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Unzip benchmark on AWS EC2 c3.large vs c4.large

29 November 2017 18 comments   Go, Mozilla, Linux, Python


Datadog monitoring of time to dump and extract zip files in staging server
This web app I'm working on gets a blob of bytes from a HTTP POST. The nature of the blob is a 100MB to 1,100MB blob of a zip file. What my app currently does is that it takes this byte buffer, uses Python's built in zipfile to extract all its content to a temporary directory. A second function then loops over the files within this extracted tree and processes each file in multiple threads with concurrent.futures.ThreadPoolExecutor. Here's the core function itself:

@metrics.timer_decorator('upload_dump_and_extract')
def dump_and_extract(root_dir, file_buffer):
    zf = zipfile.ZipFile(file_buffer)
    zf.extractall(root_dir)

So far so good.

Speed Speed Speed

I quickly noticed that this is amounting to quite a lot of time spent doing the unzip and the writing to disk. What to do????

At first I thought I'd shell out to good old unzip. E.g. unzip -d /tmp/tempdirextract /tmp/input.zip but that has two flaws:

1) I'd first have to dump the blob of bytes to disk and do the overhead of shelling out (i.e. Python subprocess)
2) It's actually not faster. Did some experimenting and got the same results at Alex Martelli in this Stackoverflow post

Compute EC2 instance types
What about disk speed? Yeah, this is likely to be a part of the total time. The servers that run the symbols.mozilla.org service runs on AWS EC2 c4.large. This only has EBS (Elastic Block Storage). However, AWS EC2 c3.large looks interesting since it's using SSD disks. That's probably a lot faster. Right?

Note! For context, the kind of .zip files I'm dealing with contain many small files and often 1-2 really large ones.

EC2s Benchmarking

I create two EC2 nodes to experiment on. One c3.large and one c4.large. Both running Ubuntu 16.04.

Next, I have this little benchmarking script which loops over a directory full of .zip files between 200MB-600MB large. Roughly 10 of them. It then loads each one, one at a time, into memory and calls the dump_and_extract. Let's run it on each EC2 instance:

On c4.large

c4.large$ python3 fastest-dumper.py /tmp/massive-symbol-zips
138.2MB/s            291.1MB              2.107s
146.8MB/s            314.5MB              2.142s
144.8MB/s            288.2MB              1.990s
84.5MB/s             532.4MB              6.302s
146.6MB/s            314.2MB              2.144s
136.5MB/s            270.7MB              1.984s
85.9MB/s             518.9MB              6.041s
145.2MB/s            306.8MB              2.113s
127.8MB/s            138.7MB              1.085s
107.3MB/s            454.8MB              4.239s
141.6MB/s            251.2MB              1.774s

Average speed: 127.7MB/s
Median speed:  138.2MB/s

Average files created:       165
Average directories created: 129

On c3.large

c3.large$ python3 fastest-dumper.py -t /mnt/extracthere /tmp/massive-symbol-zips
105.4MB/s            290.9MB              2.761s
98.1MB/s             518.5MB              5.287s
108.1MB/s            251.2MB              2.324s
112.5MB/s            294.3MB              2.615s
113.7MB/s            314.5MB              2.767s
106.3MB/s            291.5MB              2.742s
104.8MB/s            291.1MB              2.778s
114.6MB/s            248.3MB              2.166s
114.2MB/s            248.2MB              2.173s
105.6MB/s            298.1MB              2.823s
106.2MB/s            297.6MB              2.801s
98.6MB/s             521.4MB              5.289s

Average speed: 107.3MB/s
Median speed:  106.3MB/s

Average files created:       165
Average directories created: 127

What the heck!? The SSD based instance is 23% slower!

I ran it a bunch of times and the average and median numbers are steady. c4.large is faster than c3.large at unzipping large blobs to disk. So much for that SSD!

Something Weird Is Going On

It's highly likely that the unzipping work is CPU bound and that most of those, for example, 5 seconds is spent unzipping and only a small margin is the time it takes to write to disk.

If the unzipping CPU work is the dominant "time consumer" why is there a difference at all?!

Or, is the "compute power" the difference between c3 and c4 and disk writes immaterial?

