{"action":"created","issue":{"url":"https://api.github.com/repos/psi4/psi4public/issues/153","labels_url":"https://api.github.com/repos/psi4/psi4public/issues/153/labels{/name}","comments_url":"https://api.github.com/repos/psi4/psi4public/issues/153/comments","events_url":"https://api.github.com/repos/psi4/psi4public/issues/153/events","html_url":"https://github.com/psi4/psi4public/issues/153","id":97104833,"number":153,"title":"crash in Geometry Optimization","user":{"login":"dellelce","id":660211,"avatar_url":"https://avatars.githubusercontent.com/u/660211?v=3","gravatar_id":"","url":"https://api.github.com/users/dellelce","html_url":"https://github.com/dellelce","followers_url":"https://api.github.com/users/dellelce/followers","following_url":"https://api.github.com/users/dellelce/following{/other_user}","gists_url":"https://api.github.com/users/dellelce/gists{/gist_id}","starred_url":"https://api.github.com/users/dellelce/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/dellelce/subscriptions","organizations_url":"https://api.github.com/users/dellelce/orgs","repos_url":"https://api.github.com/users/dellelce/repos","events_url":"https://api.github.com/users/dellelce/events{/privacy}","received_events_url":"https://api.github.com/users/dellelce/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":4,"created_at":"2015-07-24T18:02:15Z","updated_at":"2015-07-30T14:11:25Z","closed_at":null,"body":"I had a crash for a geometry optimization, this is the stack track:\r\n\r\nReading symbols from /app/miniconda/bin/psi4...(no debugging symbols found)...done.\r\n[New LWP 7474]\r\n[Thread debugging using libthread_db enabled]\r\nUsing host libthread_db library \"/lib64/libthread_db.so.1\".\r\nCore was generated by `psi4'.\r\nProgram terminated with signal SIGABRT, Aborted.\r\n#0  0x00006a91c31f18d7 in __GI_raise (sig=sig@entry=6) at ../sysdeps/unix/sysv/linux/raise.c:55\r\n55        return INLINE_SYSCALL (tgkill, 3, pid, selftid, sig);\r\n(gdb) where\r\n#0  0x00006a91c31f18d7 in __GI_raise (sig=sig@entry=6) at ../sysdeps/unix/sysv/linux/raise.c:55\r\n#1  0x00006a91c31f353a in __GI_abort () at abort.c:89\r\n#2  0x00000000014c2e4f in opt::optking(psi::Options&) ()\r\n#3  0x0000000000a4c2fc in py_psi_optking() ()\r\n#4  0x0000000000a8993e in boost::python::objects::caller_py_function_impl<boost::python::detail::caller<int (*)(), boost::python::default_call_policies, boost::mpl::vector1<int> > >::operator()(_object*, _object*) ()\r\n#5  0x000000000554b96e in boost::python::objects::function::call(_object*, _object*) const ()\r\n#6  0x000000000554b6a5 in boost::detail::function::void_function_ref_invoker0<boost::python::objects::(anonymous namespace)::bind_return, void>::invoke(boost::detail::function::function_buffer&) ()\r\n#7  0x000000000555699d in boost::python::detail::exception_handler::operator()(boost::function0<void> const&) const ()\r\n#8  0x0000000000a6d6f5 in boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<psi::PsiException, void (*)(psi::PsiException const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(psi::PsiException const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) ()\r\n#9  0x0000000005556d54 in boost::python::handle_exception_impl(boost::function0<void>) ()\r\n#10 0x000000000554d0fe in function_call ()\r\n#11 0x00006a91c37de333 in PyObject_Call (func=0x9231260, arg=<optimized out>, kw=<optimized out>) at Objects/abstract.c:2529\r\n#12 0x00006a91c388d4b2 in do_call (nk=<optimized