Blosc Has Won Google's Open Source Peer Bonus Program












  • Support for SIMD in ARM processors.



The Lizard Codec

The past weekend I was putting some time in integrating one of the codecs that I was lately more curious about (specially since the release of its 1.0 version some months ago). I am talking about Lizard, a direct derivative of the LZ4 codec and whose author is Przemyslaw Skibinski. One should remark that Przemyslaw is not new in the compression arena as he has helped Yann Collet quite a lot during the Zstandard development, and also he is the author of lzbench, a nice and comprehensive in-memory benchmark of a series of open-source LZ77/LZSS/LZMA compressors.

The reason why I was thinking that Lizard was an interesting codec for Blosc is because it mixes some interesting optimizations of the LZ4 codec and, optionally, it can use them in combination with the Huffman coding by selecting different compression levels (currently from 10 to 49).

After the initial support for Lizard in Blosc, it took me some time to determine a decent map between the compression levels in Blosc (1-9) to the ones in Lizard (10-49), mainly for allowing fast compression and decompression (what Blosc is all about). During the way, I discovered that the most interesting compression levels in Lizard have been 10, 20 and 41. This was indeed determined using the synthetic benchamrk that comes with Blosc, but that is the usual path that gaves me quite good estimates for a first calibration (we are working on a more complete tuner that can adapt to actual data in real time, but I'll blog about it in another occasion).

A new star has born

After the calibration was done the results of the new codec are really surprising:



The interesting part of Lizard can be seen when large compression levels for Blosc are used, specially 8 and 9. Those are mapped to compression level 41 in Lizard, which means that the LIZv1 + Huffman compression method is used. Following the documentation, this matches the compression levels of Zlib and Zstd/Brotli, and it shows.

Just for reference, here it is the performance of the LZ4 codec, from which Lizard inherits a good part of its code:



And here the performance of Zstd, which also uses Huffman coding:



So, while Lizard (or at least, the current mapping that I did for it inside Blosc) in low compression levels cannot beat the speed of LZ4 or the compression ratios of Zstd, for high compression levels it clearly beats LZ4 and Zstd speed both for compression and decompression. Most specially, it works extremely well for achieving pretty reasonable compression ratios (typically better than Zlib, albeit not as good as Zstd) at very good decompression speed and exceptional compression speed (compressing at more than the memcpy() speed, at very good ratios, oh really?).

Finally, for those wondering why I have not used the LIZv1 + Huffman compression method also for the lower compression levels in Blosc, the answer is that I obviously tried that, but for some reason, this method only performs well for large buffers, whereas for small buffers (like the ones created by low compression levels in Blosc) its performance is rather poor. I was kind of getting a similar behaviour with Zstd, where performance shines for decompressing large buffers (the difference is that Lizard can compress at tremendous speed when compared with Zstd in this scenario), so I suppose this is typical when Huffman methods are used.

Finding its place among Blosc codecs

In my previous blog, I was saying that Zstd has virtually no competitor in Write Once Read Multiple scenarios. However, I think there is still a niche for codecs that, without providing the extreme compression ratios of Zstd, they still show big enough compression muscle without loosing too much compression speed. IMO, this is a good description of how Lizard performs. However, in Blosc1 we only have slots for a couple of codecs more (but that will not be a problem for Blosc2, where much more codecs will be supported), and although I am pretty enthusiastic on adding Lizard it would be nice to gather users feedback before than that. So in case you are a Blosc user, please use the lizard branch of the C-Blosc repo (UPDATE: Lizard has been merged into the C-Blosc2 repo recently) and report back your results.

Appendix: Hardware and software used



  • OS: Ubuntu 16.04

  • Compiler: GCC 6.3.0

  • C-Blosc2: (2017-07-29, lizard branch)

  • Lizard: 1.0.0

Testing PGO with LZ4 and Zstd codecs

In past week's post I was showing how the PGO (Profile Guided Optimization) capability in modern compilers allowed for a good increase in the performance of the BloscLZ codec. Today I'd like to test how the PGO optimization affected the speed of the same synthetic benchmark that comes with C-Blosc2 for the two other of the most used codecs in Blosc: LZ4 and Zstd.


First, for GCC without PGO:



Now with PGO enabled:



We can see here that, similarly to BloscLZ, although the compression speed has not improved significantly, the decompression is now reaching up to 30 GB/s, and for high compression levels, up to 20 GB/s, which is pretty good.


