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Bug #6074

closed

[API] collections are being returned too slowly + NoMemoryError

Added by Ward Vandewege over 9 years ago. Updated over 9 years ago.

Status:
Resolved
Priority:
Normal
Assigned To:
Tom Clegg
Category:
API
Target version:
2015-06-10 sprint
Story points:
1.0

Description

On Mon, May 18, 2015 at 06:51:02PM -0700, Misha Zatsman wrote:
> I've been working on the pull lists lately, using stale data because the
> api server has been frustratingly slow to respond to the data manager. Here
> you can see it taking about a minute plus to respond, before eventually
> failing:
> 
> Is there a fix in the works? If the API server takes one second per
> collection to respond, the data manager will never be able to run in a
> reasonable amount of time.
> 
> This all happened around 6:30 PM san francisco time in case you want to
> look at the qr1hi api server logs.
> 
> 2015/05/19 01:23:41 15570 collections read, 49 new in last batch,
> 2014-10-28T15:36:52Z latest modified date, 16113 8991033 250878093
> avg,max,total manifest size
> 2015/05/19 01:24:36 15619 collections read, 49 new in last batch,
> 2014-10-29T11:50:18Z latest modified date, 16064 8991033 250909919
> avg,max,total manifest size
> 2015/05/19 01:25:36 15667 collections read, 48 new in last batch,
> 2014-10-30T00:46:12Z latest modified date, 16018 8991033 250948820
> avg,max,total manifest size
> 2015/05/19 01:26:36 15716 collections read, 49 new in last batch,
> 2014-10-30T19:30:56Z latest modified date, 15976 8991033 251073129
> avg,max,total manifest size
> 2015/05/19 01:27:43 15765 collections read, 49 new in last batch,
> 2014-10-31T23:45:52Z latest modified date, 15927 8991033 251083331
> avg,max,total manifest size
> 2015/05/19 01:28:58 15814 collections read, 49 new in last batch,
> 2014-11-02T23:45:31Z latest modified date, 15879 8991033 251116752
> avg,max,total manifest size
> 2015/05/19 01:30:19 15863 collections read, 49 new in last batch,
> 2014-11-04T11:29:52Z latest modified date, 15840 8991033 251277070
> avg,max,total manifest size
> 2015/05/19 01:31:33 15912 collections read, 49 new in last batch,
> 2014-11-04T16:25:36Z latest modified date, 15798 8991033 251385001
> avg,max,total manifest size
> 2015/05/19 01:32:47 15961 collections read, 49 new in last batch,
> 2014-11-05T04:30:20Z latest modified date, 15751 8991033 251406912
> avg,max,total manifest size
> 2015/05/19 01:33:58 16010 collections read, 49 new in last batch,
> 2014-11-05T21:50:34Z latest modified date, 15705 8991033 251430464
> avg,max,total manifest size
> 2015/05/19 01:35:21 16059 collections read, 49 new in last batch,
> 2014-11-06T16:12:59Z latest modified date, 15658 8991033 251456615
> avg,max,total manifest size
> 2015/05/19 01:37:35 16108 collections read, 49 new in last batch,
> 2014-11-06T23:46:04Z latest modified date, 45871 54080537 738893606
> avg,max,total manifest size
> 2015/05/19 01:38:46 16157 collections read, 49 new in last batch,
> 2014-11-07T20:08:25Z latest modified date, 55791 54080537 901420414
> avg,max,total manifest size
> 2015/05/19 01:39:32 16206 collections read, 49 new in last batch,
> 2014-11-07T22:52:48Z latest modified date, 55637 54080537 901649169
> avg,max,total manifest size
> 2015/05/19 01:40:27 16255 collections read, 49 new in last batch,
> 2014-11-08T07:17:22Z latest modified date, 55473 54080537 901715163
> avg,max,total manifest size
> 2015/05/19 01:41:09 16303 collections read, 48 new in last batch,
> 2014-11-08T21:04:18Z latest modified date, 55314 54080537 901778597
> avg,max,total manifest size
> 2015/05/19 01:41:53 16352 collections read, 49 new in last batch,
> 2014-11-09T17:48:07Z latest modified date, 55149 54080537 901804169
> avg,max,total manifest size
> 2015/05/19 01:43:01 16401 collections read, 49 new in last batch,
> 2014-11-10T18:26:31Z latest modified date, 65035 54085104 1066634271
> avg,max,total manifest size
> 2015/05/19 01:44:01 Error querying collections: API server (
> qr1hi.arvadosapi.com) returned 422: 422 Unprocessable Entity. Additional
> details: #<NoMemoryError: failed to allocate memory>
> exit status 1
>

