Counting k-mers on EC2 - huh?

(This blog post was mightily helped by Qingpeng Zhang, the first author of the paper; he wrote the pipeline. I just ran it a bunch :)

We have been benchmarking k-mer counters in a variety of ways, in preparation for an upcoming paper. As with the diginorm paper we are automating everything, so I thought heck, why not try running it on a bunch of different EC2 machines to see how variable their performance is? Then, I ruined that idea by varying the machine configuration instead of using identical machines :).

The overall pipeline takes about 30 hours to run, and for this blog post I am focusing in on one particular benchmark -- the length of time it takes the various programs to generate and count the abundance distribution of the 22-mers present in 48.7 m short reads, or about 5 GB of data. We used Jellyfish, DSK, khmer, and Tallymer; we're planning to try out KMC, also, but didn't get to it for this post.

I ran the counting on four machines: our local server, which is your standard reasonably high performance Linux box; two m2.2xlarge Amazon EC2 instances (34 GB RAM), one with the default setup and one with a 1 TB EBS disk with 100 IOPS configuration; and an m2.4xlarge Amazon EC2 instance, with 68 GB RAM. I chose different zones for all three EC2 machines. The max memory required was about 24 GB, I think.

I analyzed everything within an IPython Notebook, which is available here. If you want to play with the data, grab the master branch of https://github.com/ged-lab/2013-khmer-counting.git, go to the notebooks/ subdirectory, run the ipython notebook server, and open the 'khmer-counting-compare' notebook. All the data necessary to run the notebook is there.

The results are a bit weird!

First, let's look at the overall walltime it took to count (Figure 1). Jellyfish did a really nice job, outperforming everything else handily. Tallymer (the oldest of the programs) was by far the slowest; DSK and khmer were in the middle, depending on machine configuration.

walltime graph

Fig 1. The time (in seconds) to count the k-mers and generate a k-mer abundance histogram for 48.7m short reads from a soil metagenome, using several different k-mer counting packages.

A few points about Figure 1 --

  1. Why no errorbars? Time is money, baby -- this already cost quite enough, thankyouverymuch.
  2. Doesn't this mean Jellyfish is just plain better? Well, read on (this and other blog posts).
  3. Why did everything perform worse on the IOPS configured EC2 instance? Heck if I know. Note that khmer has the least disk access of anything, which suggests that disk performance just downright sucked on the IOPS instance.

Now let's take a look at how efficiently the programs were using compute. Figure 2 shows the ratio of user time (which is approximately seconds spent by each core, summed, minus time spent in the OS critical sections) to walltime (how long the whole process took).

usertime ratio graph

Fig 2. The ratio of user time (seconds x cores, omitting system time) to walltime (seconds) when generating the k-mer abundance histogram for 48.7m reads. Note that Jellyfish and khmer were both run with 8 threads, while Tallymer is unthreaded and DSK was run with 1 thread by mistake.

A few points about figure 2:

  1. Wowsers! We ran both Jellyfish (red) and khmer (blue) with 8 threads, and the results suggest that they both used them very efficiently on our own server -- a factor of about 8 suggests that they were merrily blasting along doing computing, hindered little if at all by disk access! Since our local server has great I/O (I guess?), that probably accounts for it. Note: I think this also means our locking and multithreading implementations are really good (read this and this for more information; this is a general threaded API for sequence reading, hint hint).

  2. DSK and Tallymer both did a poor job of using multiple CPUs. Well, to be fair, Tallymer doesn't support threads. And while DSK does, we forgot to run it with 8 threads. Oops. Betcha performance increases!

  3. If I/O is what matters here, m2.4xlarge has what appears to be the next best I/O -- khmer got up to a ratio of 7.09. Even on the IOPS system, khmer did OK.

    In general, I think these benchmarks show that I/O is the Achilles heel of the various k-mer counting systems. I don't know why the IOPS configuration would be worse for that, though.


Finally, let's look at system time. Figure 3 shows total system time (in seconds) for each program/machine configuration. System time includes all disk access, but not, I think, cache invalidation or other things like that.

system time graph

Fig 3. System time (primarily disk access) for generating the k-mer abundance histogram for 48.7m reads.

Thoughts:

  1. This more or less confirms what we inferred from the other graphs: I/O is a bottleneck. Jellyfish, for whatever reason, disagrees with that statement, so they must be doing something clever :)

Some concluding thoughts for this initial blog post --

  1. Don't go around claiming that one k-mer counter is better, based on this! We omitted at least one good lookin' published k-mer counter (KMC) and may go take a look at BFCounter and Turtle too. Plus, we screwed up our DSK benchmarking.

  2. Note we've said nothing about memory or disk usage here. Indeed.

  3. At the end of the day, I don't understand what's going on with the IOPS-optimized EBS instances. Did I choose too low a number? (100 IOPS). Did I pick too big a hard drive? Is our access pattern lousy? Or what?

    Note that this post from Garantia Data ended up with similar questions :).

    Here, I think there are probably a variety of access patterns, but the basic thing that's going on is (a) reading a steady stream of data sequentially, and (b) for most of the programs, writing stuff to disk steadily. (khmer does not do any disk access beyond reading in the sequence file here.)


Anyway, that's the first of what will probably be several blog posts on k-mer counting performance. This is a real data set, and a real set of well-used programs, so I think it's a pretty good benchmark; let me know if you disagree and want to see something else...

--titus

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