First, for GCC without PGO:



Now with PGO enabled:



Wow, in this case we really can see important speedups in both compressing and decompressing. Specially interesting is the decompression case where, for the higher compression levels, Zstd can reach speeds exceeding 20 GB/s (whereas without PGO it was not able to exceed 12 GB/s) which seems a bit crazy provided the wonderful compression ratios that Zstd is able to achieve. Beyond any doubt, for Write Once Read Multiple scenarios there is no competitor for Zstd, most specially when PGO is used.

This confirms that, once again, when performance is critical for your applications, PGO should be part of your daily weaponery.

Appendix: Hardware and software used



  • OS: Ubuntu 16.04

  • Compiler: GCC 6.3.0 (using PGO)

  • C-Blosc2: (2017-07-11)

  • LZ4 codec: 1.7.5

  • Zstd codec: 1.3.0

Fine Tuning the BloscLZ codec

Yesterday I was reading about the exciting new CPU architectures that both AMD and Intel are introducing and I was wondering how the improved architecture of the new cores and most specially, its caches, could apply to Blosc. It turns out that I have access to a server with a relatively modern CPU (Xeon E3-1245 v5 @ 3.50GHz, with 4 physical cores) and I decided to have a go at fine-tune the included BloscLZ codec (the one that I know the best) inside C-Blosc2. Of course, I already spent some time tuning BloscLZ, but that was some years ago and provided the fast pace at which CPUs are evolving I thought that this was excellent timing for another round of fine-tuning, most specially in preparation for users adopting the forthcoming RYZEN, Threadripper, EPYC and Skylake-SP architectures.

Frankly speaking, I was expecting to get very little improvements in this front, but the results have been unexpectedly good. Keep reading.

Where we come from

Just for reference, here it is the performance of the BloscLZ codec in my server before the new tuning work:



That is the typical synthetic benchmark in Blosc, but for the plotting function in the C-Blosc2 project, the actual size of each compressed buffer is shown (and not the size of the whole dataset, as in C-Blosc1). In this case, the dataset (256 MB) is split in chunks of 4 MB, and provided that our CPU has a LLC (Last Level Cache) of 8 MB, this is sort of an optimal size for achieving maximum performance (the buffers meant for Blosc usually do not exceed 4 MB for most of its common usages).

As can be seen, performance is quite good, although compression ratios left something to be desired. Furthermore, for the maximum compression level (9), the compression ratio has a regression with respect to the previous level (8). This is not too bad, and sometimes happens in any codec, but the nice thing would be to avoid it if possible.

The new BloscLZ after fine tuning

So, after a couple of hours playing with different parameters in BloscLZ and C-Blosc2, I started to realize that the new Intel CPU performed exceedingly well when asked to compress more, to the point that high compression settings were not performing that slow in comparision with low compression ones; rather the contrary: high compression settings were operating at almost the same speed than lower ones (which was a welcome surprise indeed). Hence I tried to be set quite more aggressive parameters in BloscLZ, while trying to keep the size of internal blocks in Blosc2 below 256 KB (the typical size of L2 caches in modern CPUs). This is the result:



So the compression ratios have increased quite a bit, specially for the larger compression levels (going from less than 10x to more than 20x for this benchmark). This is courtesy of the new, more agressive compression parameters. Strikingly enough, performance has also increased in general, but specially for these large compression levels. I am not completely certain on why this is the case, but probably this new CPU architecture is much better at out-of-order execution and prefetching larger blocks of data, which benefits compressing both faster even in large buffers; similarly, I am pretty sure that improvements in compiler technology (I am using a recent GCC 6.3.0 here) is pretty important for getting faster binary code. We can also see that when using 4 threads (i.e. using all the physical cores available in our CPU at hand), BloscLZ can compress faster than a memcpy() call for most of the cases, and most specially at large compression levels, as mentioned before. Oh, and we can see that we also got rid of the regression in the compression ratio for compression level 9, which is cool.

Regarding decompression speed, we can see that the new tuning gave general speed-ups of between 10% and 20%, with no significant slowdowns in any case. All in all, quite good results indeed!

Room for more improvements? Enter PGO.