Also - qr1hi is currently running 31d8ece. That is after #5834 was merged. And still there is a NoMemoryError. Here's the backtrace from the logs:

#<NoMemoryError: failed to allocate memory>
/data/www/qr1hi.arvadosapi.com/releases/20150508140613/app/controllers/application_controller.rb:189:in `dump'
/data/www/qr1hi.arvadosapi.com/releases/20150508140613/app/controllers/application_controller.rb:189:in `send_json'
/data/www/qr1hi.arvadosapi.com/releases/20150508140613/app/controllers/application_controller.rb:487:in `render_list'
/data/www/qr1hi.arvadosapi.com/releases/20150508140613/app/controllers/application_controller.rb:76:in `index'
/var/www/qr1hi.arvadosapi.com/shared/vendor_bundle/ruby/2.1.0/gems/actionpack-3.2.17/lib/action_controller/metal/implicit_render.rb:4:in `send_action'
/var/www/qr1hi.arvadosapi.com/shared/vendor_bundle/ruby/2.1.0/gems/actionpack-3.2.17/lib/abstract_controller/base.rb:167:in `process_action'
/var/www/qr1hi.arvadosapi.com/shared/vendor_bundle/ruby/2.1.0/gems/actionpack-3.2.17/lib/action_controller/metal/rendering.rb:10:in `process_action'
/var/www/qr1hi.arvadosapi.com/shared/vendor_bundle/ruby/2.1.0/gems/actionpack-3.2.17/lib/abstract_controller/callbacks.rb:18:in `block in process_action'
/var/www/qr1hi.arvadosapi.com/shared/vendor_bundle/ruby/2.1.0/gems/activesupport-3.2.17/lib/active_support/callbacks.rb:579:in `_run__613498188452779378__process_action__1315541577497190102__callbacks'
/var/www/qr1hi.arvadosapi.com/shared/vendor_bundle/ruby/2.1.0/gems/activesupport-3.2.17/lib/active_support/callbacks.rb:405:in `__run_callback'
/var/www/qr1hi.arvadosapi.com/shared/vendor_bundle/ruby/2.1.0/gems/activesupport-3.2.17/lib/active_support/callbacks.rb:385:in `_run_process_action_callbacks'
/var/www/qr1hi.arvadosapi.com/shared/vendor_bundle/ruby/2.1.0/gems/activesupport-3.2.17/lib/active_support/callbacks.rb:81:in `run_callbacks'
/var/www/qr1hi.arvadosapi.com/shared/vendor_bundle/ruby/2.1.0/gems/actionpack-3.2.17/lib/abstract_controller/callbacks.rb:17:in `process_action'
/var/www/qr1hi.arvadosapi.com/shared/vendor_bundle/ruby/2.1.0/gems/actionpack-3.2.17/lib/action_controller/metal/rescue.rb:29:in `process_action'
/var/www/qr1hi.arvadosapi.com/shared/vendor_bundle/ruby/2.1.0/gems/actionpack-3.2.17/lib/action_controller/metal/instrumentation.rb:30:in `block in process_action'
/var/www/qr1hi.arvadosapi.com/shared/vendor_bundle/ruby/2.1.0/gems/activesupport-3.2.17/lib/active_support/notifications.rb:123:in `block in instrument'
/var/www/qr1hi.arvadosapi.com/shared/vendor_bundle/ruby/2.1.0/gems/activesupport-3.2.17/lib/active_support/notifications/instrumenter.rb:20:in `instrument'
