{"action":"created","issue":{"url":"https://api.github.com/repos/stan-dev/math/issues/529","repository_url":"https://api.github.com/repos/stan-dev/math","labels_url":"https://api.github.com/repos/stan-dev/math/issues/529/labels{/name}","comments_url":"https://api.github.com/repos/stan-dev/math/issues/529/comments","events_url":"https://api.github.com/repos/stan-dev/math/issues/529/events","html_url":"https://github.com/stan-dev/math/pull/529","id":223591373,"number":529,"title":"Do Cholesky Decomposition With the GPU","user":{"login":"SteveBronder","id":5857231,"avatar_url":"https://avatars0.githubusercontent.com/u/5857231?v=4","gravatar_id":"","url":"https://api.github.com/users/SteveBronder","html_url":"https://github.com/SteveBronder","followers_url":"https://api.github.com/users/SteveBronder/followers","following_url":"https://api.github.com/users/SteveBronder/following{/other_user}","gists_url":"https://api.github.com/users/SteveBronder/gists{/gist_id}","starred_url":"https://api.github.com/users/SteveBronder/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/SteveBronder/subscriptions","organizations_url":"https://api.github.com/users/SteveBronder/orgs","repos_url":"https://api.github.com/users/SteveBronder/repos","events_url":"https://api.github.com/users/SteveBronder/events{/privacy}","received_events_url":"https://api.github.com/users/SteveBronder/received_events","type":"User","site_admin":false},"labels":[{"id":233078045,"url":"https://api.github.com/repos/stan-dev/math/labels/feature","name":"feature","color":"bfd4f2","default":false}],"state":"open","locked":false,"assignee":{"login":"SteveBronder","id":5857231,"avatar_url":"https://avatars0.githubusercontent.com/u/5857231?v=4","gravatar_id":"","url":"https://api.github.com/users/SteveBronder","html_url":"https://github.com/SteveBronder","followers_url":"https://api.github.com/users/SteveBronder/followers","following_url":"https://api.github.com/users/SteveBronder/following{/other_user}","gists_url":"https://api.github.com/users/SteveBronder/gists{/gist_id}","starred_url":"https://api.github.com/users/SteveBronder/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/SteveBronder/subscriptions","organizations_url":"https://api.github.com/users/SteveBronder/orgs","repos_url":"https://api.github.com/users/SteveBronder/repos","events_url":"https://api.github.com/users/SteveBronder/events{/privacy}","received_events_url":"https://api.github.com/users/SteveBronder/received_events","type":"User","site_admin":false},"assignees":[{"login":"SteveBronder","id":5857231,"avatar_url":"https://avatars0.githubusercontent.com/u/5857231?v=4","gravatar_id":"","url":"https://api.github.com/users/SteveBronder","html_url":"https://github.com/SteveBronder","followers_url":"https://api.github.com/users/SteveBronder/followers","following_url":"https://api.github.com/users/SteveBronder/following{/other_user}","gists_url":"https://api.github.com/users/SteveBronder/gists{/gist_id}","starred_url":"https://api.github.com/users/SteveBronder/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/SteveBronder/subscriptions","organizations_url":"https://api.github.com/users/SteveBronder/orgs","repos_url":"https://api.github.com/users/SteveBronder/repos","events_url":"https://api.github.com/users/SteveBronder/events{/privacy}","received_events_url":"https://api.github.com/users/SteveBronder/received_events","type":"User","site_admin":false}],"milestone":null,"comments":95,"created_at":"2017-04-22T20:38:45Z","updated_at":"2017-08-13T02:17:20Z","closed_at":null,"pull_request":{"url":"https://api.github.com/repos/stan-dev/math/pulls/529","html_url":"https://github.com/stan-dev/math/pull/529","diff_url":"https://github.com/stan-dev/math/pull/529.diff","patch_url":"https://github.com/stan-dev/math/pull/529.patch"},"body":"#### Submission