To temporary end (optimization is a never ending task) this quest for speed, I am curious about the speed that we can buy by using the PGO (Profile Guided Optimization) capability that is present in most of the modern compilers. Here I am going to use the PGO of GCC in combination with our benchmark at hand so as to provide the profile for the compiler optimizer. Here are the results when PGO is applied to the new parametrization:



So, while the speed improvement for compression is not significant (albeit a bit better), the big improvement comes in the decompression speed, where we see speeds almost reaching 50 GB/s and perhaps more interestingly, more than 35 GB/s for maximum compression level, and for first time in my life as Blosc developer, I can see the speed of decompressing with one single thread being faster than memcpy() for all the compression levels.

I wonder what the PGO technique can bring to other codecs in Blosc, but that is stuff for other blog post. At any rate, the reader is encouraged to try PGO on their own setups. I am pretty sure that she will be pleased to see nice speed improvements.

Appendix: Hardware and software used



  • OS: Ubuntu 16.04

  • Compiler: GCC 6.3.0

  • C-Blosc2: (2017-07-14)

  • BloscLZ: 1.0.6 (2017-07-14)

Zstd has just landed in Blosc




A compression beast for Blosc operation










Not the fastest, but a nicely balanced one







Appendix: What can be expected in Blosc2






ARM is becoming a first-class citizen for Blosc

We are happy to announce that Blosc is receiving official support for ARM processors. Blosc has always been meant to support all platforms where a C89 compliant C compiler can be found, but until now the only hardware platforms that we were testing on a regular basis has been Intel (on top of Unix/Linux, Mac OSX and Windows).

We want this to change and the ARM architecture has been our first candidate to become a fully supported platform besides Intel/AMD. You may be wondering that we could have chosen any other architecture like MIPS or PowerPC, so why ARM?

ARM is eating the world

ARM is an increasingly popular architecture and we can find implementation exemplars of it not only in the phones, tablets or ChromeBooks, but also acting as embedded processors, as well as in providing computing power to immensely popular Raspberry Pi's and Arduinos and even environments so apparently alien to it like High Performance Computing.

Contrarily to what has been traditional for other computer platforms, one of the most important design features for ARM is to keep energy consumption under very strict limits. Nowadays, the ARM architecture can run decently powerful CPUs where each core consumes just 600 to 750 mWatt or less.

In my opinion, it is precisely this energy efficiency what makes of ARM one of the platforms with more projection to gain ground as a general computer platform in the short future. By now, we all know that ARM allows packing more cores into a single die (e.g. your phone having more cores than your laptop, anyone?). And more cores also means more combined computing throughput (albeit a bit more difficult to program), but more importantly, more cores being able to bring data from memory at the same time. Contrarily to what one might think, having different threads transmitting data from RAM to the CPU caches provides a better utilization of memory buses, and hence, a much better global memory bandwidth. This can be seen, for example, in typical Blosc benchmarks by looking at how the bandwidth grows with the number of threads in all the dots, but specially where compression ratio equals 1 (i.e. no compression is active, so Blosc is only doing a memory copy in this case).

Blosc is getting ready for ARM

So ARM is cool indeed, but what we are doing for making it a first-class citizen? For starters, we have created a new C-Blosc2 repository that is going to act as a playground for some time and where we are going to experiment with a new range of features (those will be discussed in a later post). And this is exactly the place where we have already started implementing a NEON version of the shuffle filter.

NEON is an SIMD extension in the same spirit than SSE2 or AVX2 present in Intel/AMD offerings. NEON extension was introduced in ARMv7 architecture, and is present in most of the current high-end devices (including most of the phones and tablets floating around, including the new Raspberry Pi 2). As many of you know, leveraging SIMD in modern CPUs is key for allowing Blosc to be one of the fastest compressors around, and if we wanted to be serious about ARM, NEON support had to be here, period.

The new NEON implementation of shuffle for Blosc has been entirely made by Lucian Marc, a summer student that joined the project at the beginning of July 2015. Lucian did a terrific work on implementing the shuffle filter NEON, and during the 2-months stage he did not only that, but he also had time to do a preliminary version of the bitshuffle filter as well (not completely functional yet, but as time allows, he plans to finish that).

Some hints on the measured increase in performance

So you might be asking, how fast can perform Blosc on an ARM with NEON? Well, let's start first by showing how fast it works on a Raspberry Pi 2 (Broadcom BCM2836 ARMv7 Quad Core Processor) having NEON and running Raspbian (gcc 4.7.2). To not bore people, we are going to show just decompression speeds:


It turns out that, when using the 4 cores and low compression levels, Blosc with NEON support already shows evidence that it can equal the performance of memcpy() on ARM. This is an important fact because I did not think that ARM performance was enough to allow Blosc doing that already. I was wrong.

