{"action":"created","issue":{"url":"https://api.github.com/repos/sys-bio/roadrunner/issues/346","repository_url":"https://api.github.com/repos/sys-bio/roadrunner","labels_url":"https://api.github.com/repos/sys-bio/roadrunner/issues/346/labels{/name}","comments_url":"https://api.github.com/repos/sys-bio/roadrunner/issues/346/comments","events_url":"https://api.github.com/repos/sys-bio/roadrunner/issues/346/events","html_url":"https://github.com/sys-bio/roadrunner/issues/346","id":186150340,"number":346,"title":"\"Bad Allocation\" error in getFullStoichiometryMatrix for large models","user":{"login":"hsauro","id":1054990,"avatar_url":"https://avatars.githubusercontent.com/u/1054990?v=3","gravatar_id":"","url":"https://api.github.com/users/hsauro","html_url":"https://github.com/hsauro","followers_url":"https://api.github.com/users/hsauro/followers","following_url":"https://api.github.com/users/hsauro/following{/other_user}","gists_url":"https://api.github.com/users/hsauro/gists{/gist_id}","starred_url":"https://api.github.com/users/hsauro/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/hsauro/subscriptions","organizations_url":"https://api.github.com/users/hsauro/orgs","repos_url":"https://api.github.com/users/hsauro/repos","events_url":"https://api.github.com/users/hsauro/events{/privacy}","received_events_url":"https://api.github.com/users/hsauro/received_events","type":"User","site_admin":false},"labels":[{"id":113073031,"url":"https://api.github.com/repos/sys-bio/roadrunner/labels/bug","name":"bug","color":"fc2929","default":true},{"id":199706466,"url":"https://api.github.com/repos/sys-bio/roadrunner/labels/priority","name":"priority","color":"eb6420","default":false}],"state":"open","locked":false,"assignee":{"login":"0u812","id":7402146,"avatar_url":"https://avatars.githubusercontent.com/u/7402146?v=3","gravatar_id":"","url":"https://api.github.com/users/0u812","html_url":"https://github.com/0u812","followers_url":"https://api.github.com/users/0u812/followers","following_url":"https://api.github.com/users/0u812/following{/other_user}","gists_url":"https://api.github.com/users/0u812/gists{/gist_id}","starred_url":"https://api.github.com/users/0u812/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/0u812/subscriptions","organizations_url":"https://api.github.com/users/0u812/orgs","repos_url":"https://api.github.com/users/0u812/repos","events_url":"https://api.github.com/users/0u812/events{/privacy}","received_events_url":"https://api.github.com/users/0u812/received_events","type":"User","site_admin":false},"assignees":[{"login":"0u812","id":7402146,"avatar_url":"https://avatars.githubusercontent.com/u/7402146?v=3","gravatar_id":"","url":"https://api.github.com/users/0u812","html_url":"https://github.com/0u812","followers_url":"https://api.github.com/users/0u812/followers","following_url":"https://api.github.com/users/0u812/following{/other_user}","gists_url":"https://api.github.com/users/0u812/gists{/gist_id}","starred_url":"https://api.github.com/users/0u812/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/0u812/subscriptions","organizations_url":"https://api.github.com/users/0u812/orgs","repos_url":"https://api.github.com/users/0u812/repos","events_url":"https://api.github.com/users/0u812/events{/privacy}","received_events_url":"https://api.github.com/users/0u812/received_events","type":"User","site_admin":false}],"milestone":null,"comments":1,"created_at":"2016-10-30T17:36:26Z","updated_at":"2016-10-31T19:43:08Z","closed_at":null,"body":"Download the recon1.xml model from: http://bigg.ucsd.edu:8888/models/RECON1\n\nRecon1 has 2766 metabolites and 3742 reactions.\n\nRun the scaript\nr = roadrunner.RoadRunner ('recon1.xml')\nstStr = r.getFullStoichiometryMatrix()\n\nError:\n  File \"C:\\Tellurium-Winpython\\python-2.7.10\\lib\\site-packages\\roadrunner\\roadrunner.py\", line 2903, in getFullStoichiometryMatrix\n    return _roadrunner.RoadRunner_getFullStoichiometryMatrix(self)\n\nRuntimeError: bad allocation\n\nThe smaller model. iAF1260 works fine (1668 metabolites, and 2382 reactions)\n\nRunning:\n\nOut[2]: '1.4.8; Compiler: Microsoft Visual Studio 2013, C++ version: 199711; JIT Compiler: LLVM-3.5; Date: Aug 10 2016, 15:56:47; LibSBML Version: 5.13.0'\n"},"comment":{"url":"https://api.github.com/repos/sys-bio/roadrunner/issues/comments/257398731","html_url":"https://github.com/sys-bio/roadrunner/issues/346#issuecomment-257398731","issue_url":"https://api.github.com/repos/sys-bio/roadrunner/issues/346","id":257398731,"user":{"login":"0u812","id":7402146,"avatar_url":"https://avatars.githubusercontent.com/u/7402146?v=3","gravatar_id":"","url":"https://api.github.com/users/0u812","html_url":"https://github.com/0u812","followers_url":"https://api.github.com/users/0u812/followers","following_url":"https://api.github.com/users/0u812/following{/other_user}","gists_url":"https://api.github.com/users/0u812/gists{/gist_id}","starred_url":"https://api.github.com/users/0u812/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/0u812/subscriptions","organizations_url":"https://api.github.com/users/0u812/orgs","repos_url":"https://api.github.com/users/0u812/repos","events_url":"https://api.github.com/users/0u812/events{/privacy}","received_events_url":"https://api.github.com/users/0u812/received_events","type":"User","site_admin":false},"created_at":"2016-10-31T19:43:08Z","updated_at":"2016-10-31T19:43:08Z","body":"I think this is basically Windows telling you that you have exhausted the available memory for the process. I presume you are using the 32-bit distribution of Tellurium. Like all 32-bit processes, Tellurium is limited to 4 GB of addressable memory. Every Python module that you import counts against this limit.\r\n\r\nI just tried this on my 64-bit Windows Anaconda distribution of RoadRunner and it does not have any allocation errors."}}
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