/var/www/qr1hi.arvadosapi.com/shared/vendor_bundle/ruby/2.1.0/gems/activesupport-3.2.17/lib/active_support/notifications.rb:123:in `instrument'
/var/www/qr1hi.arvadosapi.com/shared/vendor_bundle/ruby/2.1.0/gems/actionpack-3.2.17/lib/action_controller/metal/instrumentation.rb:29:in `process_action'
/var/www/qr1hi.arvadosapi.com/shared/vendor_bundle/ruby/2.1.0/gems/actionpack-3.2.17/lib/action_controller/metal/params_wrapper.rb:207:in `process_action'
/var/www/qr1hi.arvadosapi.com/shared/vendor_bundle/ruby/2.1.0/gems/activerecord-3.2.17/lib/active_record/railties/controller_runtime.rb:18:in `process_action'
/var/www/qr1hi.arvadosapi.com/shared/vendor_bundle/ruby/2.1.0/gems/actionpack-3.2.17/lib/abstract_controller/base.rb:121:in `process'
/var/www/qr1hi.arvadosapi.com/shared/vendor_bundle/ruby/2.1.0/gems/actionpack-3.2.17/lib/abstract_controller/rendering.rb:45:in `process'
/var/www/qr1hi.arvadosapi.com/shared/vendor_bundle/ruby/2.1.0/gems/actionpack-3.2.17/lib/action_controller/metal.rb:203:in `dispatch'
/var/www/qr1hi.arvadosapi.com/shared/vendor_bundle/ruby/2.1.0/gems/actionpack-3.2.17/lib/action_controller/metal/rack_delegation.rb:14:in `dispatch'
/var/www/qr1hi.arvadosapi.com/shared/vendor_bundle/ruby/2.1.0/gems/actionpack-3.2.17/lib/action_controller/metal.rb:246:in `block in action'
/var/www/qr1hi.arvadosapi.com/shared/vendor_bundle/ruby/2.1.0/gems/actionpack-3.2.17/lib/action_dispatch/routing/route_set.rb:73:in `call'
/var/www/qr1hi.arvadosapi.com/shared/vendor_bundle/ruby/2.1.0/gems/actionpack-3.2.17/lib/action_dispatch/routing/route_set.rb:73:in `dispatch'
/var/www/qr1hi.arvadosapi.com/shared/vendor_bundle/ruby/2.1.0/gems/actionpack-3.2.17/lib/action_dispatch/routing/route_set.rb:36:in `call'
/var/www/qr1hi.arvadosapi.com/shared/vendor_bundle/ruby/2.1.0/gems/journey-1.0.4/lib/journey/router.rb:68:in `block in call'
/var/www/qr1hi.arvadosapi.com/shared/vendor_bundle/ruby/2.1.0/gems/journey-1.0.4/lib/journey/router.rb:56:in `each'
/var/www/qr1hi.arvadosapi.com/shared/vendor_bundle/ruby/2.1.0/gems/journey-1.0.4/lib/journey/router.rb:56:in `call'
/var/www/qr1hi.arvadosapi.com/shared/vendor_bundle/ruby/2.1.0/gems/actionpack-3.2.17/lib/action_dispatch/routing/route_set.rb:608:in `call'
/var/www/qr1hi.arvadosapi.com/shared/vendor_bundle/ruby/2.1.0/gems/omniauth-1.1.1/lib/omniauth/strategy.rb:177:in `call!'
/var/www/qr1hi.arvadosapi.com/shared/vendor_bundle/ruby/2.1.0/gems/omniauth-1.1.1/lib/omniauth/strategy.rb:157:in `call'
/var/www/qr1hi.arvadosapi.com/shared/vendor_bundle/ruby/2.1.0/gems/omniauth-1.1.1/lib/omniauth/builder.rb:48:in `call'
/var/www/qr1hi.arvadosapi.com/shared/vendor_bundle/ruby/2.1.0/gems/actionpack-3.2.17/lib/action_dispatch/middleware/best_standards_support.rb:17:in `call'
