{"action":"closed","issue":{"url":"https://api.github.com/repos/radical-cybertools/radical.pilot/issues/910","repository_url":"https://api.github.com/repos/radical-cybertools/radical.pilot","labels_url":"https://api.github.com/repos/radical-cybertools/radical.pilot/issues/910/labels{/name}","comments_url":"https://api.github.com/repos/radical-cybertools/radical.pilot/issues/910/comments","events_url":"https://api.github.com/repos/radical-cybertools/radical.pilot/issues/910/events","html_url":"https://github.com/radical-cybertools/radical.pilot/issues/910","id":118706855,"number":910,"title":"performance of multi-core CUs","user":{"login":"antonst","id":3586211,"avatar_url":"https://avatars.githubusercontent.com/u/3586211?v=3","gravatar_id":"","url":"https://api.github.com/users/antonst","html_url":"https://github.com/antonst","followers_url":"https://api.github.com/users/antonst/followers","following_url":"https://api.github.com/users/antonst/following{/other_user}","gists_url":"https://api.github.com/users/antonst/gists{/gist_id}","starred_url":"https://api.github.com/users/antonst/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/antonst/subscriptions","organizations_url":"https://api.github.com/users/antonst/orgs","repos_url":"https://api.github.com/users/antonst/repos","events_url":"https://api.github.com/users/antonst/events{/privacy}","received_events_url":"https://api.github.com/users/antonst/received_events","type":"User","site_admin":false},"labels":[{"url":"https://api.github.com/repos/radical-cybertools/radical.pilot/labels/optimization","name":"optimization","color":"eb6420"},{"url":"https://api.github.com/repos/radical-cybertools/radical.pilot/labels/question","name":"question","color":"eb6420"}],"state":"closed","locked":false,"assignee":{"login":"antonst","id":3586211,"avatar_url":"https://avatars.githubusercontent.com/u/3586211?v=3","gravatar_id":"","url":"https://api.github.com/users/antonst","html_url":"https://github.com/antonst","followers_url":"https://api.github.com/users/antonst/followers","following_url":"https://api.github.com/users/antonst/following{/other_user}","gists_url":"https://api.github.com/users/antonst/gists{/gist_id}","starred_url":"https://api.github.com/users/antonst/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/antonst/subscriptions","organizations_url":"https://api.github.com/users/antonst/orgs","repos_url":"https://api.github.com/users/antonst/repos","events_url":"https://api.github.com/users/antonst/events{/privacy}","received_events_url":"https://api.github.com/users/antonst/received_events","type":"User","site_admin":false},"assignees":[{"login":"antonst","id":3586211,"avatar_url":"https://avatars.githubusercontent.com/u/3586211?v=3","gravatar_id":"","url":"https://api.github.com/users/antonst","html_url":"https://github.com/antonst","followers_url":"https://api.github.com/users/antonst/followers","following_url":"https://api.github.com/users/antonst/following{/other_user}","gists_url":"https://api.github.com/users/antonst/gists{/gist_id}","starred_url":"https://api.github.com/users/antonst/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/antonst/subscriptions","organizations_url":"https://api.github.com/users/antonst/orgs","repos_url":"https://api.github.com/users/antonst/repos","events_url":"https://api.github.com/users/antonst/events{/privacy}","received_events_url":"https://api.github.com/users/antonst/received_events","type":"User","site_admin":false}],"milestone":null,"comments":21,"created_at":"2015-11-24T21:29:40Z","updated_at":"2016-06-29T20:41:05Z","closed_at":"2016-06-29T20:41:05Z","body":"With RP-0.37.10 I have performed a series of experiments on both SuperMIC and Stampede using alanine-dipeptide system and AMBER (sander.MPI) as executable. For all experiments I run only 8 CU's concurrently and I allocate one extra node. Number of simulation time-steps is the same for all experiments. Below are results obtained from Amber's internal profiling while increasing the number of cores from 1 to 8 and using RP to launch tasks. These are timings obtained on superMIC, but result on Stampede are very similar:\r\n\r\n```\r\nsmic 1 core, 1000 steps, sander.MPI\r\n\r\n| Final Performance Info:\r\n| -----------------------------------------------------\r\n| Average timings for all steps:\r\n|     Elapsed(s) =     143.33 Per Step(ms) =     143.33\r\n|         ns/day =       0.60   seconds/ns =  143333.48\r\n| -----------------------------------------------------\r\n\r\nsmic 2 cores, 1000 steps, sander.MPI\r\n\r\n| Final Performance Info:\r\n| -----------------------------------------------------\r\n| Average timings for all steps:\r\n|     Elapsed(s) =     230.62 Per Step(ms) =     230.62\r\n|         ns/day =       0.37   seconds/ns =  230622.19\r\n| -----------------------------------------------------\r\n\r\nsmic 4 cores, 1000 steps, sander.MPI\r\n\r\n| Final Performance Info:\r\n| -----------------------------------------------------\r\n| Average timings for all steps:\r\n|     Elapsed(s) =     181.12 Per Step(ms) =     181.12\r\n|         ns/day =       0.48   seconds/ns =  181122.76\r\n| -----------------------------------------------------\r\n\r\nsmic 8 cores, 1000 steps, sander.MPI\r\n\r\n| Final Performance Info:\r\n| -----------------------------------------------------\r\n| Average timings for all steps:\r\n|     Elapsed(s) =     123.41 Per Step(ms) =     123.41\r\n|         ns/day =       0.70   seconds/ns =  123409.43\r\n| -----------------------------------------------------\r\n```    \r\n\r\nI have also run the same tasks, but outside of RP, e.g. simple bash script submitted to queuing system. Result can be found below:\r\n\r\n```\r\nsmic 1 core, 1000 steps, sander.MPI\r\n\r\n| Final Performance Info:\r\n| -----------------------------------------------------\r\n| Average timings for all steps:\r\n|     Elapsed(s) =      18.04 Per Step(ms) =      18.04\r\n|         ns/day =       4.79   seconds/ns =   18039.24\r\n| -----------------------------------------------------\r\n\r\nsmic 2 cores, 1000 steps, sander.MPI\r\n\r\n| Final Performance Info:\r\n| -----------------------------------------------------\r\n| Average timings for all steps:\r\n|     Elapsed(s) =       9.80 Per Step(ms) =       9.80\r\n|         ns/day =       8.81   seconds/ns =    9803.06\r\n| -----------------------------------------------------\r\n\r\nsmic 4 cores, 1000 steps, sander.MPI\r\n\r\n| Final Performance Info:\r\n| -----------------------------------------------------\r\n| Average timings for all steps:\r\n|     Elapsed(s) =       5.42 Per Step(ms) =       5.42\r\n|         ns/day =      15.95   seconds/ns =    5416.60\r\n| -----------------------------------------------------\r\n\r\n\r\nsmic 8 cores, 1000 steps, sander.MPI\r\n\r\n| Final Performance Info:\r\n| -----------------------------------------------------\r\n| Average timings for all steps:\r\n|     Elapsed(s) =       3.30 Per Step(ms) =       3.30\r\n|         ns/day =      26.15   seconds/ns =    3303.87\r\n| -----------------------------------------------------\r\n```\r\n\r\nThe difference in total simulation time is up to a factor of 41. Difference in parallel speed-up is also very significant. As of now I don't have any explanations of this behaviour.\r\n\r\n"}}
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