For the record, this test clearly demonstrates that the locally mounted SSD drive is 600% faster than ESB.

c3.large$ dd if=/dev/zero of=/tmp/1gbtest bs=16k count=65536
65536+0 records in
65536+0 records out
1073741824 bytes (1.1 GB, 1.0 GiB) copied, 16.093 s, 66.7 MB/s
c3.large$ sudo dd if=/dev/zero of=/mnt/1gbtest bs=16k count=65536
65536+0 records in
65536+0 records out
1073741824 bytes (1.1 GB, 1.0 GiB) copied, 2.62728 s, 409 MB/s

Let's try again. But instead of using c4.large and c3.large, let's use the beefier c4.4xlarge and c3.4xlarge. Both have 16 vCPUs.

c4.4xlarge

c4.4xlarge$ python3 fastest-dumper.py /tmp/massive-symbol-zips
130.6MB/s            553.6MB              4.238s
149.2MB/s            297.0MB              1.991s
129.1MB/s            529.8MB              4.103s
116.8MB/s            407.1MB              3.486s
147.3MB/s            306.1MB              2.077s
151.9MB/s            248.2MB              1.634s
140.8MB/s            292.3MB              2.076s
146.8MB/s            288.0MB              1.961s
142.2MB/s            321.0MB              2.257s

Average speed: 139.4MB/s
Median speed:  142.2MB/s

Average files created:       148
Average directories created: 117

c3.4xlarge

c3.4xlarge$ python3 fastest-dumper.py -t /mnt/extracthere /tmp/massive-symbol-zips
95.1MB/s             502.4MB              5.285s
104.1MB/s            303.5MB              2.916s
115.5MB/s            313.9MB              2.718s
105.5MB/s            517.4MB              4.904s
114.1MB/s            288.1MB              2.526s
103.3MB/s            555.9MB              5.383s
114.0MB/s            288.0MB              2.526s
109.2MB/s            251.2MB              2.300s
108.0MB/s            291.0MB              2.693s

Average speed: 107.6MB/s
Median speed:  108.0MB/s

Average files created:       150
Average directories created: 119

What's going on!? The time it takes to unzip and write to disk is, on average, the same for c3.large as c3.4xlarge!

Is Go Any Faster?

I need a break. As mentioned above, the unzip command line program is not any better than doing it in Python. But Go is faster right? Right?

Please first accept that I'm not a Go programmer even though I can use it to build stuff but really my experience level is quite shallow.

Here's the Go version. Critical function that does the unzipping and extraction to disk here:

func DumpAndExtract(dest string, buffer []byte, name string) {
    size := int64(len(buffer))
    zipReader, err := zip.NewReader(bytes.NewReader(buffer), size)
    if err != nil {
        log.Fatal(err)
    }
    for _, f := range zipReader.File {
        rc, err := f.Open()
        if err != nil {
            log.Fatal(err)
        }
        defer rc.Close()
        fpath := filepath.Join(dest, f.Name)
        if f.FileInfo().IsDir() {
            os.MkdirAll(fpath, os.ModePerm)
        } else {
            // Make File
            var fdir string
            if lastIndex := strings.LastIndex(fpath, string(os.PathSeparator)); lastIndex > -1 {
                fdir = fpath[:lastIndex]
            }
            err = os.MkdirAll(fdir, os.ModePerm)
            if err != nil {
                log.Fatal(err)
            }
            f, err := os.OpenFile(
                fpath, os.O_WRONLY|os.O_CREATE|os.O_TRUNC, f.Mode())
            if err != nil {
                log.Fatal(err)
            }
            defer f.Close()

            _, err = io.Copy(f, rc)
            if err != nil {
                log.Fatal(err)
            }
        }
    }
}

And the measurement is done like this:

size := int64(len(content))
t0 := time.Now()
DumpAndExtract(tmpdir, content, filename)
t1 := time.Now()
speed := float64(size) / t1.Sub(t0).Seconds()