Okay, so Blosc using NEON can be fast, but exactly how much when compared to a shuffle implementation in pure C? Here you have the figures for the generic C shuffle:


That means that NEON can accelerate the whole decompression process between 2x and 3x, which is pretty significant, and also speaks highly about the quality of Lucian's NEON implementation.

Does that mean that we can extrapolate these figures for all ARM processors out there? Not quite. In fact, the performance of a Raspberry Pi 2 is quite mild compared with other boards. So, let's see what is the performance on a ODROID-XU3 (although it has been replaced by ODROID-XU4, the XU3 has the same processor, so we are testing a pretty powerful CPU model here). This board comes with a Samsung Exynos5422 Cortex-A15 2.0 GHz quad core and Cortex™-A7 quad core CPUs, so it is a representative of the ARM Heterogeneous Multi-Processing solution (aka big.LITTLE). Here are its figures:


So, the first thing to note is the memcpy() speed that at 1.6 GB/s, is considerably faster than the RPi2 (< 0.9 GB/s). Yeah, this is a much more capable board from a computational point of view. The second thing is that decompression speed almost doubles the memcpy() speed. Again, I was very impressed because I did not expect this range of speeds at all. ARM definitely is getting in a situation where compression can be used for an advantage, computationally speaking.

The third thing to note is a bit disappointing though: why only 3 threads appear in the plot? Well, it turns out that the benchmark suite fails miserably when using 4 threads or more. As the Raspberry setup does not suffer from this problem at all, I presume that this is more related with the board or the libraries that come with the operating system (Ubuntu 14.04). This is rather unfortunate because I was really curious to see such an ARMv7 8-core beast running at full steam using the 8 threads. At any rate, time will tell if the problem is in the board or in Blosc itself.

Just to make the benchmarks a bit more complete, let me finish this benchmark section showing the performance using the generic C code for the shuffling algorithm:


If we compare with NEON figures for the ODROID board, we can see again an increase in speed of between 2x and 4x, which is crazy amazing (sorry if I seem a bit over-enthusiastic, but again, I was not really prepared for seeing this). Again, only figures for 2 threads are in this plot because the benchmark crashes for 3 threads (this is another hint that points to the fault being outside Blosc itself and not in its NEON implementation of the shuffle filter).

At decompression speeds of 3 GB/s and ~ 2 Watt of energy consumption, the ARM platform has one of the best bandwidth/Watt ratios that you can find in the market, and this can have (and will have) profound implications on how computations will be made in the short future (as the Mont Blanc initiative is trying to demonstrate).

What to expect from ARM/Blosc in the forthcoming months

This work on supporting ARM platforms is just the beginning. As ARM processors get more spread, and most specially, faster, we will need to refine the support for ARM in Blosc.

NEON support is only a part of the game, and things like efficient handling of ARM heterogeneous architectures (big.LITTLE) or making specific tweaks for ARM cache sizes will be critical so as to make of ARM a truly first-citizen for the Blosc ecosystem.

If you have ideas on what can be improved, and most specially how, we want to learn from you :) If you want to contribute code to the project, your pull requests are very welcome too! If you like what we are doing and want to see more of this, you can also sponsor us.

Hairy situation of Microsoft Windows compilers

Recently -- and to the requirement of a customer who recently sponsorized us -- I struggled a lot trying to get the maximum performance out of Visual Studio compilers. Here there are some quick benchmarks to show you an overview of the kind of performance that C-Blosc can reach on Windows.

First, let's use Visual Studio 2008 32-bit (extremely common platform because Python 2 still requires this compiler) and see how C-Blosc performs for decompressing on my laptop with Windows 7 Pro (64-bit) with an Intel i5-3380M @ 2.90GHz:


Now, let us see how the same benchmark performs with Visual Studio 2013:


Well, there is an important boost in speed, not only because a native 64-bit compiler has been used, but also because natural improvements in compiler technology.

At this point I wondered whether Visual Studio 2013 is doing just a decent job or if there is still some performance that can still be squeezed. So what kind of performance other compilers for Windows are reaching? For checking this, I tested the excellent MinGW-w64 compiler (thanks to Jack Pappas for suggesting this!). Here it is the result:


So, one can be seen that GCC 4.9 (included in latest Mingw-w64) can reach a performance that is still far beyond of what you can reach with modern Microsoft compilers (specially for lower compression levels, which is an important scenario when maximum speed is required), and very close to what I get on Linux.

