Difference between revisions of "Data"

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user 0m0.000s
 
user 0m0.000s
 
sys 0m0.156s
 
sys 0m0.156s
desktop$
+
 
 
desktop$ tar --use-compress-program=xz -xf linux-3.10-rc7.tar.xz
 
desktop$ tar --use-compress-program=xz -xf linux-3.10-rc7.tar.xz
 
desktop$ time cp -r linux-3.10-rc7 linux-3.10-rc7.copy
 
desktop$ time cp -r linux-3.10-rc7 linux-3.10-rc7.copy

Revision as of 11:21, 25 June 2013

Data: How to surf, rather than drown!

Introduction

Data on Disk

A Salutary Tale of Copying Files

We'll start by considering data stored on a disk drive. One thing that you might not know is that file systems and disk drives perform best when they are dealing with larger files. But how large is large? Here's a simple example, which you can try yourself:

First of all, let's get ourselves a large-ish file. A compressed tarball of the source code for the Linux kernel will do. In this case it's about 70MB in size. We can time how long it takes to create a copy of it. Below are the results of doing this experiment on BlueCrystal phase 2:

BCp2$ wget https://www.kernel.org/pub/linux/kernel/v3.x/testing/linux-3.10-rc7.tar.xz
BCp2$ time cp linux-3.10-rc7.tar.xz linux-3.10-rc7.tar.xz.copy

real	0m3.530s
user	0m0.000s
sys	0m0.068s

Now, that tar ball contains around 47,000 files, many of which are only a few hundred or thousand of bytes in size. These are files at the smaller end of the scale. Let's unpack the tarball and time how long it takes to copy these files, one-by-one:

BCp2$ tar --use-compress-program=xz -xf linux-3.10-rc7.tar.xz
BCp2$ time cp -r linux-3.10-rc7 linux-3.10-rc7.copy

real	18m17.102s
user	0m0.214s
sys	0m6.359s

Yikes! that took over 350 times longer than copying the single, large file. (These timings were taken at ~10:45 on the 25 Jun 2013. Any differences from the above values will be due to differences in load on the filesystem, which is shared with all the other users of the cluster. More of that in a moment..)

Now, we can repeat these tests on a different system. I got the values below from my very standard desktop machine:

desktop$ wget https://www.kernel.org/pub/linux/kernel/v3.x/testing/linux-3.10-rc7.tar.xz
desktop$ time cp linux-3.10-rc7.tar.xz linux-3.10-rc7.tar.xz.copy

real	0m0.192s
user	0m0.000s
sys	0m0.156s

desktop$ tar --use-compress-program=xz -xf linux-3.10-rc7.tar.xz
desktop$ time cp -r linux-3.10-rc7 linux-3.10-rc7.copy

real	0m25.961s
user	0m0.168s
sys	0m2.360s

That's a lot quicker! However, copying the small files still took over 130 times longer than copying the large file.

(Again, your mileage may vary.)

But hang on, I thought BlueCrystal was meant to be "super"?!

System Clients x1 Clients x4 Clients x8
Desktop ~65MB/s ~10MB/s ~0.5MB/s
Parallel FS ~160MB/s 130MB/s 67MB/s

Data over the Network

Filling the pipe.

Data when Writing your own Code

Memory Hierarchy

L1 Cache Picking up a book off your desk (~3s)
L2 Cache Getting up and getting a book off a shelf (~15s)
Main Memory Walking down the corridor to another room (several minutes)
Disk Walking the coastline of Britain (about a year)

Files & File Formats

Data Analytics

Some common operations you may want to perform on your data:

  • Cleaning
  • Filtering
  • Calculating summary statics (means, medians, variances)
  • Creating plots & graphics
  • Tests of statistical significance
  • Sorting and searching

Selecting the right tools.

Databases

GUI. Accessing from a program or script. Enterprise Grade The data haven.

Numerical Packages

Such as R, MATLAB & Python.

Bespoke Applications

Rolling Your Own

Principles: Sort & binary search.

Tools: Languages, libraries and packages.


When Data gets Big

Quotas.

Local Disks.

Swapping.

Data the Google way - Map-Reduce.

Hadoop & Friends.

Summary

  • Use large files whenever possible.
  • Disks are poor at servicing a large number of seek requests.
  • Check that you're making best use of a computer's memory hierarchy, i.e.:
    • Think about locality of reference.
    • Go to main memory as infrequently as possible.
    • Go to disk as infrequently as possible as possible.
  • Check that your are still using the right tools if your data grows.