It's not as sophisticated (since it's only able to use /tmp) but let's just run it see how it compares to Python:

c4.4xlarge$ mkdir ~/GO
c4.4xlarge$ export GOPATH=~/GO
c4.4xlarge$ go get github.com/pyk/byten
c4.4xlarge$ go build unzips.go
c4.4xlarge$ ./unzips /tmp/massive-symbol-zips
56MB/s         407MB          7.27804954
74MB/s         321MB          4.311504933
75MB/s         288MB          3.856798853
75MB/s         292MB          3.90972474
81MB/s         248MB          3.052652168
58MB/s         530MB          9.065985117
59MB/s         554MB          9.35237202
75MB/s         297MB          3.943132388
74MB/s         306MB          4.147176578

Average speed:    70MB/s
Median speed:     81MB/s

So... Go is, on average, 40% slower than Python in this scenario. Did not expect that.

In Conclusion

No conclusion. Only confusion.

I thought this would be a lot clearer and more obvious. Yeah, I know it's crazy to measure two things at the same time (unzip and disk write) but the whole thing started with a very realistic problem that I'm trying to solve. The ultimate question was; will the performance benefit from us moving the web servers from AWS EC2 c4.large to c3.large and I think the answer is no.

UPDATE (Nov 30, 2017)

Here's a horrible hack that causes the extraction to always go to /dev/null:

class DevNullZipFile(zipfile.ZipFile):
    def _extract_member(self, member, targetpath, pwd):
        # member.is_dir() only works in Python 3.6
        if member.filename[-1] == '/':
            return targetpath
        dest = '/dev/null'
        with self.open(member, pwd=pwd) as source, open(dest, "wb") as target:
            shutil.copyfileobj(source, target)
        return targetpath


def dump_and_extract(root_dir, file_buffer, klass):
    zf = klass(file_buffer)
    zf.extractall(root_dir)

And here's the outcome of running that:

c4.4xlarge$ python3 fastest-dumper.py --dev-null /tmp/massive-symbol-zips
170.1MB/s            297.0MB              1.746s
168.6MB/s            306.1MB              1.815s
147.1MB/s            553.6MB              3.765s
132.1MB/s            407.1MB              3.083s
145.6MB/s            529.8MB              3.639s
175.4MB/s            248.2MB              1.415s
163.3MB/s            321.0MB              1.965s
162.1MB/s            292.3MB              1.803s
168.5MB/s            288.0MB              1.709s

Average speed: 159.2MB/s
Median speed:  163.3MB/s

Average files created:       0
Average directories created: 0

I ran it a few times to make sure the numbers are stable. They are. This is on the c4.4xlarge.

So, the improvement of writing to /dev/null instead of the ESB /tmp is 15%. Kinda goes to show how much of the total time is spent reading the ZipInfo file object.

For the record, the same comparison on the c3.4xlarge was 30% improvement when using /dev/null.

Also for the record, if I replace that line shutil.copyfileobj(source, target) above with pass, the average speed goes from 159.2MB/s to 112.8GB/s but that's not a real value of any kind.

UPDATE (Nov 30, 2017)

Here's the same benchmark using c5.4xlarge instead. So, still EBS but...
"3.0 GHz Intel Xeon Platinum processors with new Intel Advanced Vector Extension 512 (AVX-512) instruction set"

Let's run it on this supposedly faster CPU:

c5.4xlarge$ python3 fastest-dumper.py /tmp/massive-symbol-zips
165.6MB/s            314.6MB              1.900s
163.3MB/s            287.7MB              1.762s
155.2MB/s            278.6MB              1.795s
140.9MB/s            513.2MB              3.643s
137.4MB/s            556.9MB              4.052s
134.6MB/s            531.0MB              3.946s
165.7MB/s            314.2MB              1.897s
158.1MB/s            301.5MB              1.907s
151.6MB/s            253.8MB              1.674s
146.9MB/s            502.7MB              3.422s
163.7MB/s            288.0MB              1.759s

Average speed: 153.0MB/s
Median speed:  155.2MB/s

Average files created:       150
Average directories created: 119

So that is, on average, 10% faster than c4.4xlarge.

Is it 10% more expensive? For a 1-year reserved instance, it's $0.796 versus $0.68 respectively. I.e. 15% more expensive. In other words, in this context it's 15% more $$$ for 10% more processing power.