Possibly the newest Visual Studio 2015 would allow more performance, but IMO, there is still some time until this is more spread, whereas GCC 4.9 (with GCC 5.1 starting to show up) is already shipping in many distributions, Windows and Mac OSX, which gives GCC a lot of advantage with respect to Visual Studio.

With regards the reason on why GCC shows that much performance for C-Blosc is probably a consequence of how it has been developed. It turns out that C-Blosc main development platform was (and still is) Linux/GCC, and after many profile/optimize cycles, this tends to favor that combination respect to others.

Provided this, and regarding the original request to reach optimal performance on Windows / Visual Studio 2013 64-bit environments, I ended implementing an example where existing Visual Studio applications can dynamically link a C-Blosc DLL that is in the PATH. You can see how this technique works at:

This is quite interesting because at compilation time you don't need to make reference to the C-Blosc DLL at all. I.e. the next is enough for compiling the example above:

cl /Ox /Fewin-dynamic-linking.exe /I..\blosc win-dynamic-linking.c

And that's all. After that, you only need to place the C-Blosc DLL anywhere in your PATH and it will be dynamically detected. I have tested that with different combinations of compilers (e.g. Visual Studio for the app, and MinGW-w64 for the DLL library) and it works beautifully. I think this is quite powerful and certainly I don't know an equivalent technique for Unix (although it probably exists also), allowing to use top-performance DLLs in your apps using different compilers in a quite easy way.

In case you have more hints on how to get better performance on Windows, please tell us.

New 'bitshuffle' filter

Although Blosc was meant for hosting more than one filter since day 0, it has traditionally came with just a single filter, known as 'shuffle', meant for shuffling bytes in binary blocks. Today this has changed, and c-blosc has officially received a new filter called 'bitshuffle' (a backport of the one included in the bithsuffle project). And you guess it, it works in a very similar way than 'shuffle', just that the shuffling happens at the bit level and not at the byte one.

Just for whetting your appetite here there are some small synthetic benchmarks on what you can expect from the newcomer. I'll start using my own laptop (Intel i5-3380M @ 2.90GHz, GCC 4.9.1, Ubuntu 14.10) and showing how the benchmark that comes with c-blosc performs with the LZ4 compressor and the regular 'shuffle' filter:

$ bench/bench lz4 shuffle single 2
Blosc version: ($Date:: 2015-05-27 #$)
List of supported compressors in this build: blosclz,lz4,lz4hc,snappy,zlib
Supported compression libraries:
  BloscLZ: 1.0.5
  LZ4: 1.7.0
  Snappy: 1.1.1
  Zlib: 1.2.8
Using compressor: lz4
Using shuffle type: shuffle
Running suite: single
--> 2, 2097152, 8, 19, lz4, shuffle
********************** Run info ******************************
Using synthetic data with 19 significant bits (out of 32)
Dataset size: 2097152 bytes     Type size: 8 bytes
Working set: 256.0 MB           Number of threads: 2
********************** Running benchmarks *********************
memcpy(write):            529.1 us, 3780.3 MB/s
memcpy(read):             245.6 us, 8143.4 MB/s
Compression level: 0
comp(write):      267.3 us, 7483.3 MB/s   Final bytes: 2097168  Ratio: 1.00
decomp(read):     200.0 us, 9997.5 MB/s   OK
Compression level: 1
comp(write):      462.8 us, 4321.1 MB/s   Final bytes: 554512  Ratio: 3.78
decomp(read):     246.6 us, 8111.5 MB/s   OK
Compression level: 2
comp(write):      506.6 us, 3947.7 MB/s   Final bytes: 498960  Ratio: 4.20
decomp(read):     331.9 us, 6025.1 MB/s   OK
Compression level: 3
comp(write):      486.8 us, 4108.8 MB/s   Final bytes: 520824  Ratio: 4.03
decomp(read):     233.5 us, 8565.2 MB/s   OK
Compression level: 4
comp(write):      497.9 us, 4017.0 MB/s   Final bytes: 332112  Ratio: 6.31
decomp(read):     258.3 us, 7743.8 MB/s   OK
Compression level: 5
comp(write):      474.6 us, 4214.5 MB/s   Final bytes: 327112  Ratio: 6.41
decomp(read):     287.8 us, 6949.0 MB/s   OK
Compression level: 6
comp(write):      558.0 us, 3584.4 MB/s   Final bytes: 226308  Ratio: 9.27
decomp(read):     284.8 us, 7022.7 MB/s   OK
Compression level: 7
comp(write):      689.9 us, 2899.1 MB/s   Final bytes: 211880  Ratio: 9.90
decomp(read):     363.0 us, 5509.1 MB/s   OK
Compression level: 8
comp(write):      691.9 us, 2890.6 MB/s   Final bytes: 220464  Ratio: 9.51
decomp(read):     385.5 us, 5188.5 MB/s   OK
Compression level: 9
comp(write):      567.0 us, 3527.6 MB/s   Final bytes: 132154  Ratio: 15.87
decomp(read):     627.3 us, 3188.2 MB/s   OK

