Collection API - Performance enhancements¶

Problem description¶

Currently, we are experiencing severe performance issues when working with large collections in Arvados. Below are a few scenario descriptions.

1. Fetching a large collection¶

Fetching a collection with large manifest text from API server results in timeout errors. This is suspected to be either the root cause or contributing largely to the other issues listed below. Several issues are reported which are the side effects of this issue: #4953, #4943, #5614, #5901, #5902

2. Collection#show in workbench¶

Often times, we see timeout errors in workbench when showing a collection page with large manifest text. It may be mostly due to the above listed concern about fetching the large collections. #5902, #5908

3. Create a collection by combining¶

Creating new collections by combining other collections or several files from a collection almost always fail when one of more of the involved collections contain large manifest texts. A few issues about this: #4943, #5614

Proposed solutions¶

Various operations dealing with these large manifest texts are certainly the cause of these performance issues. Sending and receiving the manifest text to and from the api server to clients, json encoding and decoding of these large manifest texts could be contributing to this performance issues. Reducing the amount of data and the number of times this data is exchanged can greatly help.

1. Fetching a large collection¶

• Compress the data transferred (We recently enabled gzip compression between API and workbench)

• Use efficient json encoding / decoding
  • We are using Oj between API server and Workbench. Is there room for further improvement? (http://devblog.agworld.com.au/post/42586025923/the-performance-of-to-json-in-rails-sucks-and)
  • Are we consistently using Oj in Ruby SDK? (Radhika: I need to do further research to answer this question)

• Send the data in smaller chunks (?)
  • Is it possible for us to implement some form of “paging” strategy in sending the manifest text to the clients from the API server?

2. Collection#show in workbench¶

Collection#show responses are profiled using rack-mini-profiler. When pointed the development environment to qr1hi api server, the following observations are made (based on about 20+ reloads of the page):

• On average it took about 70s for to show the collection qr1hi-4zz18-tcnxylwkxg0nfhi

• The most expensive operations (on average) are:
  • collections/_show_source_summary -- 30 seconds
  • collections/show (api request to get collection) -- 15 sec
    • It took on average .2 sec to parse response (json)
  • collections/_show_files -- 15 sec
  • applications/_projects_tree_menu -- 3 to 4 sec
    • For this collection, 6 requests were made to /groups each taking .2 to .5sec

<p><img src="qr1hi-4zz18-tcnxylwkxg0nfhi.png&quot;">https://arvados.org/attachments/download/595/perf-profile-qr1hi-4zz18-tcnxylwkxg0nfhi.png&quot; alt="" /></p>