UPDATE (Jan 24, 2018)

I can almost not believe it!

Thanks you Oliver who discovered (see comment below) a blaring mistake in my last conclusion. The for reserved instances (which is what we use on my Mozilla production servers) the c5.4xlarge is actually cheaper than c4.4xlarge. What?!

In my previous update I compared c4.4xlarge and c5.4xlarge and concluded that c5.4xlarge is 10% faster but 15% more expensive. That actually made sense. Fancier servers, more $$$. But it's not like that in the real world. See for yourself:

c4.4xlarge
c4.4xlarge

c5.4xlarge
c5.4xlarge

Why didn't I know about machma?!

07 June 2017 0 comments   Go, MacOSX, Linux


"machma - Easy parallel execution of commands with live feedback"

This is so cool! https://github.com/fd0/machma

It's a command line program that makes it really easy to run any command line program in parallel. I.e. in separate processes with separate CPUs.

Something network bound

Suppose I have a file like this:

▶ wc -l urls.txt
      30 urls.txt

▶ cat urls.txt | head -n 3
https://s3-us-west-2.amazonaws.com/org.mozilla.crash-stats.symbols-public/v1/wntdll.pdb/D74F79EB1F8D4A45ABCD2F476CCABACC2/wntdll.sym
https://s3-us-west-2.amazonaws.com/org.mozilla.crash-stats.symbols-public/v1/firefox.pdb/448794C699914DB8A8F9B9F88B98D7412/firefox.sym
https://s3-us-west-2.amazonaws.com/org.mozilla.crash-stats.symbols-public/v1/d2d1.pdb/CB8FADE9C48E44DA9A10B438A33114781/d2d1.sym

If I wanted to download all of these files with wget the traditional way would be:

▶ time cat urls.txt | xargs wget -q -P ./downloaded/
cat urls.txt  0.00s user 0.00s system 53% cpu 0.005 total
xargs wget -q -P ./downloaded/  0.07s user 0.24s system 2% cpu 14.913 total

▶ ls downloaded | wc -l
      30

▶ du -sh downloaded
 21M    downloaded

So it took 15 seconds to download 30 files that totals 21MB.

Now, let's do it with machama instead:

▶ time cat urls.txt | machma -- wget -q -P ./downloaded/ {}
cat urls.txt  0.00s user 0.00s system 55% cpu 0.004 total
machma -- wget -q -P ./downloaded/ {}  0.53s user 0.45s system 12% cpu 7.955 total

That uses 8 separate processors (because my laptop has 8 CPUs).
Because 30 / 8 ~= 4, it roughly does 4 iterations.

But note, it took 15 seconds to download 30 files synchronously. That's an average of 0.5s per file. The reason it doesn't take 4x0.5 seconds (instead of 8 seconds) is because it's at the mercy of bad luck and some of those 30 spiking a bit.

Something CPU bound

Now let's do something really CPU intensive; Guetzli compression.


▶ ls images | wc -l
  7

▶ time find images -iname '*.jpg' | xargs -I {} guetzli --quality 85 {} compressed/{}
find images -iname '*.jpg'  0.00s user 0.00s system 40% cpu 0.009 total
xargs -I {} guetzli --quality 85 {} compressed/{}  35.74s user 0.68s system 99% cpu 36.560 total

And now the same but with machma:

▶ time find images -iname '*.jpg' | machma -- guetzli --quality 85 {} compressed/{}

processed 7 items (0 failures) in 0:10
find images -iname '*.jpg'  0.00s user 0.00s system 51% cpu 0.005 total
machma -- guetzli --quality 85 {} compressed/{}  58.47s user 0.91s system 546% cpu 10.857 total

Basically, it took only 11 seconds. This time there were fewer images (7) than there was CPUs (8), so basically the poor computer is doing super intensive CPU (and memory) work across all CPUs at the same time. The average time for each of these files is ~5 seconds so it's really interesting that even if you try to do this in parallel execution instead of taking a total of ~5 seconds, it took almost double that.

In conclusion

Such a handy tool to have around for command line stuff. I haven't looked at its code much but it's almost a shame that the project only has 300+ GitHub stars. Perhaps because it's kinda complete and doesn't need much more work.

