Archive

Archive for the ‘Performance’ Category

MongoDB Indexing, count(), and unique validations

11/10/2012 Comments off

Slow Queries in MongoDB

I rebuilt the database tier powering App Cloud earlier this week and uncovered some performance problems caused by slow queries. As usual, two or three were caused by missing indexes and were easily fixed by adding index coverage. MongoDB has decent index functionality for most use cases.

Investigating Slow count() queries

Unfortunately, I noticed a large variety of slow queries issuing complex count() queries like:

{ 
  count: "users", 
  query: { 
    email: "bob@company.com", 
    _id: { $ne: ObjectId('509e83e132a5752f5f000001') }
  }, 
  fields: null 
}

Investigating our users collection, I saw a proper index on _id and email. Unfortunately, MongoDB can’t use indexes properly for count() operations. That’s a serious drawback, but not one I can change.

Where were these odd looking queries coming from? Why would we be looking for a user with a given email but NOT a given id?

The uniqueness validation on the email key of the User document and many other models was the culprit. Whenever a User is created/updated, ActiveModel is verifying there are no other Users with the given email:

class User
  include MongoMapper::Document

  key :email, String, unique: true
end

Use the Source!

Why is a unique validation triggering this type of count() query? Within Rails 3.x, this functionality is handled by the UniquenessValidator#validate_each implementation, which checks for records using the model’s exists?() query:

  finder_class.unscoped.where(relation).exists?

The exists?() method is a convention in both ActiveRecord and MongoMapper, checking for any records within the given scope. MongoMapper delegates it’s querying capability to the Plucky gem, where we can find the exists?() implementation using count():

  def exists?(query_options={})
    !count(query_options).zero?
  end

Root Cause and a Patch to work-around MongoMapper/Plucky

In SQL, using count() is a nice way to check for the existence of records. Unfortunately, since MongoDB won’t use indices properly for count(), this incurs a big performance hit on large collections.

I added a MongoMapper patch to work-around the issue. We can patch the exists?() method to use find_one() without any fields instead of the expensive count() path:

module MongoMapper
  module Plugins
    module Querying
      module ClassMethods
        # Performance Hack: count() operations can't use indexes properly.
        # Use find() instead of count() for faster queries via indexes.
        def exists?(query_options={})
          !!only(:_id).find_one(query_options)
        end
      end
    end
  end 
end
Advertisements

How PatientsLikeMe.com Monitors Ops w/ PagerDuty

04/26/2011 1 comment

PagerDuty Dispatch

Summary (TL;DR)
We have a network of production monitoring tools at patientslikeme.com, where monit, NewRelic, and Pingdom feed alerts through PagerDuty to produce e-mail, SMS, and Pager alerts for production issues. PagerDuty has a ticketing system to assign a given problem to a single person. It’s awesome.

Life Before PagerDuty
Whenever a background worker was automatically restarted, we deployed a fix, or any minor system event occurred a handful of e-mails would be generated to our whole Ops team and most of them would get SMS messages for each. We mostly ignored all of this noise. When a genuine emergency occurred, we often didn’t react immediately. Because we were all getting alerted, often 2-3 of us would respond in a piling-on effect. This sucks.

Principles of Proper Ops Monitoring

  1. People only get alerts for serious issues requiring human intervention
  2. Only One Person Alerted at a Time
  3. Serious Issues Should Wake You Up at 4AM

Read more…

Rails Tests Run in 2/3 Time w/ GC Tuning

12/10/2010 Comments off

Run Your Unit Tests in 2/3 the Time
Tweaking the Ruby Enterprise Edition (REE) garbage collection (GC) parameters, I was able to run my unit tests in 2/3 the normal time. Total test time w/ Ruby 1.8.7 down from 20mins to approx 6mins on tuned REE 1.8.7.

This data was measured on the PatientsLikeMe Rails codebase, a very mature and large Rails app. The hardware is a MacBook Pro w/ Rails 2.3.5 on OSX 10.6.4. Your mileage may vary.

