{"action":"created","issue":{"url":"https://api.github.com/repos/dealii/dealii/issues/3853","repository_url":"https://api.github.com/repos/dealii/dealii","labels_url":"https://api.github.com/repos/dealii/dealii/issues/3853/labels{/name}","comments_url":"https://api.github.com/repos/dealii/dealii/issues/3853/comments","events_url":"https://api.github.com/repos/dealii/dealii/issues/3853/events","html_url":"https://github.com/dealii/dealii/issues/3853","id":203309518,"number":3853,"title":"PETSCERROR: Caught signal number 4 Illegal instruction: Likely due to memory corruption","user":{"login":"ilovezfs","id":5268928,"avatar_url":"https://avatars.githubusercontent.com/u/5268928?v=3","gravatar_id":"","url":"https://api.github.com/users/ilovezfs","html_url":"https://github.com/ilovezfs","followers_url":"https://api.github.com/users/ilovezfs/followers","following_url":"https://api.github.com/users/ilovezfs/following{/other_user}","gists_url":"https://api.github.com/users/ilovezfs/gists{/gist_id}","starred_url":"https://api.github.com/users/ilovezfs/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ilovezfs/subscriptions","organizations_url":"https://api.github.com/users/ilovezfs/orgs","repos_url":"https://api.github.com/users/ilovezfs/repos","events_url":"https://api.github.com/users/ilovezfs/events{/privacy}","received_events_url":"https://api.github.com/users/ilovezfs/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":3,"created_at":"2017-01-26T07:42:36Z","updated_at":"2017-01-27T07:02:39Z","closed_at":null,"body":"We're seeing this error during `brew test dealii` on our MacStadium CI nodes but not on our Mac Mini CI nodes. Any idea what the problem might be and how we might be able to fix it?\r\n\r\nHere's the successful log: https://bot.brew.sh/job/Homebrew%20Testing/1292/version=sierra_positive/consoleText\r\n\r\nHere's the unsuccessful log: https://bot.brew.sh/job/Homebrew%20Testing/1292/version=sierra_stadium_1/consoleText\r\n\r\n```\r\n==> mpirun -np 4 step-40\r\nCycle 0:\r\n   Number of active cells:       1024\r\n   Number of degrees of freedom: 4225\r\n[0]PETSC ERROR: ------------------------------------------------------------------------\r\n[0]PETSC ERROR: Caught signal number 4 Illegal instruction: Likely due to memory corruption\r\n[0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger\r\n[0]PETSC ERROR: or see http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind\r\n[0]PETSC ERROR: [2]PETSC ERROR: ------------------------------------------------------------------------\r\n[2]PETSC ERROR: Caught signal number 4 Illegal instruction: Likely due to memory corruption\r\n[2]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger\r\n[2]PETSC ERROR: or see http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind\r\n[2]PETSC ERROR: or try http://valgrind.org on GNU/linux and Apple Mac OS X to find memory corruption errors\r\n[0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and run \r\n[0]PETSC ERROR: to get more information on the crash.\r\nor try http://valgrind.org on GNU/linux and Apple Mac OS X to find memory corruption errors\r\n[2]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and run \r\n[2]PETSC ERROR: to get more information on the crash.\r\n[2]PETSC ERROR: --------------------- Error Message --------------------------------------------------------------\r\n[2]PETSC ERROR: Signal received\r\n[2]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html for trouble shooting.