Compress Me, Stupid!

Francesc Alted — Thu, 28 Aug 2014 17:01:20 GMT

How it all started

I think I began to become truly interested in compression when, back in 1992, I was installing C-News, a news server package meant to handle Usenet News articles in our university. For younger audiences, Usenet News was a very popular way to discuss about all kind of topics, but at the same time it was pretty difficult to cope with the huge amount of articles, specially because spam practices started to appear by that time. As Gene Spafford put it in 1992:

"Usenet is like a herd of performing elephants with diarrhea. Massive, difficult to redirect, awe-inspiring, entertaining, and a source of mind-boggling amounts of excrement when you least expect it."

But one thing was clear: Usenet brought massive amounts of data that had to be transmitted through the typical low-bandwidth data lines of that time: 64 Kbps shared for everyone at our university.

My mission then was to bring the Usenet News feed by making use of as low of resources as possible. Of course, one of the first things that I did was to start news transmission during the night, when everyone was warm at bed and nobody was going to complain about others stealing the precious and scarce Internet bandwidth. Another measure was to subscribe to just a selection of groups so that the transmission would end before the new day would start. And of course, I started experimenting with compression for maximizing the number of groups that we could bring to our community.

Compressing Usenet News

The most used compressor by 1992 was compress, a Unix program based on the LZW compression algorithm. But LZW had patents issues, so by that time Jean-Loup Gailly and Mark Adler started the work with gzip. At the beginning of 1993 gzip 1.0 was ready for consumption and I find it exciting not only because it was not patent-encumbered, but also because it compressed way better than the previous compress program, allowed different compression levels, and it was pretty fast too (although compress still had an advantage here, IIRC).

So I talked with the university that was providing us with the News feed and we manage to start compressing it, first with compress and then with gzip. Shortly after that, while making measurements on the new gzip improvements, I discovered that the bottleneck was in our News workstation (an HP 9000-730 with a speedy PA-7000 RISC microprocessor @ 66 MHz) being unable to decompress all the gzipped stream of subscribed news on-time. The bottleneck suddenly changed from the communication line to the CPU!

I remember spending large hours playing with different combinations of data chunk sizes and gzip compression levels, plotting the results (with the fine gnuplot) before finally coming with a combination that stroked a fair balance between available bandwidth and CPU speed, maximizing the amount of news articles hitting our university. I think this was my first realization of how compression could help bringing data faster to the system, making some processes more effective. In fact, that actually blew-up my mind and made me passionate about compression technologies for the years to come.

LZO and the explosion of compression technology

During 1996, Markus F.X.J. Oberhumer started to announce the availability of his own set of LZO compressors. These consisted in many different compressors, all of them being variations of his own compression algorithm (LZO), but tweaked to achieve either better compression ratios or compression speed. The suite was claimed to being able to achieve speeds reaching 1/3 of the memory speed of the typical Pentium-class computers available at that time. An entire set of compressors being able to approach memory speed? boy, that was a very exciting news for me.

LZO was in the back of my mind when I started my work on PyTables in August 2002 and shortly after, in May 2003, PyTables gained support for LZO. My goal was indeed to accelerate data transmission from disk to the CPU (and back), and these plots are testimonial of how beneficial LZO was for achieving that goal. Again, compression was demonstrating that it could effectively increase disk bandwidth, and not only slow internet lines.

However, although LZO was free of patent issues and fast as hell, it had a big limitation for a project like PyTables: the licensing. LZO was using the GPL license, and that prevented the inclusion of its sources in distributions without re-licensing PyTables itself as GPL, a thing that I was not willing to do (PyTables has a BSD license, as it is usual in the NumPy ecosystem). Because of that, LZO was a nice compressor to be included in GPL projects like the Linux kernel itself, but not a good fit for PyTables (although support for LZO still exists, as long as it is downloaded and installed separately).

By that time (mid 2000's) it started to appear a plethora of fast compressors with the same spirit than LZO, but with more permissive licenses (typically BSD/MIT), many of them being a nice fit for PyTables.

A new compressor for PyTables/HDF5

By 2008 it was clear that PyTables needed a compressor whose sources could be included in the PyTables tarball, so minimizing the installation requirements. For this I started considering a series of libraries and immediately devised FastLZ as a nice candidate because of its simplicity and performance. Also, FastLZ had a permissive MIT license, which was what I was looking for.

But pure FastLZ was not completely satisfactory because it was not simple enough. It had 2 compression levels that complicated the implementation quite a bit, so I decided to keep just the highest level, and then optimize certain parts of it so that speed would be acceptable. These modifications gave birth to BloscLZ, which is still being default compressor in Blosc.

But I had more ideas on what other features the new Blosc compressor should have, namely, multi-threading and an integrated shuffle filter. Multi-threading made a lot of sense by 2008 because both Intel and AMD already had a wide range of multi-core processors by then, and it was clear that the race for throwing more and more cores into systems was going to intensify. A fast compressor had to be able to use all these cores dancing around, period.

Shuffle (see slide 71 of this presentation) was the other important component of the new compressor. This algorithm relies on neighboring elements of a dataset being highly correlated to improve data compression. A shuffle filter already came as part of the HDF5 library but it was implemented in pure C, and as it had an important overhead in terms of computation, I decided to do an SIMD version using the powerful SSE2 instructions present in all Intel and AMD processors since 2003. The result is that this new shuffle implementation adds almost zero overhead compared with the compression/decompression stages.

Once all of these features were implemented, I designed a pretty comprehensive suite of tests and asked the PyTables community to help me testing the new compressor in as much systems as possible. After some iterations, we were happy when the new compressor worked flawlessly compressing and decompressing hundreds of terabytes on many different Windows and Unix boxes, both in 32-bit and 64-bit. The new beast was ready to ship.

Blosc was born

I then grabbed BloscLZ, the multi-threading support and the SSE2-powered shuffle and put it all in the same package. That also became a standalone, pure C library, with no attachments to PyTables or HDF5, so any application could make use of it. I have got the first stable version (1.0) of Blosc released by July 2010. Before this, I already introduced Blosc publicly in my EuroSciPy 2009 keynote and also made a small reference to it in an article about Starving CPUs where I stated:

"As the gap between CPU and memory speed continues to widen, I expect Blosc to improve memory-to-CPU data transmission rates over an increasing range of datasets."

And that is the thing. As CPUs are getting faster, the chances for using compression for an advantage can be applied to more and more scenarios, to the point that improving the bandwidth of main memory (RAM) is becoming possible now. And surprisingly enough, the methodology for achieving that is the same than back in the C-news ages: strike a good balance between data block sizes and compression speed, and let compression make your applications handle data faster and not only making it more compact.

When seen in perspective, it has been a long quest over the last decades. During the 90's, compression was useful to improve the bandwidth of slow internet connections. In the 2000's, it made possible accelerating disk I/O operation. In the 2010's Blosc goal is making the memory subsystem faster and whether it is able to achieve this or not will be the subject of future blogs (hint: data arrangement is critical too). But one thing is clear, achieving this (by Blosc or any other compressor out there) is just a matter of time. Such is the fate of the ever increasing gap in CPU versus memory speeds.

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