{"action":"created","issue":{"url":"https://api.github.com/repos/Homebrew/homebrew-science/issues/1814","labels_url":"https://api.github.com/repos/Homebrew/homebrew-science/issues/1814/labels{/name}","comments_url":"https://api.github.com/repos/Homebrew/homebrew-science/issues/1814/comments","events_url":"https://api.github.com/repos/Homebrew/homebrew-science/issues/1814/events","html_url":"https://github.com/Homebrew/homebrew-science/issues/1814","id":57312963,"number":1814,"title":"Petsc dependency sundials: segmentation fault","user":{"login":"aancel","id":5362942,"avatar_url":"https://avatars.githubusercontent.com/u/5362942?v=3","gravatar_id":"","url":"https://api.github.com/users/aancel","html_url":"https://github.com/aancel","followers_url":"https://api.github.com/users/aancel/followers","following_url":"https://api.github.com/users/aancel/following{/other_user}","gists_url":"https://api.github.com/users/aancel/gists{/gist_id}","starred_url":"https://api.github.com/users/aancel/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/aancel/subscriptions","organizations_url":"https://api.github.com/users/aancel/orgs","repos_url":"https://api.github.com/users/aancel/repos","events_url":"https://api.github.com/users/aancel/events{/privacy}","received_events_url":"https://api.github.com/users/aancel/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":4,"created_at":"2015-02-11T13:02:44Z","updated_at":"2015-02-13T08:44:25Z","closed_at":null,"body":"While trying to install petsc on Yosemite 10.10.2, brew installs sundials as a dependency and adds the `--with-mpi` flag. If my understanding is correct, when we add a flag, brew automatically recompiles the dependency with the correct flags and do not use bottles. The compilation of sundials ends up with an error.\r\n\r\nUsing the `--debug` flag for `install`, I noticed that the sundial installation ends up with a segfault when executing `./cvodes/serial/cvsHessian_ASA_FSA`.\r\n\r\nThis can be worked around by adding the `without-check` flag to the dependency in petsc, but does not solves this segmentation fault issue.\r\nAccording to their [website](https://computation.llnl.gov/casc/sundials/download/download.php), the version of sundial provided in homebrew is the latest (the release date of 2.5.0 is March 2012).\r\n\r\nWhat could be the solution to this problem ?\r\n- removing the dependency on sundials from petsc ?\r\n- adding the `without-check` flag (might not be safe as the segfault could come from the library itself)"},"comment":{"url":"https://api.github.com/repos/Homebrew/homebrew-science/issues/comments/74221877","html_url":"https://github.com/Homebrew/homebrew-science/issues/1814#issuecomment-74221877","issue_url":"https://api.github.com/repos/Homebrew/homebrew-science/issues/1814","id":74221877,"user":{"login":"aancel","id":5362942,"avatar_url":"https://avatars.githubusercontent.com/u/5362942?v=3","gravatar_id":"","url":"https://api.github.com/users/aancel","html_url":"https://github.com/aancel","followers_url":"https://api.github.com/users/aancel/followers","following_url":"https://api.github.com/users/aancel/following{/other_user}","gists_url":"https://api.github.com/users/aancel/gists{/gist_id}","starred_url":"https://api.github.com/users/aancel/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/aancel/subscriptions","organizations_url":"https://api.github.com/users/aancel/orgs","repos_url":"https://api.github.com/users/aancel/repos","events_url":"https://api.github.com/users/aancel/events{/privacy}","received_events_url":"https://api.github.com/users/aancel/received_events","type":"User","site_admin":false},"created_at":"2015-02-13T08:44:25Z","updated_at":"2015-02-13T08:44:25Z","body":"I have redone an installation starting from scratch (removed all the brew installed software).\r\nI used the following command to install petsc:\r\n```\r\nbrew -v install petsc\r\n```\r\n\r\nWhen it reaches the installation of sundials, the installation fails and I get:\r\n```\r\nError: sundials 2.5.0 did not build\r\n```\r\nThen I launch brew in debug mode to check what failed:\r\n```\r\nbrew -v install --debug petsc\r\n```\r\nWhen the installation of sundials fails at `./cvodes/serial/cvsHessian_ASA_FSA` and brew ask me what to do, I choose the drop down to shell option, and tries to execute the application manually, then I end up with:\r\n```\r\n$/private/tmp/sundials-DBRwBC/sundials-2.5.0/examples: ./cvodes/serial/cvsHessian_ASA_FSA\r\n-------------------\r\nForward integration\r\n-------------------\r\n\r\nncheck = 1\r\n\r\n     y:      2.2732e-01   1.3534e-01   3.1472e-02     G:      5.3088e-01\r\n\r\n     yS1:   -1.6714e-01   0.0000e+00   0.0000e+00\r\n     yS2:    2.1339e-01   0.0000e+00  -1.0885e-01\r\n\r\n   dG/dp:   -1.2838e-01   1.8037e-02\r\n\r\nFinal Statistics for forward pb.\r\n--------------------------------\r\n Number steps:   142\r\n\r\n Function evaluations:\r\n  f:          165\r\n  fQ:         147\r\n  fS:         165\r\n  fQS:        147\r\n Error test failures:\r\n  netf:         1\r\n  netfQ:        0\r\n  netfS:        0\r\n  netfQS:       1\r\n Linear solver setups:\r\n  nsetups:     27\r\n  nsetupsS:     0\r\n Nonlinear iterations:\r\n  nni:        161\r\n  nniS:         0\r\n Convergence failures:\r\n  ncfn:         0\r\n  ncfnS:        0\r\n\r\n---------------------------------------------\r\nBackward integration ... (2 adjoint problems)\r\n---------------------------------------------\r\n\r\nzsh: segmentation fault  ./cvodes/serial/cvsHessian_ASA_FSA\r\n```\r\n\r\nDo you think it might come from other softwares that I might have installed locally ? or my configuration ?"}}