Also, if you attempt all the examples above you'll notice that when you use the ... | xargs ... approach the stdout and stderr is a mess. For wget, that's why I used -q to silence it a bit. With machma you get a really pleasant color coded live output that tells you the state of the queue, possible failures and an ETA.

Autocompeter is Dead. Long live Autocompeter!

09 January 2017 0 comments   Go, Web development, Python

https://github.com/peterbe/autocompeter/commit/dfe2db128e628d6dd300385cc6e422e6e1bed57e


About 2 years ago I launched Autocompeter.com. It was two parts:

1) A autocompeter.js pure JavaScript solution to add autocomplete to a search input field.
2) A REST API where you can submit titles with a HTTP header key, and a fancy autocomplete search.

Only Rewrote the Go + Redis part

The second part has now been completely re-written. The server was originally written in Go and used Redis. Now it's Django and ElasticSearch.

The ultimate reason for this was that Redis was, by far, the biggest memory consumer on my shared DigitalOcean server. The way it worked was that every prefix of every word in every title was indexes as a key. For example the words p, pe, pet, pete, peter and peter$ are all keys and they point to an array of IDs that you then look up to get the distinct set of titles and their URLs. This makes it really really fast but since redis doesn't support namespaces, or multiple columns it means that for every prefix it needs a prefix of its own for the domain they belong to. So the hash for www.peterbe.com is eb9f747 so the strings to store are instead eb9f747p, eb9f747pe, eb9f747pet, eb9f747pete , eb9f747peter and eb9f747peter$.

ElasticSearch on the other hand has ALL of this built in deep in Lucene. AND you can filter. So the way it's queried now instead is something like this:

search = TitleDoc.search()
search = search.filter('term', domain=domain.name)
search = search.query(Q('match_phrase', title=request.GET['q']))
search = search.sort('-popularity', '_score')
search = search[:size]
response = search.execute()
...

And here's how the mapping is defined:

from elasticsearch_dsl import (
    DocType,
    Float,
    Text,
    Index,
    analyzer,
    Keyword,
    token_filter,
)


edge_ngram_analyzer = analyzer(
    'edge_ngram_analyzer',
    type='custom',
    tokenizer='standard',
    filter=[
        'lowercase',
        token_filter(
            'edge_ngram_filter', type='edgeNGram',
            min_gram=1, max_gram=20
        )
    ]
)


class TitleDoc(DocType):
    id = Keyword()
    domain = Keyword(required=True)
    url = Keyword(required=True, index=False)
    title = Text(
        required=True,
        analyzer=edge_ngram_analyzer,
        search_analyzer='standard'
    )
    popularity = Float()
    group = Keyword()

I'm learning ElasticSearch rapidly but I still feel like I have so much to learn. This solution I have here is quite good and I'm pretty happy with the results but I bet there's a lot of things I can learn to make it even better.

Why Ditch Go?

I actually had a lot of fun building the first server version of Autocompeter in Go but Django is just so many times more convenient. It's got management commands, ORM, authentication system, CSRF protection, awesome error reporting, etc. All built in! With Go I had to build everything from scratch.

Also, I felt like the important thing here is the JavaScript client and the database. Now that I've proven this to work with Django and elasticsearch-dsl I think it wouldn't be too hard to re-write the critical query API in Go or in something like Sanic for maximum performance.

All Dockerized

Oh, one of the reasons I wanted to do this new server in Python is because I want to learn Docker better and in particular Docker with Python projects.

The project is now entirely contained in Docker so you can start the PostgreSQL, ElasticSearch 5.1.1 and Django with docker-compose up. There might be a couple of things I've forgot to document for how to configure things but this is actually the first time I've developed something entirely in Docker.

Benchmarking Autocompeter

12 April 2015 0 comments   Go


Now that Autocompeter.com is launched I can publish some preliminary benchmarks of "real" usage. It's all on my MacBook Pro on a local network with a local Redis but it's quite telling that it's pretty fast.

What I did was I started with a completely empty Redis database then I did the following things:

First of all, I bulk load in 1035 "documents" (110Kb of data). This takes about 0.44 seconds consistently!