Round-trip compr/decompr on 7.5 GB
Elapsed time:       3.6 s, 4755.3 MB/s

Now, look at what bitshuffle can do with the same datasets and compressor:

$ bench/bench lz4 bitshuffle single 2
Supported compression libraries:
  BloscLZ: 1.0.5
  LZ4: 1.7.0
  Snappy: 1.1.1
  Zlib: 1.2.8
Using compressor: lz4
Using shuffle type: bitshuffle
Running suite: single
--> 2, 2097152, 8, 19, lz4, bitshuffle
Using synthetic data with 19 significant bits (out of 32)
Dataset size: 2097152 bytes     Type size: 8 bytes
Working set: 256.0 MB           Number of threads: 2
memcpy(write):            518.5 us, 3857.3 MB/s
memcpy(read):             248.6 us, 8045.7 MB/s
Compression level: 0
comp(write):      259.5 us, 7706.1 MB/s   Final bytes: 2097168  Ratio: 1.00
decomp(read):     217.5 us, 9196.3 MB/s   OK
Compression level: 1
comp(write):     1099.0 us, 1819.9 MB/s   Final bytes: 72624  Ratio: 28.88
decomp(read):     824.2 us, 2426.5 MB/s   OK
Compression level: 2
comp(write):     1093.2 us, 1829.5 MB/s   Final bytes: 71376  Ratio: 29.38
decomp(read):    1293.2 us, 1546.5 MB/s   OK
Compression level: 3
comp(write):     1084.5 us, 1844.2 MB/s   Final bytes: 69200  Ratio: 30.31
decomp(read):    1331.2 us, 1502.4 MB/s   OK
Compression level: 4
comp(write):     1193.2 us, 1676.2 MB/s   Final bytes: 42480  Ratio: 49.37
decomp(read):     833.8 us, 2398.7 MB/s   OK
Compression level: 5
comp(write):     1190.9 us, 1679.4 MB/s   Final bytes: 42928  Ratio: 48.85
decomp(read):     880.2 us, 2272.2 MB/s   OK
Compression level: 6
comp(write):      969.7 us, 2062.5 MB/s   Final bytes: 32000  Ratio: 65.54
decomp(read):     854.8 us, 2339.8 MB/s   OK
Compression level: 7
comp(write):     1056.2 us, 1893.6 MB/s   Final bytes: 40474  Ratio: 51.81
decomp(read):     960.8 us, 2081.7 MB/s   OK
Compression level: 8
comp(write):     1018.5 us, 1963.8 MB/s   Final bytes: 28050  Ratio: 74.76
decomp(read):     966.8 us, 2068.7 MB/s   OK
Compression level: 9
comp(write):     1161.7 us, 1721.6 MB/s   Final bytes: 25188  Ratio: 83.26
decomp(read):    1245.5 us, 1605.8 MB/s   OK

Round-trip compr/decompr on 7.5 GB
Elapsed time:       7.8 s, 2161.7 MB/s

Amazing! the compression ratios are much higher (up to 83x vs 16x) which is very exciting. The drawback is that with 'bitshuffle' the compression/decompression speed is between 2x and 4x slower than with the regular 'shuffle'. In fact, this slowdown is unusually light because the additional work should be much more (1 byte has 8 bits), so that's not too bad.

