{"action":"created","comment":{"url":"https://api.github.com/repos/idaholab/moose/pulls/comments/68824246","id":68824246,"diff_hunk":"@@ -939,7 +943,12 @@ Assembly::prepare()\n     unsigned int vi = ivar.number();\n     unsigned int vj = jvar.number();\n \n-    jacobianBlock(vi, vj).resize(ivar.dofIndices().size(), jvar.dofIndices().size());\n+    AllLocalDofIndicesThread aldit(_sys.system(), {jvar.name()});","path":"framework/src/base/Assembly.C","position":26,"original_position":26,"commit_id":"332547ec6de646c78f76451d5903b26c473a0c5a","original_commit_id":"332547ec6de646c78f76451d5903b26c473a0c5a","user":{"login":"friedmud","id":870705,"avatar_url":"https://avatars.githubusercontent.com/u/870705?v=3","gravatar_id":"","url":"https://api.github.com/users/friedmud","html_url":"https://github.com/friedmud","followers_url":"https://api.github.com/users/friedmud/followers","following_url":"https://api.github.com/users/friedmud/following{/other_user}","gists_url":"https://api.github.com/users/friedmud/gists{/gist_id}","starred_url":"https://api.github.com/users/friedmud/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/friedmud/subscriptions","organizations_url":"https://api.github.com/users/friedmud/orgs","repos_url":"https://api.github.com/users/friedmud/repos","events_url":"https://api.github.com/users/friedmud/events{/privacy}","received_events_url":"https://api.github.com/users/friedmud/received_events","type":"User","site_admin":false},"body":"Actually - it turns out that this _IS_ the problem.  We currently don't allow threaded loops to run within other threaded loops.\r\n\r\nThe mechanism that forbids this is here: https://github.com/libMesh/libmesh/blob/master/include/parallel/threads_pthread.h#L335\r\n\r\nThat is essentially a \"lock\" that doesn't allow two different threaded loops to execute.\r\n\r\nYou need to move this whole dof_indices finding thing somewhere more suitable... like maybe into the variable's themselves or into one of the `initialSetup()` routines in Assembly or FEProblem","created_at":"2016-06-28T19:18:40Z","updated_at":"2016-06-28T19:18:40Z","html_url":"https://github.com/idaholab/moose/pull/7216#discussion_r68824246","pull_request_url":"https://api.github.com/repos/idaholab/moose/pulls/7216","_links":{"self":{"href":"https://api.github.com/repos/idaholab/moose/pulls/comments/68824246"},"html":{"href":"https://github.com/idaholab/moose/pull/7216#discussion_r68824246"},"pull_request":{"href":"https://api.github.com/repos/idaholab/moose/pulls/7216"}}},"pull_request":{"url":"https://api.github.com/repos/idaholab/moose/pulls/7216","id":74500233,"html_url":"https://github.com/idaholab/moose/pull/7216","diff_url":"https://github.com/idaholab/moose/pull/7216.diff","patch_url":"https://github.com/idaholab/moose/pull/7216.patch","issue_url":"https://api.github.com/repos/idaholab/moose/issues/7216","number":7216,"state":"open","locked":false,"title":"Jacobian Contribution corresponding to non-local 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case,\r\nhttp://www.mooseframework.org/wiki/PhysicsModules/PhaseField/DevelopingModels/GrainMotion/Derivations/ \r\n(refer to the \"Simple test case for the jacobian implementation\" part)\r\n\r\nNote: \r\n- Residual has a term that is integrated over the whole simulation domain, both residual and the jacobian calculations are done in UserObject\r\n- Introduces ShapeElementUserObject to make shape functions available to userobjects (previous PR: https://github.com/idaholab/moose/pull/5914)\r\n- kernel should be able to write jacobian terms corresponding to non-local dofs \r\n\r\n- Work in progress #5913 \r\n\r\nTagging @dschwen @permcody @friedmud @andrsd for design discussion. 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