Checklist\r\n\r\n- [ ] 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\n\r\nPasses Cholesky Decompositions to the GPU using ViennaCL\r\n\r\n#### Intended Effect:\r\n\r\nGives users the ability to pass computation for Cholesky Decompositions to the GPU\r\n\r\n#### How to Verify:\r\n\r\nTODO: Make and run tests\r\n\r\n#### Side Effects:\r\n\r\nTODO\r\n\r\n#### Documentation:\r\n\r\nTODO\r\n\r\n#### Reviewer Suggestions: \r\n\r\n#### Copyright and Licensing\r\n\r\nSteve Bronder\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\r\nYes"},"comment":{"url":"https://api.github.com/repos/stan-dev/math/issues/comments/322017408","html_url":"https://github.com/stan-dev/math/pull/529#issuecomment-322017408","issue_url":"https://api.github.com/repos/stan-dev/math/issues/529","id":322017408,"user":{"login":"bgoodri","id":3386282,"avatar_url":"https://avatars2.githubusercontent.com/u/3386282?v=4","gravatar_id":"","url":"https://api.github.com/users/bgoodri","html_url":"https://github.com/bgoodri","followers_url":"https://api.github.com/users/bgoodri/followers","following_url":"https://api.github.com/users/bgoodri/following{/other_user}","gists_url":"https://api.github.com/users/bgoodri/gists{/gist_id}","starred_url":"https://api.github.com/users/bgoodri/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/bgoodri/subscriptions","organizations_url":"https://api.github.com/users/bgoodri/orgs","repos_url":"https://api.github.com/users/bgoodri/repos","events_url":"https://api.github.com/users/bgoodri/events{/privacy}","received_events_url":"https://api.github.com/users/bgoodri/received_events","type":"User","site_admin":false},"created_at":"2017-08-13T02:17:19Z","updated_at":"2017-08-13T02:17:19Z","body":"When debugging, you don't want -03. Do -O0 or -Og.\n\nOn Sat, Aug 12, 2017 at 10:14 PM, Steve Bronder <notifications@github.com>\nwrote:\n\n> Compiling the programs with the following\n>\n> g++ -I . -isystem lib/eigen_3.3.3 -isystem lib/boost_1.62.0 -isystem lib/cvodes_2.9.0/include -std=c++1y -DBOOST_RESULT_OF_USE_TR1 -DBOOST_NO_DECLTYPE -DBOOST_DISABLE_ASSERTS -D STAN_GPU -isystem lib/viennacl_1.7.1 -DGTEST_USE_OWN_TR1_TUPLE -DGTEST_HAS_PTHREAD=0 -isystem lib/gtest_1.7.0/include -isystem lib/gtest_1.7.0 -O3 -DGTEST_USE_OWN_TR1_TUPLE -DGTEST_HAS_PTHREAD=0 -isystem lib/gtest_1.7.0/include -isystem lib/gtest_1.7.0 -O3 -Wall -DNO_FPRINTF_OUTPUT -pipe  -c -o test/unit/math/rev/mat/fun/cholesky_decompose_gpu_test.o test/unit/math/rev/mat/fun/cholesky_decompose_gpu_test.cpp -lOpenCL\n>\n>\n> g++ -I . -isystem lib/eigen_3.3.3 -isystem lib/boost_1.62.0 -isystem lib/cvodes_2.9.0/include -std=c++1y -DBOOST_RESULT_OF_USE_TR1 -DBOOST_NO_DECLTYPE -DBOOST_DISABLE_ASSERTS -D STAN_GPU -isystem lib/viennacl_1.7.1 -lOpenCL -DGTEST_USE_OWN_TR1_TUPLE -DGTEST_HAS_PTHREAD=0 -isystem lib/gtest_1.7.0/include -isystem lib/gtest_1.7.0 -O3 -Wall -DNO_FPRINTF_OUTPUT -pipe -lpthread  -o test/unit/math/rev/mat/fun/cholesky_decompose_gpu_test test/unit/math/rev/mat/fun/cholesky_decompose_gpu_test.o -lOpenCL lib/gtest_1.7.0/src/gtest_main.cc lib/gtest_1.7.0/src/gtest-all.o\n>\n> and doing a traceback on the segfault gives\n>\n> $: gdb test/unit/math/rev/mat/fun/cholesky_decompose_gpu_test\n> (gdb) start\n> Temporary breakpoint 1 at 0xef10\n> Starting program: /home/steve/Statistics/opensource/stan/math/test/unit/math/rev/mat/fun/cholesky_decompose_gpu_test\n>\n> Program received signal SIGSEGV, Segmentation fault.0x00007ffff78e983a in ?? () from /usr/lib/x86_64-linux-gnu/libstdc++.so.6\n> (gdb) bt\n>\n> Temporary breakpoint 1 at 0xef10\n> Starting program: /home/steve/Statistics/opensource/stan/math/test/unit/math/rev/mat/fun/cholesky_decompose_gpu_test\n>\n> Program received signal SIGSEGV, Segmentation fault.0x00007ffff78e983a in ?? () from /usr/lib/x86_64-linux-gnu/libstdc++.so.6\n> (gdb) bt#0  0x00007ffff78e983a in ?? () from /usr/lib/x86_64-linux-gnu/libstdc++.so.6#1  0x00005555555a8f66 in std::_Rb_tree<long, std::pair<long const, bool>, std::_Select1st<std::pair<long const, bool> >, std::less<long>, std::allocator<std::pair<long const, bool> > >::_M_get_insert_unique_pos(long const&) ()#2  0x00005555555a901f in std::_Rb_tree<long, std::pair<long const, bool>, std::_Select1st<std::pair<long const, bool> >, std::less<long>, std::allocator<std::pair<long const, bool> > >::_M_get_insert_hint_unique_pos(std::_Rb_tree_const_iterator<std::pair<long const, bool> >, long const&) ()#3  0x00005555555a9f8c in viennacl::ocl::backend<false>::context(long) ()#4  0x000055555556244c in _GLOBAL__sub_I_in ()#5  0x000055555561a5cd in __libc_csu_init ()#6  0x00007ffff6f7b380 in __libc_start_main (main=0x555555562f10 <main>, argc=1, argv=0x7fffffffde48, init=0x55555561a580 <__libc_csu_init>,\n>     fini=<optimized out>, rtld_fini=<optimized out>, stack_end=0x7fffffffde38) at ../csu/libc-start.c:247#7  0x00005555555632aa in _start ()\n>\n> So it seems like main() -> viennacl::ocl -> libstdc++.so.6 -> error?\n> Really not sure what is going on here.\n>\n> g++ version below\n>\n> $: g++ -v\n> Using built-in specs.\n> COLLECT_GCC=g++\n> COLLECT_LTO_WRAPPER=/usr/lib/gcc/x86_64-linux-gnu/6/lto-wrapper\n> Target: x86_64-linux-gnu\n> Configured with: ../src/configure -v --with-pkgversion='Ubuntu 6.3.0-12ubuntu2' --with-bugurl=file:///usr/share/doc/gcc-6/README.Bugs --enable-languages=c,ada,c++,java,go,d,fortran,objc,obj-c++ --prefix=/usr --program-suffix=-6 --program-prefix=x86_64-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --with-sysroot=/ --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-vtable-verify --enable-libmpx --enable-plugin --enable-default-pie --with-system-zlib --disable-browser-plugin --enable-java-awt=gtk --enable-gtk-cairo --with-java-home=/usr/lib/jvm/java-1.5.0-gcj-6-amd64/jre --enable-java-home --with-jvm-root-dir=/usr/lib/jvm/java-1.5.0-gcj-6-amd64 --with-jvm-jar-dir=/usr/lib/jvm-exports/java-1.5.0-gcj-6-amd64 --with-arch-directory=amd64 --with-ecj-jar=/usr/share/java/eclipse-ecj.jar --with-target-system-zlib --enable-objc-gc=auto --enable-multiarch --disable-werror --with-arch-32=i686 --with-abi=m64 --with-multilib-list=m32,m64,mx32 --enable-multilib --with-tune=generic --enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu\n> Thread model: posix\n> gcc version 6.3.0 20170406 (Ubuntu 6.3.0-12ubuntu2)\n>\n> Sys Info:\n>\n> $: lsb_release -a\n> No LSB modules are available.\n> Distributor ID:\tUbuntu\n> Description:\tUbuntu 17.04\n> Release:\t17.04\n> Codename:\tzesty\n>\n> —\n> You are receiving this because you were mentioned.\n> Reply to this email directly, view it on GitHub\n> <https://github.com/stan-dev/math/pull/529#issuecomment-322017311>, or mute\n> the thread\n> <https://github.com/notifications/unsubscribe-auth/ADOrqv5jqdGFKK4eaiIJ8-xaV3Ej0iWCks5sXlvqgaJpZM4NFNUg>\n> .\n>\n"}}
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