/var/www/qr1hi.arvadosapi.com/shared/vendor_bundle/ruby/2.1.0/gems/rack-1.4.5/lib/rack/etag.rb:23:in `call'
/var/www/qr1hi.arvadosapi.com/shared/vendor_bundle/ruby/2.1.0/gems/rack-1.4.5/lib/rack/conditionalget.rb:25:in `call'
/var/www/qr1hi.arvadosapi.com/shared/vendor_bundle/ruby/2.1.0/gems/actionpack-3.2.17/lib/action_dispatch/middleware/head.rb:14:in `call'
/var/www/qr1hi.arvadosapi.com/shared/vendor_bundle/ruby/2.1.0/gems/actionpack-3.2.17/lib/action_dispatch/middleware/params_parser.rb:21:in `call'
/var/www/qr1hi.arvadosapi.com/shared/vendor_bundle/ruby/2.1.0/gems/actionpack-3.2.17/lib/action_dispatch/middleware/flash.rb:242:in `call'
/var/www/qr1hi.arvadosapi.com/shared/vendor_bundle/ruby/2.1.0/gems/rack-1.4.5/lib/rack/session/abstract/id.rb:210:in `context'
/var/www/qr1hi.arvadosapi.com/shared/vendor_bundle/ruby/2.1.0/gems/rack-1.4.5/lib/rack/session/abstract/id.rb:205:in `call'
/var/www/qr1hi.arvadosapi.com/shared/vendor_bundle/ruby/2.1.0/gems/actionpack-3.2.17/lib/action_dispatch/middleware/cookies.rb:341:in `call'
/var/www/qr1hi.arvadosapi.com/shared/vendor_bundle/ruby/2.1.0/gems/activerecord-3.2.17/lib/active_record/query_cache.rb:64:in `call'
/var/www/qr1hi.arvadosapi.com/shared/vendor_bundle/ruby/2.1.0/gems/activerecord-3.2.17/lib/active_record/connection_adapters/abstract/connection_pool.rb:479:in `call'
/var/www/qr1hi.arvadosapi.com/shared/vendor_bundle/ruby/2.1.0/gems/actionpack-3.2.17/lib/action_dispatch/middleware/callbacks.rb:28:in `block in call'
/var/www/qr1hi.arvadosapi.com/shared/vendor_bundle/ruby/2.1.0/gems/activesupport-3.2.17/lib/active_support/callbacks.rb:405:in `_run__2522496659413941100__call__2134072409839546070__callbacks'
/var/www/qr1hi.arvadosapi.com/shared/vendor_bundle/ruby/2.1.0/gems/activesupport-3.2.17/lib/active_support/callbacks.rb:405:in `__run_callback'
/var/www/qr1hi.arvadosapi.com/shared/vendor_bundle/ruby/2.1.0/gems/activesupport-3.2.17/lib/active_support/callbacks.rb:385:in `_run_call_callbacks'
/var/www/qr1hi.arvadosapi.com/shared/vendor_bundle/ruby/2.1.0/gems/activesupport-3.2.17/lib/active_support/callbacks.rb:81:in `run_callbacks'
/var/www/qr1hi.arvadosapi.com/shared/vendor_bundle/ruby/2.1.0/gems/actionpack-3.2.17/lib/action_dispatch/middleware/callbacks.rb:27:in `call'
/var/www/qr1hi.arvadosapi.com/shared/vendor_bundle/ruby/2.1.0/gems/actionpack-3.2.17/lib/action_dispatch/middleware/debug_exceptions.rb:16:in `call'
/var/www/qr1hi.arvadosapi.com/shared/vendor_bundle/ruby/2.1.0/gems/actionpack-3.2.17/lib/action_dispatch/middleware/show_exceptions.rb:56:in `call'
/var/www/qr1hi.arvadosapi.com/shared/vendor_bundle/ruby/2.1.0/gems/railties-3.2.17/lib/rails/rack/logger.rb:32:in `call_app'