  1. GET on the home page (not part of the API and thus quite unimportant in terms of performance)
  2. GET on a search with a single character ("p") expecting 10 results (e.g. /v1?d=mydomain&q=p)
  3. GET on a search with a full word ("python") expecting 10 results
  4. GET on a search with a full word that isn't in the index ("xxxxxxxx") expecting 0 results
  5. GET on a search with two words ("python", "te") expecting 4 results
  6. GET on a search with two words that aren't in the index ("xxxxxxx", "yyyyyy") expecting 0 results

In each benchmark I use wrk with 10 connections, lasting 5 seconds, using 5 threads.

And for each round I try with 1 processor, 2 processors and 8 processors (my laptop's max according to runtime.NumCPU()).

I ran it a bunch of times and recorded the last results for each number of processors.
The results are as follows:

Autocompeter Benchmark v1

Notes

Basically, this is a benchmark of Redis more so than Go but it's quite telling that running it in multiple processors does help.

If you're curious, the benchmark code is here and I'm sure there's things one can do to speed it up even more. It's just interesting that it's so freakin' fast out of the box!

In particular I'm very pleased with the fact that it takes less than half a second to bulk load in over 1,000 documents.

Autocompeter 1.1.8 and smooth typing

06 April 2015 0 comments   Go, Javascript


One of the most constructive pieces of feedback I got when Autocompeter was on Hacker News was that when you type something with lots of predictable results the results overlay would "flicker".

E.g. you type "javascript" in a nice and steady pace and the overlay would shrink and grow and shrink and grow very rapidly.

The reason it happened was due to a bug in the javascript code that filtered results whilst waiting for the next AJAX request from the latest typed character. E.g. you type "ash" and the results comes back with "ashley", "ashes", "Ashford". Then you add a "l" so now we start a new AJAX query for "ashl" and whilst waiting for that output from the server we can start filtering out "ashes" and "Ashford" because we can pre-emptively know that that won't be in the new result set.

The bug was a bad function that filtered the existing results on a second rendering whilst waiting for the next AJAX. It was easy to fix and this is included in version 1.1.8 .

The reason I failed to notice this was because I had inserted some necessary optimizations when the network latency was very very slow but hadn't tested it in a realistic network latency environment. E.g. a decent DSL connection but nevertheless something more advanced that just connecting to localhost.

Autocompeter.com

02 April 2015 8 comments   Go, Javascript

https://autocompeter.com/


About a year ago I found a great article about how to use Redis to index every prefix of every word as an index and thus a super fast way of building an autocomplete service. The idea is that you take all your titles and index them like this; if the title is "My Title" you store a key for m, my, t, ti, tit, titl and title. That means you can do very fast lookups as someone is typing unfinished words.

Anyway. I was running this merrily here on my personal blog but I liked it so much and I wanted to use it on aother site for work that I thought it'd be time to extract it into its own little microservice. All I needed was a name and my friend and colleague jezdez suggested I call it "autocompeter". So that it became.

The original implementation was written in Python and at the time I was learning Go and was eager to have something to build in Go. So I built this microservice in Go using the Negroni web framework.

The idea is that you own and run a website. You have a search feature on your website but you don't have a nifty autocomplete (aka. live search) thing on it. So, you send me all your titles, URLs and optionally their "popularity ranking" (basically a score). I'll index them on autocompeter.com under your domain. You have to sign in with GitHub to set up an API Auth Key.

Then, you put this into your HTML:

<script src="//cdn.jsdelivr.net/autocompeter/1/autocompeter.min.js"></script>
<script>
Autocompeter(document.querySelector('input[name="q"]');
</script>

Also, you'll need to download the CSS and put into your site. I don't recommend pointing to a CDN for CSS.

And that's all you have to do. The REST API, options for the Javascript integration and CSS integration in the documentation.

The Javascript is framework-free meaning it's just pure DOM manipulation and works in IE and modern browsers. The minified file is only 4.2Kb minified (2Kb gzipped).

All code is Open Source under a BSD license. Everything is free but there's no SLA as of yet.

I'm going to be blogging more and more about feature development, benchmarks and other curious things I learn developing this further.