[Beowulf] Accelerator for data compressing

Joe Landman landman at scalableinformatics.com
Fri Oct 3 11:45:43 EDT 2008


Carsten Aulbert wrote:

> If 7-zip can only compress data at a rate of less than say 5 MB/s (input
> data) I can much much faster copy the data over uncompressed regardless
> of how many unused cores I have in the system. Exactly for these cases I
> would like to use all cores available to compress the data fast in order
> to increase the throughput.

This is fundamentally the issue.  If the compression time plus the 
tranmit time for the compressed data is greater than the transmit time 
for the uncompressed data, then the compression may not be worth it. 
Sure, if it is nothing but text files, you may get 60-80+% compression 
rates.  But for the case of (non-pathological) binary data, it might be 
only a few percent.   So in this case, even if you could get a few 
percent delta from the compression, is that worth all the extra time you 
spend to get it?

At the end of the day the question is how much lossless compression can 
you do in a short enough time for it to be meaningful in terms of 
transmitting the data?

> 
> Do I miss something vital?

Nope.  You got it nailed.

Several months ago, I tried moving about 600 GB of data from an old 
server to a JackRabbit.  The old server and the JackRabbit had a gigabit 
link between them.  We regularly saw 45 MB scp rates (one of the chips 
in the older server was a Broadcom).

I tried this with and without compression.  With compression (simple 
gzip), the copy took something like 28 hours ( a little more than a 
day).  Without compression, it was well under 10 hours.

In this case, compression (gzip) was not worth it.  The command I used 
for the test was

uncompressed:

	cd /directory
	tar -cpf - ./ | ssh jackrabbit "cd /directory ; tar -xpvf - "

compressed:

	cd /directory
	tar -czpf - ./ | ssh jackrabbit "cd /directory ; tar -xzpvf - "

if you want to spend more time, use "j" rather than "z" in the options.

YMMV, but I have been convinced that, apart from specific use cases with 
text only documents or documents known to compress quickly/well, that 
compression prior to transfer may waste more time than it saves.

This said, if someone has a parallel hack of gzip or similar we can pipe 
through, by all means, I would be happy to try it. But it would have to 
be pretty darned efficient.

100MB/s means 1 byte transmitted,on average, in 10 nanoseconds.  Which 
means for compression to be meaningful, you would need to compute for 
less time than that to increase the information density.  Put another 
way, 1 MB takes about 10 ms to send over a gigabit link.  For 
compression to be meaningful, you need to compress this 1MB in far less 
than 10 ms and still transmit it in that time.  Assuming that any 
compression algorithm has to walk through data at least once,  A 1 GB/s 
memory subsystem takes about 1 ms to walk through this data at least 
once, so you need as few passes as possible through the data set to 
construct the compressed representation, as you will still have on the 
order of 1E+5 bytes to send.

I am not saying it is hopeless, just hard for complex compression 
schemes (bzip2, etc).  When we get enough firepower in the CPU (or maybe 
GPU ... hmmmm) the situation may improve.

GPU as a compression engine?  Interesting ...

Joe

> 
> Cheers
> 
> Carsten

-- 
Joseph Landman, Ph.D
Founder and CEO
Scalable Informatics LLC,
email: landman at scalableinformatics.com
web  : http://www.scalableinformatics.com
        http://jackrabbit.scalableinformatics.com
phone: +1 734 786 8423 x121
fax  : +1 866 888 3112
cell : +1 734 612 4615
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