/var/www/qr1hi.arvadosapi.com/shared/vendor_bundle/ruby/2.1.0/gems/railties-3.2.17/lib/rails/rack/logger.rb:16:in `block in call'
/var/www/qr1hi.arvadosapi.com/shared/vendor_bundle/ruby/2.1.0/gems/activesupport-3.2.17/lib/active_support/tagged_logging.rb:22:in `tagged'
/var/www/qr1hi.arvadosapi.com/shared/vendor_bundle/ruby/2.1.0/gems/railties-3.2.17/lib/rails/rack/logger.rb:16:in `call'
/var/www/qr1hi.arvadosapi.com/shared/vendor_bundle/ruby/2.1.0/gems/actionpack-3.2.17/lib/action_dispatch/middleware/request_id.rb:22:in `call'
/var/www/qr1hi.arvadosapi.com/shared/vendor_bundle/ruby/2.1.0/gems/rack-1.4.5/lib/rack/methodoverride.rb:21:in `call'
/var/www/qr1hi.arvadosapi.com/shared/vendor_bundle/ruby/2.1.0/gems/rack-1.4.5/lib/rack/runtime.rb:17:in `call'
/var/www/qr1hi.arvadosapi.com/shared/vendor_bundle/ruby/2.1.0/gems/activesupport-3.2.17/lib/active_support/cache/strategy/local_cache.rb:72:in `call'
/var/www/qr1hi.arvadosapi.com/shared/vendor_bundle/ruby/2.1.0/gems/rack-1.4.5/lib/rack/lock.rb:15:in `call'
/var/www/qr1hi.arvadosapi.com/shared/vendor_bundle/ruby/2.1.0/gems/rack-cache-1.2/lib/rack/cache/context.rb:136:in `forward'
/var/www/qr1hi.arvadosapi.com/shared/vendor_bundle/ruby/2.1.0/gems/rack-cache-1.2/lib/rack/cache/context.rb:245:in `fetch'
/var/www/qr1hi.arvadosapi.com/shared/vendor_bundle/ruby/2.1.0/gems/rack-cache-1.2/lib/rack/cache/context.rb:185:in `lookup'
/var/www/qr1hi.arvadosapi.com/shared/vendor_bundle/ruby/2.1.0/gems/rack-cache-1.2/lib/rack/cache/context.rb:66:in `call!'
/var/www/qr1hi.arvadosapi.com/shared/vendor_bundle/ruby/2.1.0/gems/rack-cache-1.2/lib/rack/cache/context.rb:51:in `call'
/data/www/qr1hi.arvadosapi.com/releases/20150508140613/app/middlewares/arvados_api_token.rb:59:in `call'
/var/www/qr1hi.arvadosapi.com/shared/vendor_bundle/ruby/2.1.0/gems/actionpack-3.2.17/lib/action_dispatch/middleware/remote_ip.rb:31:in `call'
/var/www/qr1hi.arvadosapi.com/shared/vendor_bundle/ruby/2.1.0/gems/railties-3.2.17/lib/rails/engine.rb:484:in `call'
/var/www/qr1hi.arvadosapi.com/shared/vendor_bundle/ruby/2.1.0/gems/railties-3.2.17/lib/rails/application.rb:231:in `call'
/var/www/qr1hi.arvadosapi.com/shared/vendor_bundle/ruby/2.1.0/gems/railties-3.2.17/lib/rails/railtie/configurable.rb:30:in `method_missing'
/usr/lib/ruby/vendor_ruby/phusion_passenger/rack/thread_handler_extension.rb:74:in `process_request'
/usr/lib/ruby/vendor_ruby/phusion_passenger/request_handler/thread_handler.rb:141:in `accept_and_process_next_request'
/usr/lib/ruby/vendor_ruby/phusion_passenger/request_handler/thread_handler.rb:109:in `main_loop'
/usr/lib/ruby/vendor_ruby/phusion_passenger/request_handler.rb:455:in `block (3 levels) in start_threads'