But we have some good news: besides SSE2, 'bitshuffle' also supports AVX2 SIMD instructions (as 'shuffle' itself) but unfortunately my laptop does not have them (pre-Haswell). So let's run the benchmark above in a AVX2 server (Intel Xeon E3-1240 v3 @ 3.40GHz, GCC 4.9.3, Gentoo 2.2):

$ bench/bench lz4 bitshuffle single 8
Supported compression libraries:
  BloscLZ: 1.0.5
  LZ4: 1.7.0
  Snappy: 1.1.1
  Zlib: 1.2.8
Using compressor: lz4
Using shuffle type: bitshuffle
Running suite: single
--> 8, 2097152, 8, 19, lz4, bitshuffle
Using synthetic data with 19 significant bits (out of 32)
Dataset size: 2097152 bytes     Type size: 8 bytes
Working set: 256.0 MB           Number of threads: 8
memcpy(write):            264.9 us, 7551.1 MB/s
memcpy(read):             174.1 us, 11488.6 MB/s
Compression level: 0
comp(write):      173.1 us, 11551.7 MB/s          Final bytes: 2097168  Ratio: 1.00
decomp(read):     119.3 us, 16765.2 MB/s          OK
Compression level: 1
comp(write):      271.8 us, 7358.1 MB/s   Final bytes: 72624  Ratio: 28.88
decomp(read):     225.7 us, 8862.7 MB/s   OK
Compression level: 2
comp(write):      275.7 us, 7253.7 MB/s   Final bytes: 71376  Ratio: 29.38
decomp(read):     229.2 us, 8724.8 MB/s   OK
Compression level: 3
comp(write):      274.5 us, 7285.9 MB/s   Final bytes: 69200  Ratio: 30.31
decomp(read):     238.8 us, 8374.6 MB/s   OK
Compression level: 4
comp(write):      249.5 us, 8015.5 MB/s   Final bytes: 42480  Ratio: 49.37
decomp(read):     229.8 us, 8701.6 MB/s   OK
Compression level: 5
comp(write):      249.1 us, 8028.1 MB/s   Final bytes: 42928  Ratio: 48.85
decomp(read):     243.9 us, 8198.8 MB/s   OK
Compression level: 6
comp(write):      332.4 us, 6017.5 MB/s   Final bytes: 32000  Ratio: 65.54
decomp(read):     322.2 us, 6206.4 MB/s   OK
Compression level: 7
comp(write):      431.9 us, 4630.2 MB/s   Final bytes: 40474  Ratio: 51.81
decomp(read):     437.6 us, 4570.7 MB/s   OK
Compression level: 8
comp(write):      421.5 us, 4745.0 MB/s   Final bytes: 28050  Ratio: 74.76
decomp(read):     437.2 us, 4574.5 MB/s   OK
Compression level: 9
comp(write):      941.1 us, 2125.2 MB/s   Final bytes: 25188  Ratio: 83.26
decomp(read):     674.7 us, 2964.2 MB/s   OK

Round-trip compr/decompr on 7.5 GB
Elapsed time:       2.8 s, 6047.8 MB/s

Wow, in this case we are having compression speed peaks even higher than a memcpy (8 GB/s vs 7.5 GB/s), and decompression speed is pretty good too (8.8 GB/s vs 11.5 GB/s memcpy). With AVX2 support, 'bitshuffle' does have a pretty good performance. But yeah, this server has 8 physical cores, so we are not actually comparing pears with pears. So let's re-run the benchmark with just 2 threads:

$ bench/bench lz4 bitshuffle single 2
Supported compression libraries:
  BloscLZ: 1.0.5
  LZ4: 1.7.0
  Snappy: 1.1.1
  Zlib: 1.2.8
Using compressor: lz4
Using shuffle type: bitshuffle
Running suite: single
Using synthetic data with 19 significant bits (out of 32)
Dataset size: 2097152 bytes     Type size: 8 bytes
Working set: 256.0 MB           Number of threads: 2
memcpy(write):            253.9 us, 7877.5 MB/s
memcpy(read):             174.1 us, 11488.8 MB/s
Compression level: 0
comp(write):      133.4 us, 14995.6 MB/s          Final bytes: 2097168  Ratio: 1.00
decomp(read):     117.5 us, 17026.6 MB/s          OK
Compression level: 1
comp(write):      604.1 us, 3310.7 MB/s   Final bytes: 72624  Ratio: 28.88
decomp(read):     431.2 us, 4638.3 MB/s   OK
Compression level: 2
comp(write):      624.3 us, 3203.5 MB/s   Final bytes: 71376  Ratio: 29.38
decomp(read):     452.3 us, 4421.5 MB/s   OK
Compression level: 3
comp(write):      623.7 us, 3206.8 MB/s   Final bytes: 69200  Ratio: 30.31
decomp(read):     442.3 us, 4521.9 MB/s   OK
Compression level: 4
comp(write):      585.2 us, 3417.6 MB/s   Final bytes: 42480  Ratio: 49.37
decomp(read):     395.3 us, 5058.9 MB/s   OK
Compression level: 5
comp(write):      530.0 us, 3773.4 MB/s   Final bytes: 42928  Ratio: 48.85
decomp(read):     400.5 us, 4994.0 MB/s   OK
Compression level: 6
comp(write):      542.6 us, 3686.0 MB/s   Final bytes: 32000  Ratio: 65.54
decomp(read):     426.7 us, 4687.2 MB/s   OK
Compression level: 7
comp(write):      605.6 us, 3302.4 MB/s   Final bytes: 40474  Ratio: 51.81
decomp(read):     494.5 us, 4044.5 MB/s   OK
Compression level: 8
comp(write):      588.1 us, 3400.7 MB/s   Final bytes: 28050  Ratio: 74.76
decomp(read):     487.3 us, 4104.6 MB/s   OK
Compression level: 9
comp(write):      692.5 us, 2888.2 MB/s   Final bytes: 25188  Ratio: 83.26
decomp(read):     591.4 us, 3381.8 MB/s   OK

Round-trip compr/decompr on 7.5 GB
Elapsed time:       3.9 s, 4294.1 MB/s

Now, for 2 threads we are getting times that are about 2x slower than for 8 threads. But the interesting thing here is that the compression speed is still ~2x faster than my laptop (peaks at 3.7 GB/s vs 1.8 GB/s) and the same goes for decompression (peaks at 5 GB/s vs 2.4 GB/s). Agreed, the server can run at 3.4GHz vs 2.9 GHz of my laptop, but this alone cannot explain the difference in speed, so the big responsible for the speedup is the AVX2 support in 'bitshuffle'.

In summary, the new 'bitshuffle' filter is very good news for the users of the Blosc ecosystem because it adds yet another powerful resource that will help in the fight for storing datasets with less space, but still keeping good performance. Of course, this is just a quick experiment with synthetic data, but I am pretty sure that the new 'bitshuffle' filter will find a good niche in real world datasets. Anyone interested in contributing some real data benchmark?

I'd like to thank Kiyo Masui for his help in this 'bitshuffle' backport.

Seeking Sponsorship for Bcolz/Blosc

Dear Everyone,

as you may or may not know, the Blosc compressor has become the basis for some novel, innovative technological experiments in the PyData space. Especially the Bcolz and Bloscpack projects which provide a way to perform out-of-core computations on column based datasets have become particularly interesting for the analysis of medium-sized time-series datasets.

In this post, we would like to convince you to give us some money to foster the project, development and accelerate growth of our community. Historically, it has always been a difficult endeavour to monetize open-source development and so, below is a non-exhaustive list of potential models that we are considering:

  • Direct sponsoring / Donations

    This involves paying either a single lump-sum or monthly installments to foster continued development and innovation. This type of sponsoring isn't bound to any specific goal or feature and would allow us for example maintain and release the projects regularly.

  • Feature-driven sponsoring

    Paying for specific features to be implemented, bugs to be fixed or paying to have a voice when it comes to prioritizing items in the issue-tracker(s).

  • Hiring us as freelancers for Blosc/Bcolz projects

    This means that you hire one or both of us to implement a project that uses bcolz inside your company. Any bugs we find or improvements that need to be made would flow back into the open source code-base.

  • Hiring us as part-time freelancers for general projects

    This means you hire one or both of us as part-time freelancers for two to three days a week to work on general projects. These can be related to Python and data or open-source work on other projects. This would allow us to spend the remaining days on Blosc/Bcolz.

  • PhD positions

    There are still a few interesting theoretical aspects to be unlocked, for example certain mathematical properties of the shuffle filter and a compressed extension of the external-memory-model (EMM) to analyse the runtime of Blosc style out-of-core algorithms and Bcolz operations in general.

We welcome any feedback regarding the above options and please do tell us about any additional models that may be interesting to us or for you.

With best wishes and looking forward to your input,

Francesc Alted and Valentin Haenel

Compress Me, Stupid!

How it all started





Compressing Usenet News




LZO and the explosion of compression technology





A new compressor for PyTables/HDF5






Blosc was born