• Workbench console log
  

  Started GET "/collections/qr1hi-4zz18-tcnxylwkxg0nfhi" for 127.0.0.1 at 2015-05-11 14:47:03 -0400
  Processing by CollectionsController#show as HTML
    Parameters: {"id"=>"qr1hi-4zz18-tcnxylwkxg0nfhi"}
  API client: 0.0007654 Prepare request https://qr1hi.arvadosapi.com/arvados/v1/users/current    
  API client: 0.313339245 API transaction
  API client: 0.000289537 Parse response
  API client: 9.8434e-05 Prepare request https://qr1hi.arvadosapi.com/discovery/v1/apis/arvados/v1/rest    
  API client: 0.250356943 API transaction
  API client: 0.005898489 Parse response
  API client: 0.000356541 Prepare request https://qr1hi.arvadosapi.com/arvados/v1/collections/qr1hi-4zz18-tcnxylwkxg0nfhi    
  API client: 21.405180053 API transaction
  API client: 0.170310714 Parse response
  API client: 0.000316374 Prepare request https://qr1hi.arvadosapi.com/arvados/v1/jobs  {"output":"55152d2b989c6b174e298dba10ae3ff7+57708684"}  
  API client: 0.221916151 API transaction
  API client: 0.000178293 Parse response
  API client: 0.000356427 Prepare request https://qr1hi.arvadosapi.com/arvados/v1/jobs  {"log":"55152d2b989c6b174e298dba10ae3ff7+57708684"}  
  API client: 0.078525257 API transaction
  API client: 0.00017414 Parse response
  API client: 0.000424393 Prepare request https://qr1hi.arvadosapi.com/arvados/v1/links  {"head_uuid":"qr1hi-4zz18-tcnxylwkxg0nfhi","link_class":"name"}  modified_at DESC
  API client: 0.059534807 API transaction
  API client: 0.000152869 Parse response
  API client: 0.000302943 Prepare request https://qr1hi.arvadosapi.com/arvados/v1/groups  {"uuid":[]}  
  API client: 0.06070466 API transaction
  API client: 0.000145646 Parse response
  API client: 0.00029954 Prepare request https://qr1hi.arvadosapi.com/arvados/v1/links  {"head_uuid":"qr1hi-4zz18-tcnxylwkxg0nfhi","link_class":"permission","name":"can_read"}  modified_at DESC
  API client: 0.062907368 API transaction
  API client: 0.000149375 Parse response
  API client: 0.00028907 Prepare request https://qr1hi.arvadosapi.com/arvados/v1/logs  {"object_uuid":"qr1hi-4zz18-tcnxylwkxg0nfhi"}  created_at DESC
  API client: 0.079528074 API transaction
  API client: 0.00016842 Parse response
  API client: 0.000523936 Prepare request https://qr1hi.arvadosapi.com/arvados/v1/links  {"head_uuid":"qr1hi-4zz18-tcnxylwkxg0nfhi","tail_uuid":"qr1hi-tpzed-ktpvhqu89qoib9f","link_class":"resources","name":"wants"}  
  API client: 0.062874638 API transaction
  API client: 0.000175978 Parse response
  API client: 0.000377932 Prepare request https://qr1hi.arvadosapi.com/arvados/v1/api_client_authorizations   [["scopes","=",["GET /arvados/v1/collections/qr1hi-4zz18-tcnxylwkxg0nfhi","GET /arvados/v1/collections/qr1hi-4zz18-tcnxylwkxg0nfhi/","GET /arvados/v1/keep_services/accessible"]]] 
  API client: 0.158867905 API transaction
    Rendered application/_show_autoselect_text.html.erb (0.9ms)
    Rendered application/_show_autoselect_text.html.erb (0.2ms)
    Rendered collections/_show_source_summary.html.erb (26534.7ms)
    Rendered collections/_sharing_button.html.erb (1.1ms)
  API client: 0.000270093 Prepare request https://qr1hi.arvadosapi.com/arvados/v1/groups/qr1hi-j7d0g-ixtfnxccvzm7ui4    
  API client: 0.227171335 API transaction
  API client: 0.000226508 Parse response
    Rendered application/_title_and_buttons.html.erb (239.8ms)
    Rendered collections/_show_files.html.erb (14531.8ms)
    Rendered application/_loading_modal.html.erb (1.5ms)
    Rendered application/_content.html.erb (14545.1ms)
    Rendered application/show.html.erb (14790.7ms)
    Rendered collections/show.html.erb within layouts/application (41352.7ms)
  API client: 0.000296285 Prepare request https://qr1hi.arvadosapi.com/arvados/v1/authorized_keys  {"authorized_user_uuid":"qr1hi-tpzed-ktpvhqu89qoib9f"}  
  API client: 0.151415184 API transaction
  API client: 0.000207343 Parse response
  API client: 0.000238512 Prepare request https://qr1hi.arvadosapi.com/arvados/v1/collections  {"created_by":"qr1hi-tpzed-ktpvhqu89qoib9f"}  
  API client: 0.330716574 API transaction
  API client: 0.000160901 Parse response
  API client: 0.000376137 Prepare request https://qr1hi.arvadosapi.com/arvados/v1/pipeline_instances  {"created_by":"qr1hi-tpzed-ktpvhqu89qoib9f"}  
  API client: 0.263794223 API transaction
  API client: 0.000841214 Parse response
  API client: 0.000266079 Prepare request https://qr1hi.arvadosapi.com/arvados/v1/groups   [["group_class","=","project"]] name
  API client: 0.968549864 API transaction
  API client: 0.001104326 Parse response
  API client: 0.001218433 Prepare request https://qr1hi.arvadosapi.com/arvados/v1/groups   [["group_class","=","project"]] name
  API client: 1.214942211 API transaction
  API client: 0.001293295 Parse response
  API client: 0.001586803 Prepare request https://qr1hi.arvadosapi.com/arvados/v1/groups   [["group_class","=","project"]] name
  API client: 0.737031104 API transaction
  API client: 0.000921665 Parse response
  API client: 0.000487645 Prepare request https://qr1hi.arvadosapi.com/arvados/v1/groups   [["group_class","=","project"]] name
  API client: 0.848679769 API transaction
  API client: 0.002339424 Parse response
  API client: 0.000264704 Prepare request https://qr1hi.arvadosapi.com/arvados/v1/groups   [["group_class","=","project"]] name
  API client: 0.681490624 API transaction
  API client: 0.000958536 Parse response
  API client: 0.000484713 Prepare request https://qr1hi.arvadosapi.com/arvados/v1/groups   [["group_class","=","project"]] name
  API client: 0.412487956 API transaction
  API client: 0.000900607 Parse response
    Rendered application/_projects_tree_menu.html.erb (5474.8ms)
  API client: 0.00045925 Prepare request https://qr1hi.arvadosapi.com/arvados/v1/groups/qr1hi-tpzed-rv6f0l8lbvdzkog    
  API client: 0.078490258 API transaction
    Rendered application/_browser_unsupported.html (0.6ms)
    Rendered getting_started/_getting_started_popup.html.erb (2.7ms)
    Rendered layouts/body.html.erb (6343.2ms)
  Completed 200 OK in 70876ms (Views: 47804.5ms | ActiveRecord: 0.0ms)
  

*

• Implement paging (?) in the collection#show? Get “pages” of collection and display them as needed.

• Avoid making multiple calls to the API server for the same data by caching or preloading data (See #5908)

• Show less information in the collection page (such as not linking images that are going to 404)? (See #5908)

3. Create a collection by combining¶

• Offer an API server method that accepts the selections array (and optionally owner_uuid and name) and performs the creation of the new collection in the backend. Doing so can help as follows:
  • When combining entire collections: We can completely eliminate the need to fetch the manifest text for the collections in workbench. Also, workbench would no longer need to work through the combining logic and generate the manifest text for the new collection to be created. No need to do JSON decode and encode the manifest text. Lastly, it would not need to send this manifest text to the API server on the wire. Instead, the API server can do all these steps on the server and create the new collection and send the generated collection uuid to workbench (which will then reduce the performance issue down to collection#show issue; yay)
  • When combining selected files from within a collection: Here also, we can see significant performance improvements by eliminating need to generate the combined manifest text and sending it on wire.

4. Implement caching using a framework such as Memcache¶

• One of the issues listed above (#5901) is around being able to access collection in multiple threads in parallel. Also, #5908 highlights several API requests being repeated within one page display. In fact, we have this issue in several areas of workbench implementation.

• By implementing caching, we will be able to reduce the need to make round trip API requests to fetch these objects. Instead, we can improve performance by fetching these objects from the shared cache.

• Question: Not sure how caching would work if / when we cache these huge collections.