{"action":"created","issue":{"url":"https://api.github.com/repos/stan-dev/math/issues/744","repository_url":"https://api.github.com/repos/stan-dev/math","labels_url":"https://api.github.com/repos/stan-dev/math/issues/744/labels{/name}","comments_url":"https://api.github.com/repos/stan-dev/math/issues/744/comments","events_url":"https://api.github.com/repos/stan-dev/math/issues/744/events","html_url":"https://github.com/stan-dev/math/pull/744","id":292959822,"number":744,"title":"Update cvodes to 3.1.0","user":{"login":"yizhang-cae","id":33104304,"avatar_url":"https://avatars0.githubusercontent.com/u/33104304?v=4","gravatar_id":"","url":"https://api.github.com/users/yizhang-cae","html_url":"https://github.com/yizhang-cae","followers_url":"https://api.github.com/users/yizhang-cae/followers","following_url":"https://api.github.com/users/yizhang-cae/following{/other_user}","gists_url":"https://api.github.com/users/yizhang-cae/gists{/gist_id}","starred_url":"https://api.github.com/users/yizhang-cae/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/yizhang-cae/subscriptions","organizations_url":"https://api.github.com/users/yizhang-cae/orgs","repos_url":"https://api.github.com/users/yizhang-cae/repos","events_url":"https://api.github.com/users/yizhang-cae/events{/privacy}","received_events_url":"https://api.github.com/users/yizhang-cae/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":{"login":"syclik","id":425751,"avatar_url":"https://avatars2.githubusercontent.com/u/425751?v=4","gravatar_id":"","url":"https://api.github.com/users/syclik","html_url":"https://github.com/syclik","followers_url":"https://api.github.com/users/syclik/followers","following_url":"https://api.github.com/users/syclik/following{/other_user}","gists_url":"https://api.github.com/users/syclik/gists{/gist_id}","starred_url":"https://api.github.com/users/syclik/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/syclik/subscriptions","organizations_url":"https://api.github.com/users/syclik/orgs","repos_url":"https://api.github.com/users/syclik/repos","events_url":"https://api.github.com/users/syclik/events{/privacy}","received_events_url":"https://api.github.com/users/syclik/received_events","type":"User","site_admin":false},"assignees":[{"login":"syclik","id":425751,"avatar_url":"https://avatars2.githubusercontent.com/u/425751?v=4","gravatar_id":"","url":"https://api.github.com/users/syclik","html_url":"https://github.com/syclik","followers_url":"https://api.github.com/users/syclik/followers","following_url":"https://api.github.com/users/syclik/following{/other_user}","gists_url":"https://api.github.com/users/syclik/gists{/gist_id}","starred_url":"https://api.github.com/users/syclik/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/syclik/subscriptions","organizations_url":"https://api.github.com/users/syclik/orgs","repos_url":"https://api.github.com/users/syclik/repos","events_url":"https://api.github.com/users/syclik/events{/privacy}","received_events_url":"https://api.github.com/users/syclik/received_events","type":"User","site_admin":false},{"login":"yizhang-cae","id":33104304,"avatar_url":"https://avatars0.githubusercontent.com/u/33104304?v=4","gravatar_id":"","url":"https://api.github.com/users/yizhang-cae","html_url":"https://github.com/yizhang-cae","followers_url":"https://api.github.com/users/yizhang-cae/followers","following_url":"https://api.github.com/users/yizhang-cae/following{/other_user}","gists_url":"https://api.github.com/users/yizhang-cae/gists{/gist_id}","starred_url":"https://api.github.com/users/yizhang-cae/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/yizhang-cae/subscriptions","organizations_url":"https://api.github.com/users/yizhang-cae/orgs","repos_url":"https://api.github.com/users/yizhang-cae/repos","events_url":"https://api.github.com/users/yizhang-cae/events{/privacy}","received_events_url":"https://api.github.com/users/yizhang-cae/received_events","type":"User","site_admin":false}],"milestone":null,"comments":24,"created_at":"2018-01-30T22:21:54Z","updated_at":"2018-02-25T20:20:50Z","closed_at":null,"author_association":"CONTRIBUTOR","pull_request":{"url":"https://api.github.com/repos/stan-dev/math/pulls/744","html_url":"https://github.com/stan-dev/math/pull/744","diff_url":"https://github.com/stan-dev/math/pull/744.diff","patch_url":"https://github.com/stan-dev/math/pull/744.patch"},"body":"#### Submission Checklist\r\n\r\n- [x] Run unit tests: `./runTests.py test/unit`\r\n- [x] Run cpplint: `make cpplint`\r\n- [x] Declare copyright holder and open-source license: see below\r\n\r\n#### Summary:\r\nThis PR address issue #743 .\r\n\r\nUse CVODES 3.1.0 for its new matrix & linsol API. This makes linear solver tuning more accessible, as well as provides CUDA API support.\r\n\r\nDue to change of API, the initialization of the matrix solver in BDF is changed. The original workflow includes generating dense linsol using `CVDense`, which has been removed since SUNDIALS 3.0.0.\r\nThe updated approach is: \r\n- create Jacobian matrix skeleton using `SUNDenseMatrix`\r\n- create linsol object using `SUNDenseLinearSolver`\r\n- attach linsol object to CVODES pointers\r\n\r\nThe makefile changes accordingly by including `sunmatrix` and `sunlinsol` headers.\r\n\r\n#### Intended Effect:\r\nUsing new CVODES API\r\n\r\n#### How to Verify:\r\nunit tests\r\n\r\n#### Side Effects:\r\nN/A\r\n\r\n#### Copyright and Licensing\r\n\r\nPlease list the copyright holder for the work you are submitting (this will be you or your assignee, such as a university or company):\r\nMetrum Research Group, LLC\r\n\r\nBy submitting this pull request, the copyright holder is agreeing to license the submitted work under the following licenses:\r\n- Code: BSD 3-clause (https://opensource.org/licenses/BSD-3-Clause)\r\n- Documentation: CC-BY 4.0 (https://creativecommons.org/licenses/by/4.0/)\r\n"},"comment":{"url":"https://api.github.com/repos/stan-dev/math/issues/comments/368341087","html_url":"https://github.com/stan-dev/math/pull/744#issuecomment-368341087","issue_url":"https://api.github.com/repos/stan-dev/math/issues/744","id":368341087,"user":{"login":"bob-carpenter","id":3383807,"avatar_url":"https://avatars1.githubusercontent.com/u/3383807?v=4","gravatar_id":"","url":"https://api.github.com/users/bob-carpenter","html_url":"https://github.com/bob-carpenter","followers_url":"https://api.github.com/users/bob-carpenter/followers","following_url":"https://api.github.com/users/bob-carpenter/following{/other_user}","gists_url":"https://api.github.com/users/bob-carpenter/gists{/gist_id}","starred_url":"https://api.github.com/users/bob-carpenter/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/bob-carpenter/subscriptions","organizations_url":"https://api.github.com/users/bob-carpenter/orgs","repos_url":"https://api.github.com/users/bob-carpenter/repos","events_url":"https://api.github.com/users/bob-carpenter/events{/privacy}","received_events_url":"https://api.github.com/users/bob-carpenter/received_events","type":"User","site_admin":false},"created_at":"2018-02-25T20:20:50Z","updated_at":"2018-02-25T20:20:50Z","author_association":"CONTRIBUTOR","body":"Sounds like a good plan to me.  Anything to cut down on size and linking/compiling time."}}
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