\r\n[2]PETSC ERROR: Petsc Release Version 3.7.4, Oct, 02, 2016 \r\n[2]PETSC ERROR: step-40 on a real named Sierra.local by brew Thu Jan 26 07:17:41 2017\r\n[0]PETSC ERROR: --------------------- Error Message --------------------------------------------------------------\r\n[0]PETSC ERROR: Signal received\r\n[0]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html for trouble shooting.\r\n[0]PETSC ERROR: Petsc Release Version 3.7.4, Oct, 02, 2016 \r\n[0]PETSC ERROR: step-40 on a real named Sierra.local by brew Thu Jan 26 07:17:41 2017\r\n[0]PETSC ERROR: [1]PETSC ERROR: ------------------------------------------------------------------------\r\n[1]PETSC ERROR: Caught signal number 4 Illegal instruction: Likely due to memory corruption\r\n[1]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger\r\nConfigure options CC=/usr/local/bin/mpicc CXX=/usr/local/bin/mpicxx F77=/usr/local/bin/mpif77 FC=/usr/local/bin/mpif90 --with-shared-libraries=1 --with-pthread=0 --with-openmp=0 --with-debugging=0 --with-ssl=0 --with-superlu_dist-include=/usr/local/opt/superlu_dist/include --with-superlu_dist-lib=\"-L/usr/local/opt/superlu_dist/lib -lsuperlu_dist\" --with-fftw-dir=/usr/local/opt/fftw --with-netcdf-dir=/usr/local/opt/netcdf --with-suitesparse-dir=/usr/local/opt/suite-sparse --with-hdf5-dir=/usr/local/opt/hdf5 --with-metis-dir=/usr/local/opt/metis --with-parmetis-dir=/usr/local/opt/parmetis --with-scalapack-dir=/usr/local/opt/scalapack --with-mumps-dir=/usr/local/opt/mumps/libexec --with-x=0 --prefix=/usr/local/Cellar/petsc/3.7.4_1/real --with-scalar-type=real --with-hypre-dir=/usr/local/opt/hypre --with-sundials-dir=/usr/local/opt/sundials --with-hwloc-dir=/usr/local/opt/hwloc\r\n[0]PETSC ERROR: #1 User provided function() line 0 in  unknown file\r\n[1]PETSC ERROR: or see http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind\r\n[1]PETSC ERROR: or try http://valgrind.org on GNU/linux and Apple Mac OS X to find memory corruption errors\r\n[1]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and run \r\n[1]PETSC ERROR: to get more information on the crash.\r\n[2]PETSC ERROR: Configure options CC=/usr/local/bin/mpicc CXX=/usr/local/bin/mpicxx F77=/usr/local/bin/mpif77 FC=/usr/local/bin/mpif90 --with-shared-libraries=1 --with-pthread=0 --with-openmp=0 --with-debugging=0 --with-ssl=0 --with-superlu_dist-include=/usr/local/opt/superlu_dist/include --with-superlu_dist-lib=\"-L/usr/local/opt/superlu_dist/lib -lsuperlu_dist\" --with-fftw-dir=/usr/local/opt/fftw --with-netcdf-dir=/usr/local/opt/netcdf --with-suitesparse-dir=/usr/local/opt/suite-sparse --with-hdf5-dir=/usr/local/opt/hdf5 --with-metis-dir=/usr/local/opt/metis --with-parmetis-dir=/usr/local/opt/parmetis --with-scalapack-dir=/usr/local/opt/scalapack --with-mumps-dir=/usr/local/opt/mumps/libexec --with-x=0 --prefix=/usr/local/Cellar/petsc/3.7.4_1/real --with-scalar-type=real --with-hypre-dir=/usr/local/opt/hypre --with-sundials-dir=/usr/local/opt/sundials --with-hwloc-dir=/usr/local/opt/hwloc\r\n[2]PETSC ERROR: #1 User provided function() line 0 in  unknown file\r\n[1]PETSC ERROR: --------------------- Error Message --------------------------------------------------------------\r\n[1]PETSC ERROR: Signal received\r\n[1]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html for trouble shooting.