{"action":"created","issue":{"url":"https://api.github.com/repos/ablab/spades/issues/19","repository_url":"https://api.github.com/repos/ablab/spades","labels_url":"https://api.github.com/repos/ablab/spades/issues/19/labels{/name}","comments_url":"https://api.github.com/repos/ablab/spades/issues/19/comments","events_url":"https://api.github.com/repos/ablab/spades/issues/19/events","html_url":"https://github.com/ablab/spades/issues/19","id":227459851,"number":19,"title":"Determining optimal -m Memory and -t Threads setting","user":{"login":"md5sam","id":12861419,"avatar_url":"https://avatars1.githubusercontent.com/u/12861419?v=4","gravatar_id":"","url":"https://api.github.com/users/md5sam","html_url":"https://github.com/md5sam","followers_url":"https://api.github.com/users/md5sam/followers","following_url":"https://api.github.com/users/md5sam/following{/other_user}","gists_url":"https://api.github.com/users/md5sam/gists{/gist_id}","starred_url":"https://api.github.com/users/md5sam/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/md5sam/subscriptions","organizations_url":"https://api.github.com/users/md5sam/orgs","repos_url":"https://api.github.com/users/md5sam/repos","events_url":"https://api.github.com/users/md5sam/events{/privacy}","received_events_url":"https://api.github.com/users/md5sam/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":1,"created_at":"2017-05-09T18:41:20Z","updated_at":"2017-08-14T20:43:06Z","closed_at":null,"body":"While trying to run a mammalian (chromosome-specific) assembly with ~20 million reads, stages with k=21 and k=33 complete successfully. Subsequently, the k=55 step fails with \r\n\r\n`<jemalloc>: Error in malloc(): out of memory. Requested: 64, active: 210579226624`\r\n\r\nI've tried playing with the memory parameters, setting -m to 120, 256, 500 etc. but this continues to throw an error without completion. \r\n\r\nCould you provide any ideas on how to determine optimal -m ? The node I'm using has 64 processors and max of 512 GB memory.  \r\n\r\nWould reducing the number of threads help ? How does SPAdes decide the total RAM requested ? \r\nCan I try any other parameters to get this assembly to complete? I'm open to any suggestions. \r\n\r\nParameters : \r\n\r\n`System information:\r\n  SPAdes version: 3.6.1\r\n  Threads: 64\r\n  Memory limit (in Gb): 250\r\n  Python version: 2.7.13\r\n  OS: Linux-3.2.0-4-amd64-x86_64-with-debian-7.5\r\n  k: [21, 33, 55]\r\n  Mismatch careful mode is turned OFF\r\n  Repeat resolution is enabled\r\n  MismatchCorrector will be SKIPPED\r\n  Coverage cutoff is turned OFF\r\n`\r\n\r\n"},"comment":{"url":"https://api.github.com/repos/ablab/spades/issues/comments/322303872","html_url":"https://github.com/ablab/spades/issues/19#issuecomment-322303872","issue_url":"https://api.github.com/repos/ablab/spades/issues/19","id":322303872,"user":{"login":"TomHarrop","id":5971975,"avatar_url":"https://avatars3.githubusercontent.com/u/5971975?v=4","gravatar_id":"","url":"https://api.github.com/users/TomHarrop","html_url":"https://github.com/TomHarrop","followers_url":"https://api.github.com/users/TomHarrop/followers","following_url":"https://api.github.com/users/TomHarrop/following{/other_user}","gists_url":"https://api.github.com/users/TomHarrop/gists{/gist_id}","starred_url":"https://api.github.com/users/TomHarrop/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/TomHarrop/subscriptions","organizations_url":"https://api.github.com/users/TomHarrop/orgs","repos_url":"https://api.github.com/users/TomHarrop/repos","events_url":"https://api.github.com/users/TomHarrop/events{/privacy}","received_events_url":"https://api.github.com/users/TomHarrop/received_events","type":"User","site_admin":false},"created_at":"2017-08-14T20:43:06Z","updated_at":"2017-08-14T20:43:06Z","body":"I'm having this problem too on our compute server with 1 TB of RAM. Here's the Spades error:\r\n\r\n```<jemalloc>: Error in malloc(): out of memory. Requested: 365790526992, active: 127263571968```\r\n\r\nHere's the free memory on the server:\r\n\r\n```\r\n              total        used        free      shared  buff/cache   available\r\nMem:           1.0T        7.1G        991G         21M        9.2G        998G\r\nSwap:          4.0G          0B        4.0G\r\n```\r\n\r\nSystem info:\r\n\r\n```\r\nSystem information:\r\n  SPAdes version: 3.10.1\r\n  Python version: 3.4.5\r\n  OS: Linux-3.10.0-514.10.2.el7.x86_64-x86_64-with-redhat-7.3-Maipo\r\n```"}}
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