numpy

● Compressing Data

● What is HDF5?

● Querying your data in many different ways, fast

● Design goals

Agenda:

Outline

innfinision.netLarge Data Analyze with PyTables

Outline


The Starving CPU Problem● Getting the Most Out of Computers

● Caches and Data Locality

● Techniques For Fighting Data

Starvation

High Performance Libraries● Why Should You Use Them?

● In-Core High Performance

● Out-of-Core High Performance

Libraries

Getting the Most Out of Computers


Getting the Most Out of Computers


Computers nowadays are very powerful:● Extremely fast CPU’s (multicores)

● Large amounts of RAM

● Huge disk capacities

But they are facing a pervasive problem:An ever-increasing mismatch between CPU, memory and disk speeds (the

so-called “Starving CPU problem”)

This introduces tremendous difficulties in getting the most out of

computers.

CPU vs Memory cycle Trend


Cycle time is the time, usually measured in nanosecond s, between the start of

one random access memory ( RAM ) access to the time when the next access can

be started

History

● In the 1970s and 1980s the memory subsystem was able to

deliver all the data that processors required in time.

● In the good old days, the processor was the key bottleneck.

● But in the 1990s things started to change...

CPU vs Memory cycle Trend


dd

The CPU Starvation Problem


Known facts (in 2010):

● Memory latency is much higher (around 250x) than processors and it has been

an essential bottleneck for the past twenty years.

● Memory throughput is improving at a better rate than memory latency, but it

is also much slower than processors (about 25x).

The result is that CPUs in our current computers are suffering from

a serious data starvation problem: they could consume (much!)

more data than the system can possibly deliver.

What Is the Industry Doing to Alleviate CPU Starvation?


● They are improving memory throughput: cheap to implement

(more data is transmitted on each clock cycle).

● They are adding big caches in the CPU dies.

Why Is a Cache Useful?


● Caches are closer to the processor (normally in the same die),

so both the latency and throughput are improved.

● However: the faster they run the smaller they must be.

● They are effective mainly in a couple of scenarios:

● Time locality: when the dataset is reused.

● Spatial locality: when the dataset is accessed sequentially.

Time Locality


Parts of the dataset are reused

Spatial Locality


Dataset is accessed sequentially

Why High Performance Libraries?


● High performance libraries are made by people that knows very

well the different optimization techniques.

● You may be tempted to create original algorithms that can be

faster than these, but in general, it is very difficult to beat

them.

● In some cases, it may take some time to get used to them, but

the effort pays off in the long run.

Some In-Core High Performance Libraries


● ATLAS/MKL (Intel’s Math Kernel Library): Uses memory efficient algorithms as well

as SIMD and multi-core algorithms linear algebra operations.→

● VML (Intel’s Vector Math Library): Uses SIMD and multi-core to compute basic math

functions (sin, cos, exp, log...) in vectors.

● Numexpr: Performs potentially complex operations with NumPy arrays without the

overhead of temporaries. Can make use of multi-cores.

● Blosc: A multi-threaded compressor that can transmit data from caches to memory,

and back, at speeds that can be larger than a OS memcpy().

What is PyTables ?


PyTables


PyTables is a package for managing hierarchical datasets and designed to efficiently

and easily cope with extremely large amounts of data. You can download PyTables

and use it for free. You can access documentation, some examples of use and

presentations in the HowToUse section.

PyTables is built on top of the HDF5 library, using the Python language and the

NumPy package. It features an object-oriented interface that, combined with C

extensions for the performance-critical parts of the code (generated using Cython),

makes it a fast, yet extremely easy to use tool for interactively browse, process and

search very large amounts of data. One important feature of PyTables is that it

optimizes memory and disk resources so that data takes much less space (specially if

on-flight compression is used) than other solutions such as relational or object

oriented databases.

Numexpr & Numpy


Numexpr: Dealing with Complex Expressions


● Wears a specialized virtual machine for evaluating expressions.

● It accelerates computations by using blocking and by avoiding

temporaries.

● Multi-threaded: can use several cores automatically.

● It has support for Intel’s VML (Vector Math Library), so you

can accelerate the evaluation of transcendental (sin, cos,

atanh, sqrt. . . ) functions too.

NumPy: A Powerful Data Container for Python


NumPy provides a very powerful, object oriented, multi dimensional data container:

● array[index]: retrieves a portion of a data container

● (array1**3 / array2) - sin(array3): evaluates potentially complex

expressions

● numpy.dot(array1, array2): access to optimized BLAS (*GEMM) functions

NumPy And Temporaries


Computing “a*b+c” with numpy. Temporaries goes to memory

Numexpr Avoids (Big) Temporaries


Computing “a*b+c” with numexpr. Temporaries in memory are avoided.

Numexpr Performance (Using Multiple Threads)


Time to evaluate polynomial : ((.25*x + .75)*x – 1.5)*x -2

Compression


Why Compression


● Lets you store more data using the same space

● Uses more CPU, but CPU time is cheap compared with disk access

● Different compressors for different uses:

Bzip2, zlib, lzo, Blosc

Why Compression


3X more data

Why Compression


Less data needs to be transmitted to the CPU

Transmission + decompression faster than direct transfer?

Blosc: Compressing faster than Memory Speed


What is HDF5 ?


HDF5


HDF5 is a data model, library, and file format for storing and managing data. It

supports an unlimited variety of datatypes, and is designed for flexible and

efficient I/O and for high volume and complex data. HDF5 is portable and is

extensible, allowing applications to evolve in their use of HDF5. The HDF5

Technology suite includes tools and applications for managing, manipulating,

viewing, and analyzing data in the HDF5 format.

The HDF5 technology suite includes:


● A versatile data model that can represent very complex data objects and a wide

variety of metadata.

● A completely portable file format with no limit on the number or size of data

objects in the collection.

● A software library that runs on a range of computational platforms, from laptops to

massively parallel systems, and implements a high-level API with C, C++,

Fortran 90, and Java interfaces.

● A rich set of integrated performance features that allow for access time and

storage space optimizations.

● Tools and applications for managing, manipulating, viewing, and analyzing the data

in the collection.

Data structures


High level of flexibility for structuring your data:

● Datatypes: scalars (numerical & strings), records, enumerated, time...

● Table support multidimensional cells and nested records

● Multidimensional arrays

● Variable lengths arrays

Attributes:


Metadata about data

● Dataset hierarchy


Querying your data in many different

ways, fast


PyTables Query


One characteristic that sets PyTables apart from similar tools is its capability to

perform extremely fast queries on your tables in order to facilitate as much as

possible your main goal: get important information *out* of your datasets.

PyTables achieves so via a very flexible and efficient query iterator, named

Table.where(). This, in combination with OPSI, the powerful indexing engine that

comes with PyTables, and the efficiency of underlying tools like NumPy, HDF5,

Numexpr and Blosc, makes of PyTables one of the fastest and more powerful query

engines available.

Different query modes


Regular query:

● [ r[‘c1’] for r in table

if r[‘c2’] > 2.1 and r[‘c3’] == True)) ]

In- kernel query:

● [ r[‘c1’] for r in table.where(‘(c2>2.1)&(c3==True)’) ]

Indexed query:

● table.cols.c2.createIndex()

● table.cols.c3.createIndex()

● [ r[‘c1’] for r in table.where(‘(c2>2.1)&(c3==True)’) ]


This presentation has been collected from several other presentations(PyTables presentation). For more presentation refer to this link (http://pytables.org/moin/HowToUse#Presentations).

Ali Hallaji

[email protected]

innfinision.net

Thank you

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