\r\n[1]PETSC ERROR: Petsc Release Version 3.7.4, Oct, 02, 2016 \r\n[1]PETSC ERROR: step-40 on a real named Sierra.local by brew Thu Jan 26 07:17:41 2017\r\n[1]PETSC ERROR: Configure options CC=/usr/local/bin/mpicc CXX=/usr/local/bin/mpicxx F77=/usr/local/bin/mpif77 FC=/usr/local/bin/mpif90 --with-shared-libraries=1 --with-pthread=0 --with-openmp=0 --with-debugging=0 --with-ssl=0 --with-superlu_dist-include=/usr/local/opt/superlu_dist/include --with-superlu_dist-lib=\"-L/usr/local/opt/superlu_dist/lib -lsuperlu_dist\" --with-fftw-dir=/usr/local/opt/fftw --with-netcdf-dir=/usr/local/opt/netcdf --with-suitesparse-dir=/usr/local/opt/suite-sparse --with-hdf5-dir=/usr/local/opt/hdf5 --with-metis-dir=/usr/local/opt/metis --with-parmetis-dir=/usr/local/opt/parmetis --with-scalapack-dir=/usr/local/opt/scalapack --with-mumps-dir=/usr/local/opt/mumps/libexec --with-x=0 --prefix=/usr/local/Cellar/petsc/3.7.4_1/real --with-scalar-type=real --with-hypre-dir=/usr/local/opt/hypre --with-sundials-dir=/usr/local/opt/sundials --with-hwloc-dir=/usr/local/opt/hwloc\r\n[1]PETSC ERROR: #1 User provided function() line 0 in  unknown file\r\n[3]PETSC ERROR: ------------------------------------------------------------------------\r\n[3]PETSC ERROR: Caught signal number 4 Illegal instruction: Likely due to memory corruption\r\n[3]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger\r\n[3]PETSC ERROR: or see http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind\r\n[3]PETSC ERROR: or try http://valgrind.org on GNU/linux and Apple Mac OS X to find memory corruption errors\r\n[3]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and run \r\n[3]PETSC ERROR: to get more information on the crash.\r\n[3]PETSC ERROR: --------------------- Error Message --------------------------------------------------------------\r\n[3]PETSC ERROR: Signal received\r\n[3]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html for trouble shooting.\r\n[3]PETSC ERROR: Petsc Release Version 3.7.4, Oct, 02, 2016 \r\n[3]PETSC ERROR: step-40 on a real named Sierra.local by brew Thu Jan 26 07:17:41 2017\r\n[3]PETSC ERROR: Configure options CC=/usr/local/bin/mpicc CXX=/usr/local/bin/mpicxx F77=/usr/local/bin/mpif77 FC=/usr/local/bin/mpif90 --with-shared-libraries=1 --with-pthread=0 --with-openmp=0 --with-debugging=0 --with-ssl=0 --with-superlu_dist-include=/usr/local/opt/superlu_dist/include --with-superlu_dist-lib=\"-L/usr/local/opt/superlu_dist/lib -lsuperlu_dist\" --with-fftw-dir=/usr/local/opt/fftw --with-netcdf-dir=/usr/local/opt/netcdf --with-suitesparse-dir=/usr/local/opt/suite-sparse --with-hdf5-dir=/usr/local/opt/hdf5 --with-metis-dir=/usr/local/opt/metis --with-parmetis-dir=/usr/local/opt/parmetis --with-scalapack-dir=/usr/local/opt/scalapack --with-mumps-dir=/usr/local/opt/mumps/libexec --with-x=0 --prefix=/usr/local/Cellar/petsc/3.7.4_1/real --with-scalar-type=real --with-hypre-dir=/usr/local/opt/hypre --with-sundials-dir=/usr/local/opt/sundials --with-hwloc-dir=/usr/local/opt/hwloc\r\n[3]PETSC ERROR: #1 User provided function() line 0 in  unknown file\r\n--------------------------------------------------------------------------\r\nMPI_ABORT was invoked on rank 3 in communicator MPI_COMM_WORLD\r\nwith errorcode 59.\r\n\r\nNOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.\r\nYou may or may not see output from other processes, depending on\r\nexactly when Open MPI kills them.