{"action":"created","issue":{"url":"https://api.github.com/repos/elemental/Elemental/issues/181","repository_url":"https://api.github.com/repos/elemental/Elemental","labels_url":"https://api.github.com/repos/elemental/Elemental/issues/181/labels{/name}","comments_url":"https://api.github.com/repos/elemental/Elemental/issues/181/comments","events_url":"https://api.github.com/repos/elemental/Elemental/issues/181/events","html_url":"https://github.com/elemental/Elemental/issues/181","id":176553679,"number":181,"title":"Seg fault in Cholesky","user":{"login":"haimav","id":7327450,"avatar_url":"https://avatars.githubusercontent.com/u/7327450?v=3","gravatar_id":"","url":"https://api.github.com/users/haimav","html_url":"https://github.com/haimav","followers_url":"https://api.github.com/users/haimav/followers","following_url":"https://api.github.com/users/haimav/following{/other_user}","gists_url":"https://api.github.com/users/haimav/gists{/gist_id}","starred_url":"https://api.github.com/users/haimav/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/haimav/subscriptions","organizations_url":"https://api.github.com/users/haimav/orgs","repos_url":"https://api.github.com/users/haimav/repos","events_url":"https://api.github.com/users/haimav/events{/privacy}","received_events_url":"https://api.github.com/users/haimav/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":16,"created_at":"2016-09-13T05:35:55Z","updated_at":"2016-09-21T04:51:31Z","closed_at":null,"body":"In my larger code, the following code generates a seg fault in Elemental.\r\n\r\n        El::Identity(C, 100, 100);\r\n        El::Cholesky(El::LOWER, C);\r\n\r\n(original code was more complex, but even this generated the seg fault).\r\n\r\nHere is a stack trace:\r\n\r\nProgram received signal SIGSEGV, Segmentation fault.\r\n0x00007fff8af9a2da in stack_not_16_byte_aligned_error () from /usr/lib/system/libdyld.dylib\r\n(gdb) where\r\n#0  0x00007fff8af9a2da in stack_not_16_byte_aligned_error () from /usr/lib/system/libdyld.dylib\r\n#1  0x00007fff5fbfcb80 in ?? ()\r\n#2  0x00000001028d2398 in ?? () from /usr/local/lib/libEl.dylib\r\n#3  0x0000000000137ad6 in ?? ()\r\n#4  0x00000001012cbf6e in El::Matrix<double>::operator()(El::Range<int>, El::Range<int>) () from /usr/local/lib/libEl.dylib\r\n#5  0x000000010152ecfc in void El::cholesky::UVar3<double>(El::Matrix<double>&) () from /usr/local/lib/libEl.dylib\r\n#6  0x0000000101537f15 in void El::cholesky::UVar3<double>(El::AbstractDistMatrix<double>&) () from /usr/local/lib/libEl.dylib\r\n#7  0x00000001000a01b6 in skylark::ml::feature_map_precond_t<El::DistMatrix<double, (El::DistNS::Dist)0, (El::DistNS::Dist)2, (El::DistWrapNS::DistWrap)0> >::feature_map_precond_t<skylark::ml::kernel_container_t, El::DistMatrix<double, (El::DistNS::Dist)0, (El::DistNS::Dist)2, (El::DistWrapNS::DistWrap)0> > (this=0x105757490, k=..., lambda=<optimized out>, X=..., s=<optimized out>, context=..., params=...)\r\n    at /Users/haimav/Coding/libskylark/ml/krr.hpp:385\r\n#8  0x00000001000a44c1 in skylark::ml::FasterKernelRidge<double, skylark::ml::kernel_container_t> (direction=<optimized out>, k=..., X=...,\r\n    Y=..., lambda=0.01, A=..., s=50, context=..., params=...) at /Users/haimav/Coding/libskylark/ml/krr.hpp:501\r\n#9  0x000000010012a280 in skylark::ml::FasterKernelRLSC<double, int, skylark::ml::kernel_container_t> (direction=COLUMNS, k=..., X=..., L=...,\r\n    lambda=0.01, A=..., rcoding=..., s=50, context=..., params=...) at /Users/haimav/Coding/libskylark/ml/rlsc.hpp:244\r\n#10 0x000000010012f243 in execute_classification<double> (context=...) at /Users/haimav/Coding/libskylark/examples/kernel_regression.cpp:401\r\n#11 0x00000001001309b9 in main (argc=9, argv=0x7fff5fbff978) at /Users/haimav/Coding/libskylark/examples/kernel_regression.cpp:882"},"comment":{"url":"https://api.github.com/repos/elemental/Elemental/issues/comments/248511058","html_url":"https://github.com/elemental/Elemental/issues/181#issuecomment-248511058","issue_url":"https://api.github.com/repos/elemental/Elemental/issues/181","id":248511058,"user":{"login":"jeffhammond","id":406118,"avatar_url":"https://avatars.githubusercontent.com/u/406118?v=3","gravatar_id":"","url":"https://api.github.com/users/jeffhammond","html_url":"https://github.com/jeffhammond","followers_url":"https://api.github.com/users/jeffhammond/followers","following_url":"https://api.github.com/users/jeffhammond/following{/other_user}","gists_url":"https://api.github.com/users/jeffhammond/gists{/gist_id}","starred_url":"https://api.github.com/users/jeffhammond/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jeffhammond/subscriptions","organizations_url":"https://api.github.com/users/jeffhammond/orgs","repos_url":"https://api.github.com/users/jeffhammond/repos","events_url":"https://api.github.com/users/jeffhammond/events{/privacy}","received_events_url":"https://api.github.com/users/jeffhammond/received_events","type":"User","site_admin":false},"created_at":"2016-09-21T04:51:31Z","updated_at":"2016-09-21T04:51:31Z","body":"I too am unable to reproduce.\r\n\r\nI saw the following issue:\r\n```\r\n/var/folders/tz/3sxkhvt90632mzr6fxm1cd0h0000gp/T//ccRiuRgy.s:235666:11: warning: section \"__const_coal\" is deprecated\r\n        .section __DATA,__const_coal,coalesced\r\n                 ^      ~~~~~~~~~~~~\r\n/var/folders/tz/3sxkhvt90632mzr6fxm1cd0h0000gp/T//ccRiuRgy.s:235666:11: note: change section name to \"__const\"\r\n        .section __DATA,__const_coal,coalesced\r\n                 ^      ~~~~~~~~~~~~\r\n```\r\nThis was solved exactly as described on http://stackoverflow.com/questions/39502921/warning-section-const-coal-is-deprecated-error-after-updating-xcode-to-la.\r\n\r\nThe test I ran successful was:\r\n\r\n```c++\r\n#include \"El.hpp\"\r\nint main(int argc, char* argv[]){\r\nEl::Initialize(argc, argv);\r\nEl::Matrix<double> C;\r\nEl::Identity(C, 1000, 1000);\r\nEl::Cholesky(El::LOWER, C);\r\n}\r\n```\r\n\r\n```sh\r\n/opt/mpich/dev/gcc/default/bin/mpicxx \\\r\n-I$HOME/Work/Elemental/git/install-gcc/include \\\r\n-std=c++11 toy.cc  \\\r\n-L$HOME/Work/Elemental/git/install-gcc/lib -lEl \\\r\n-Wl,-rpath -Wl,$HOME/Work/Elemental/git/install-gcc/lib\r\n```\r\n\r\nI am running OS X 10.11.6 with the following GCC and MPICH.\r\n```\r\n$ g++-6 -v\r\nUsing built-in specs.\r\nCOLLECT_GCC=g++-6\r\nCOLLECT_LTO_WRAPPER=/usr/local/Cellar/gcc/6.2.0/libexec/gcc/x86_64-apple-darwin15.6.0/6.2.0/lto-wrapper\r\nTarget: x86_64-apple-darwin15.6.0\r\nConfigured with: ../configure --build=x86_64-apple-darwin15.6.0 --prefix=/usr/local/Cellar/gcc/6.2.0 --libdir=/usr/local/Cellar/gcc/6.2.0/lib/gcc/6 --enable-languages=c,c++,objc,obj-c++,fortran --program-suffix=-6 --with-gmp=/usr/local/opt/gmp --with-mpfr=/usr/local/opt/mpfr --with-mpc=/usr/local/opt/libmpc --with-isl=/usr/local/opt/isl --with-system-zlib --enable-libstdcxx-time=yes --enable-stage1-checking --enable-checking=release --enable-lto --with-build-config=bootstrap-debug --disable-werror --with-pkgversion='Homebrew gcc 6.2.0 --without-multilib' --with-bugurl=https://github.com/Homebrew/homebrew/issues --enable-plugin --disable-nls --disable-multilib\r\nThread model: posix\r\ngcc version 6.2.0 (Homebrew gcc 6.2.0 --without-multilib) \r\n```\r\n\r\n```\r\n$ /opt/mpich/dev/gcc/default/bin/mpichversion \r\nMPICH Version:    \t3.3a1\r\nMPICH Release date:\tunreleased development copy\r\nMPICH Device:    \tch3:nemesis\r\nMPICH configure: \tCC=gcc-6 CXX=g++-6 FC=gfortran-6 F77=gfortran-6 --enable-cxx --enable-fortran --enable-threads=runtime --enable-g=dbg --with-pm=hydra --prefix=/opt/mpich/dev/gcc/default --enable-wrapper-rpath --disable-static --enable-shared\r\nMPICH CC: \tgcc-6    -g -O2\r\nMPICH CXX: \tg++-6   -g\r\nMPICH F77: \tgfortran-6   -g\r\nMPICH FC: \tgfortran-6   -g\r\nMPICH Custom Information: \r\n```"}}
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