{"action":"created","issue":{"url":"https://api.github.com/repos/ontodev/robot/issues/418","repository_url":"https://api.github.com/repos/ontodev/robot","labels_url":"https://api.github.com/repos/ontodev/robot/issues/418/labels{/name}","comments_url":"https://api.github.com/repos/ontodev/robot/issues/418/comments","events_url":"https://api.github.com/repos/ontodev/robot/issues/418/events","html_url":"https://github.com/ontodev/robot/issues/418","id":391664417,"node_id":"MDU6SXNzdWUzOTE2NjQ0MTc=","number":418,"title":"Ideas? Loading NCIt not possible using reasonable memory resources","user":{"login":"matentzn","id":7070631,"node_id":"MDQ6VXNlcjcwNzA2MzE=","avatar_url":"https://avatars1.githubusercontent.com/u/7070631?v=4","gravatar_id":"","url":"https://api.github.com/users/matentzn","html_url":"https://github.com/matentzn","followers_url":"https://api.github.com/users/matentzn/followers","following_url":"https://api.github.com/users/matentzn/following{/other_user}","gists_url":"https://api.github.com/users/matentzn/gists{/gist_id}","starred_url":"https://api.github.com/users/matentzn/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/matentzn/subscriptions","organizations_url":"https://api.github.com/users/matentzn/orgs","repos_url":"https://api.github.com/users/matentzn/repos","events_url":"https://api.github.com/users/matentzn/events{/privacy}","received_events_url":"https://api.github.com/users/matentzn/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":0,"created_at":"2018-12-17T11:14:02Z","updated_at":"2018-12-17T13:00:16Z","closed_at":null,"author_association":"NONE","body":"When running\r\n\r\n```\r\n./run.sh robot convert -I http://purl.obolibrary.org/obo/ncit.owl -o ncit.owl\r\n```\r\n\r\nin a container with 10GB max memory (ROBOT release 1.2.0), we get \r\n\r\n```\r\nException in thread \"main\" java.lang.OutOfMemoryError: GC overhead limit exceeded\r\n```\r\n\r\nSince that is the absolute maximum of what we can assume any client having available, and this particular process is merely loading the ontology and serialising: Is there any way we can deal with this? Being able to deal with larger ontologies becomes increasingly important now, at the very least to extract modules from them.\r\n\r\nrun.sh:\r\n```\r\n#!/bin/sh\r\ndocker run -v $PWD/../../:/work -w /work/src/ontology --rm -ti obolibrary/odkfull \"$@\"\r\n```"},"comment":{"url":"https://api.github.com/repos/ontodev/robot/issues/comments/447837570","html_url":"https://github.com/ontodev/robot/issues/418#issuecomment-447837570","issue_url":"https://api.github.com/repos/ontodev/robot/issues/418","id":447837570,"node_id":"MDEyOklzc3VlQ29tbWVudDQ0NzgzNzU3MA==","user":{"login":"jamesaoverton","id":292409,"node_id":"MDQ6VXNlcjI5MjQwOQ==","avatar_url":"https://avatars2.githubusercontent.com/u/292409?v=4","gravatar_id":"","url":"https://api.github.com/users/jamesaoverton","html_url":"https://github.com/jamesaoverton","followers_url":"https://api.github.com/users/jamesaoverton/followers","following_url":"https://api.github.com/users/jamesaoverton/following{/other_user}","gists_url":"https://api.github.com/users/jamesaoverton/gists{/gist_id}","starred_url":"https://api.github.com/users/jamesaoverton/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jamesaoverton/subscriptions","organizations_url":"https://api.github.com/users/jamesaoverton/orgs","repos_url":"https://api.github.com/users/jamesaoverton/repos","events_url":"https://api.github.com/users/jamesaoverton/events{/privacy}","received_events_url":"https://api.github.com/users/jamesaoverton/received_events","type":"User","site_admin":false},"created_at":"2018-12-17T13:00:16Z","updated_at":"2018-12-17T13:00:16Z","author_association":"MEMBER","body":"Most of ROBOT is a thin wrapper over OWLAPI, and the `convert` command is probably the thinnest part of all. We just call OWLAPI load and save. I don't think we're keeping anything extra in memory -- if we are then that would be a bug.\r\n\r\nDoes this work in Protege?\r\n\r\nSuggestions are welcome, but I think you're hitting an OWLAPI limitation."}}
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