Error 1431999841+3bb31288: 422
  Rendered text template (0.0ms)
Completed 422 Unprocessable Entity in 60139.7ms (Views: 1.1ms | ActiveRecord: 48283.5ms)

Subtasks 2 (0 open — 2 closed)

Task #6123: Determine why still NoMemoryError even with API memory-limiting featureResolvedTom Clegg06/03/2015Actions
Task #6110: Review 6074-collections-index @ 22c8b63ResolvedTom Clegg06/03/2015Actions

Related issues 2 (0 open — 2 closed)

Related to Arvados - Bug #5834: [API] Be careful about memory usage when responding to collections#index queriesResolvedBrett Smith04/30/2015Actions
Blocks Arvados - Idea #3408: [Keep] Implement Production Data ManagerResolvedPeter Amstutz07/29/2014Actions
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 #1

Updated by Ward Vandewege over 9 years ago

  • Description updated (diff)
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 #2

Updated by Ward Vandewege over 9 years ago

  • Description updated (diff)
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 #3

Updated by Ward Vandewege over 9 years ago

  • Subject changed from [API] collections are being returned too slowly to [API] collections are being returned too slowly + NoMemoryError
  • Description updated (diff)
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 #4

Updated by Brett Smith over 9 years ago

  • Category set to API
  • Target version changed from Bug Triage to Arvados Future Sprints
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 #5

Updated by Brett Smith over 9 years ago

  • Target version changed from Arvados Future Sprints to 2015-06-10 sprint
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 #6

Updated by Tom Clegg over 9 years ago

  • Assigned To set to Tom Clegg
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 #7

Updated by Tom Clegg over 9 years ago

  • Story points set to 1.0
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 #8

Updated by Tom Clegg over 9 years ago

At least part of the slowness is fixed by using octet_length() instead of length() in ApplicationController#limit_database_read, 69f592e

Before

arvados_production=> explain analyze SELECT  collections."manifest_text", collections."owner_uuid", collections."uuid", collections."modified_at", (length(manifest_text)) as read_length FROM "collections"  WHERE (expires_at IS NULL or expires_at > CURRENT_TIMESTAMP) AND ((collections.modified_at >= '2014-11-08 07:17:22.000000')) ORDER BY "collections"."id" ASC LIMIT 1000 OFFSET 0;
                                                                   QUERY PLAN                                                                   
------------------------------------------------------------------------------------------------------------------------------------------------
 Limit  (cost=562.06..564.56 rows=1000 width=212) (actual time=4721.771..4723.577 rows=1000 loops=1)
   ->  Sort  (cost=562.06..568.73 rows=2667 width=212) (actual time=4721.764..4722.385 rows=1000 loops=1)
         Sort Key: id
         Sort Method: top-N heapsort  Memory: 352kB
         ->  Seq Scan on collections  (cost=0.00..415.84 rows=2667 width=212) (actual time=0.026..4717.554 rows=3633 loops=1)
               Filter: ((modified_at >= '2014-11-08 07:17:22'::timestamp without time zone) AND ((expires_at IS NULL) OR (expires_at > now())))
 Total runtime: 4724.374 ms
(7 rows)

After

arvados_production=> explain analyze SELECT  collections."manifest_text", collections."owner_uuid", collections."uuid", collections."modified_at", (octet_length(manifest_text)) as read_length FROM "collections"  WHERE (expires_at IS NULL or expires_at > CURRENT_TIMESTAMP) AND ((collections.modified_at >= '2014-11-08 07:17:22.000000')) ORDER BY "collections"."id" ASC LIMIT 1000 OFFSET 0;
                                                                   QUERY PLAN                                                                   
------------------------------------------------------------------------------------------------------------------------------------------------
 Limit  (cost=562.06..564.56 rows=1000 width=212) (actual time=11.248..13.639 rows=1000 loops=1)
   ->  Sort  (cost=562.06..568.73 rows=2667 width=212) (actual time=11.247..12.075 rows=1000 loops=1)
         Sort Key: id
         Sort Method: top-N heapsort  Memory: 352kB
         ->  Seq Scan on collections  (cost=0.00..415.84 rows=2667 width=212) (actual time=0.006..6.007 rows=3633 loops=1)
               Filter: ((modified_at >= '2014-11-08 07:17:22'::timestamp without time zone) AND ((expires_at IS NULL) OR (expires_at > now())))
 Total runtime: 14.570 ms
(7 rows)

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 #9

Updated by Brett Smith over 9 years ago

  • Category deleted (API)

Reviewing 22c8b63. To be clear upfront: this is a worthwhile change, and the code is good to merge. My points are more about understanding context than anything.