\r\n--------------------------------------------------------------------------\r\n[Sierra.local:14811] 3 more processes have sent help message help-mpi-api.txt / mpi-abort\r\n[Sierra.local:14811] Set MCA parameter \"orte_base_help_aggregate\" to 0 to see all help / error messages\r\nError: homebrew/science/dealii: failed\r\nFailed executing: mpirun -np 4 step-40\r\n/usr/local/Homebrew/Library/Homebrew/formula.rb:1834:in `block in system'\r\n/usr/local/Homebrew/Library/Homebrew/formula.rb:1772:in `open'\r\n/usr/local/Homebrew/Library/Homebrew/formula.rb:1772:in `system'\r\n/usr/local/Homebrew/Library/Taps/homebrew/homebrew-science/dealii.rb:120:in `block (2 levels) in <class:Dealii>'\r\n/System/Library/Frameworks/Ruby.framework/Versions/2.0/usr/lib/ruby/2.0.0/fileutils.rb:125:in `chdir'\r\n/System/Library/Frameworks/Ruby.framework/Versions/2.0/usr/lib/ruby/2.0.0/fileutils.rb:125:in `cd'\r\n/usr/local/Homebrew/Library/Taps/homebrew/homebrew-science/dealii.rb:116:in `block in <class:Dealii>'\r\n/usr/local/Homebrew/Library/Homebrew/formula.rb:1671:in `block (2 levels) in run_test'\r\n/usr/local/Homebrew/Library/Homebrew/formula.rb:884:in `with_logging'\r\n/usr/local/Homebrew/Library/Homebrew/formula.rb:1670:in `block in run_test'\r\n/usr/local/Homebrew/Library/Homebrew/extend/fileutils.rb:14:in `block in mktemp'\r\n/usr/local/Homebrew/Library/Homebrew/extend/fileutils.rb:74:in `block in run'\r\n/usr/local/Homebrew/Library/Homebrew/extend/fileutils.rb:74:in `chdir'\r\n/usr/local/Homebrew/Library/Homebrew/extend/fileutils.rb:74:in `run'\r\n/usr/local/Homebrew/Library/Homebrew/extend/fileutils.rb:13:in `mktemp'\r\n/usr/local/Homebrew/Library/Homebrew/formula.rb:1664:in `run_test'\r\n/usr/local/Homebrew/Library/Homebrew/test.rb:28:in `block in <main>'\r\n/System/Library/Frameworks/Ruby.framework/Versions/2.0/usr/lib/ruby/2.0.0/timeout.rb:66:in `timeout'\r\n/usr/local/Homebrew/Library/Homebrew/test.rb:27:in `<main>'\r\n```"},"comment":{"url":"https://api.github.com/repos/dealii/dealii/issues/comments/275601968","html_url":"https://github.com/dealii/dealii/issues/3853#issuecomment-275601968","issue_url":"https://api.github.com/repos/dealii/dealii/issues/3853","id":275601968,"user":{"login":"ilovezfs","id":5268928,"avatar_url":"https://avatars.githubusercontent.com/u/5268928?v=3","gravatar_id":"","url":"https://api.github.com/users/ilovezfs","html_url":"https://github.com/ilovezfs","followers_url":"https://api.github.com/users/ilovezfs/followers","following_url":"https://api.github.com/users/ilovezfs/following{/other_user}","gists_url":"https://api.github.com/users/ilovezfs/gists{/gist_id}","starred_url":"https://api.github.com/users/ilovezfs/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ilovezfs/subscriptions","organizations_url":"https://api.github.com/users/ilovezfs/orgs","repos_url":"https://api.github.com/users/ilovezfs/repos","events_url":"https://api.github.com/users/ilovezfs/events{/privacy}","received_events_url":"https://api.github.com/users/ilovezfs/received_events","type":"User","site_admin":false},"created_at":"2017-01-27T07:02:39Z","updated_at":"2017-01-27T07:02:39Z","body":"It looks like there was something wrong with the PETSc bottle, though I'm not sure why the problem didn't trigger on positive.\r\n\r\nI rebuilt the PETSc bottle (https://github.com/Homebrew/homebrew-science/commit/3b03395ce78477c898b50365bce2f64f38b9ffbf) and now deal.II CI is passing on both positive and stadium: https://bot.brew.sh/job/Homebrew%20Testing/1299/\r\n\r\nAnimal spirits?"}}
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