Background: Garbage Collection & Tuning
Ruby is a dynamic language with GC managing dynamic memory allocation. Most Ruby programmers have the benefit of ignoring the garbage collector during development, but tuning the GC parameters can have dramatic benefits in production and running your tests locally. Using REE allows the tuning of many GC parameters.

37Signals Production Settings

# NOTE: These only take effect when running Ruby Enterprise Edition

export RUBY_HEAP_MIN_SLOTS=600000
export RUBY_GC_MALLOC_LIMIT=59000000
export RUBY_HEAP_FREE_MIN=100000

Measured Performance

# Before (REE, no GC settings)
#
$> ruby -v
ruby 1.8.7 (2010-04-19 patchlevel 253) [i686-darwin10.4.0], MBARI 0x6770, Ruby Enterprise Edition 2010.02
$> rake test:units
#Snip...
Finished in 666.310269 seconds.

3883 tests, 11523 assertions, 0 failures, 0 errors, 0 pendings, 0 omissions, 0 notifications
# After (REE, w/ 37Signals GC tuning)
#
$> ruby -v
ruby 1.8.7 (2010-04-19 patchlevel 253) [i686-darwin10.4.0], MBARI 0x6770, Ruby Enterprise Edition 2010.02
$> env | grep RUBY
RUBY_HEAP_FREE_MIN=100000
RUBY_HEAP_MIN_SLOTS=600000
RUBY_GC_MALLOC_LIMIT=59000000
$> rake test:units
#Snip...
Finished in 411.319884 seconds.

3883 tests, 11523 assertions, 0 failures, 0 errors, 0 pendings, 0 omissions, 0 notifications

Why? What Do These Settings Mean?

  • RUBY_HEAP_MIN_SLOTS – Number of slots in Ruby heap, directly controls initial heap size in your VM. Should be large enough to hold entire Rails environment. This is 6x the default heap size.
  • RUBY_GC_MALLOC_LIMIT – Wait until # of malloc() calls to trigger GC, this is much longer wait than Ruby default period for less collections. The value above collects every 59mil malloc()s
  • RUBY_HEAP_FREE_MIN – Minimum free heap post-collection, if not met will allocate a whole new heap. We’ve set it here to 17% the size of the heap. Default is 25% of heap.

REE Cuts Rails Test Time in Half

12/07/2010 Comments off

Ruby Enterprise Edition (REE)
I spent the night after work switching our build/stage server to Ruby Enterprise Edition. I switched both our Hudson based builds and our Passenger staging servers.

REE is well known for it’s superior garbage collection and memory management, but I was shocked to see how much faster it executed in Ruby CPU-bound contexts. We saw about a 55% drop in runtime, taking our average build times from 55min to 30min.

Build/Test Times Cut Almost in Half
Hudson Screen Shot

Performance Drill-down

  • Unit Tests: From 1036s to 579s (to run 3880 tests)
  • Functional Tests: From 844s to 448s (to run 860 tests)
  • Cucumber Tests: From 498s to 255s (to run 1078 steps)

The nginx/REE/Passenger stack is known as the best of breed production Rails stack, but I can’t believe how much of a benefit we’ve gotten from introducing the same components into our build and staging systems.

This effort was initially a functional testing pass to verify our system performed correctly under REE, I never expected to achieve such massive performance gains on it’s own merits.

Tips/Tricks & Gotchas

  • RVM is the best way to test/incrementally introduce a new ruby interpreter
  • If you’re using bundler w/ file-system bundles (via –path) you need to completely rebuild them when you switch Ruby interpreters
  • If you have a previous Passenger Apache module installer, you need to rebuild/reinstall the REE based Apache module

Footnotes:
Original Ruby Version
ruby 1.8.7 (2009-06-12 patchlevel 174) [x86_64-linux]
REE Version
ruby 1.8.7 (2010-04-19 patchlevel 253) [x86_64-linux], MBARI 0x6770, Ruby Enterprise Edition 2010.02