This change should help mitigate Misha's concern about slowness, but it doesn't seem to do anything to mitigate the memory pressure that Ward observed. Do I understand correctly? Is this branch expected to close the ticket, or just one improvement of several?

Related to the change to make max_index_database_read a hard limit:

  • It'd be good to update or remove the comment in application.default.yml, "Note this is a threshold, not a limit. Record collection stops after reading this much data."
  • Off-by-one concerns: Should the if read_total condition use > instead of >=? Or at least not decrement new_limit when read_total == max_index_database_read?

Thanks.

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 #10

Updated by Brett Smith over 9 years ago

  • Category set to API
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 #11

Updated by Tom Clegg over 9 years ago

Brett Smith wrote:

This change should help mitigate Misha's concern about slowness, but it doesn't seem to do anything to mitigate the memory pressure that Ward observed. Do I understand correctly? Is this branch expected to close the ticket, or just one improvement of several?

Sorry for missing explanation. Here's what I should have offered.

Two memory-impacting problems are fixed here:
  1. Our "scouting" query was unintentionally retrieving manifest_text, because
    • the client-provided @select was applied to the @objects query before limit_database_read, and
    • ActiveRecord's #select method adds to the list of selected fields, rather than replacing it.
  2. The effective maximum size was the configured maximum (default 128 MiB) plus the maximum manifest_text size.

The first problem might not have contributed to the observed OOM problem, if Ruby's garbage collection was doing well. But even if it didn't, it was wasteful, so I fixed it.

The second problem, again, might not have caused the observed OOM problem, but it seems clear that it makes the effective limit much larger than anticipated. The new behavior still provides the same non-starvation guarantee (i.e., you will always make progress with each page) but limits the result to approximately max(configured,max(actual)) instead of configured+max(actual). IOW, if you have enough memory to return your biggest record, then you have enough memory to do every "index" query.

Related to the change to make max_index_database_read a hard limit:

  • It'd be good to update or remove the comment in application.default.yml, "Note this is a threshold, not a limit. Record collection stops after reading this much data."

Indeed, thanks. Updated.

  • Off-by-one concerns: Should the if read_total condition use > instead of >=? Or at least not decrement new_limit when read_total == max_index_database_read?
I considered that, and yes that would be more closely adhere to the config knob documentation, but
  • The number is already at a much higher precision than is sensible. Will anyone really care whether we stop at 134217727 or 134217728?
  • The row will have a bunch of other stuff besides manifest_text, so this means we'll be using more than max_index_database_read bytes when we fetch it.

But if you still think it's worth adding the extra test "return the last one too if it fills the max right down to the byte", saying "yes please" will be enough to twist my arm.

...and now for the good stuff

Meanwhile, I decided I'd made the use of #find_each superfluous, so I changed it to #each. And then I read the docs. And then things really started getting good. I ended up at 602706e.

I still think the above changes are worth keeping, but they pale in comparison to the find_each bug. I confirmed that find_each was checking the manifest sizes on the wrong records, which obviously would have made the "prevent OOM" mechanism ineffective in many cases like the one at hand which uses "order":"modified_at". (To see this, you can change it back to find_each and run the new test on it. Looking at the length() queries in your older log files doesn't demonstrate it very well because of the testing bugs.)

Underneath it all was another oddity/bug, "order params are silently ignored if you use "select" and don't include the columns you're ordering on" but I think that can be dealt with separately so I added #6240.

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 #12

Updated by Brett Smith over 9 years ago

Thanks for the detailed explanation, and for fixing my bugs. 602706ef is good to merge.

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 #13

Updated by Tom Clegg over 9 years ago

  • Status changed from New to Resolved

Applied in changeset arvados|commit:a12cf91db3ececed782d9718af30553f8866ad81.

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