out>, na=<optimized out>, pp_stack=0x712c327ea368, func=0x9231260) at Python/ceval.c:4253\r\n#13 call_function (oparg=<optimized out>, pp_stack=0x712c327ea368) at Python/ceval.c:4058\r\n#14 PyEval_EvalFrameEx (f=<optimized out>, throwflag=<optimized out>) at Python/ceval.c:2681\r\n#15 0x00006a91c388fdbe in PyEval_EvalCodeEx (co=0x6a91b94db9b0, globals=<optimized out>, locals=<optimized out>, args=<optimized out>, argcount=1, kws=0x92f85c8, kwcount=1, defs=0x0, defcount=0, closure=0x0) at Python/ceval.c:3267\r\n#16 0x00006a91c388e3fa in fast_function (nk=<optimized out>, na=1, n=<optimized out>, pp_stack=0x712c327ea568, func=0x6a91b8cca488) at Python/ceval.c:4131\r\n#17 call_function (oparg=<optimized out>, pp_stack=0x712c327ea568) at Python/ceval.c:4056\r\n#18 PyEval_EvalFrameEx (f=<optimized out>, throwflag=<optimized out>) at Python/ceval.c:2681\r\n#19 0x00006a91c388fdbe in PyEval_EvalCodeEx (co=0x6a91c45356b0, globals=<optimized out>, locals=<optimized out>, args=<optimized out>, argcount=0, kws=0x0, kwcount=0, defs=0x0, defcount=0, closure=0x0) at Python/ceval.c:3267\r\n#20 0x00006a91c388fed2 in PyEval_EvalCode (co=<optimized out>, globals=<optimized out>, locals=<optimized out>) at Python/ceval.c:669\r\n#21 0x00006a91c38ae38c in run_mod (arena=0x93cee40, flags=<optimized out>, locals=0x6a91c4610d70, globals=0x6a91c4610d70, filename=0x6a91c38de42d \"<string>\", mod=<optimized out>) at Python/pythonrun.c:1371\r\n#22 PyRun_StringFlags (\r\n    str=0x92f8a04 \"from psi4 import *\\nfrom p4const import *\\nfrom p4util import *\\nfrom molutil import *\\nfrom aliases import *\\npsi4_io = psi4.IOManager.shared_object()\\npsi4.efp_init()\\npsi4_io.set_default_path(\\\"/app/scienc\"..., \r\n    start=257, globals=0x6a91c4610d70, locals=0x6a91c4610d70, flags=<optimized out>) at Python/pythonrun.c:1334\r\n#23 0x000000000555a8aa in boost::python::exec(boost::python::str, boost::python::api::object, boost::python::api::object) ()\r\n#24 0x0000000000a67f25 in psi::Python::run(_IO_FILE*) ()\r\n#25 0x00000000009937e0 in main ()\r\n(gdb) \r\n\r\nthe input file:\r\n\r\nmemory 2500 mb\r\n\r\nmolecule struct {\r\n symmetry c1\r\n no_reorient   #\r\n no_com   # whether to move the origin to the center of masses\r\n units angstrom\r\n0 1   \r\n      C                    0.008240    0.001327    0.000310\r\n      C                    1.553694    0.001373    0.000036\r\n      N                   -0.700795   -1.157242   -0.001319\r\n      N                   -2.008585   -1.428031    0.002174\r\n      N                   -0.699812    1.158389   -0.000832\r\n      N                   -2.008322    1.432822    0.001677\r\n      N                    2.267238    1.156444   -0.001011\r\n      N                    3.565803    1.436891    0.001896\r\n      N                    2.266013   -1.155613   -0.000583\r\n      N                    3.563003   -1.435099    0.001415\r\n      B                   -1.131831   -2.605160   -0.011643\r\n      B                   -1.129410    2.608511   -0.010295\r\n      B                    2.669048   -2.603366   -0.007508\r\n      B                    2.671738    2.604971   -0.007555\r\n}\r\n\r\nset  {\r\n  basis       6-31G*\r\n  # Do use pure angular momentum basis functions?\r\n #  PUREAM false\r\n\r\n #  SCF_TYPE DIRECT  # An out-of-core, presorted algorithm using exact ERIs.\r\n\r\n #  MOLDEN_WRITE true\r\n\r\n}\r\n\r\noptimize('scf', dertype='energy')\r\n\r\npsi4 is installed through miniconda:\r\n\r\n[root@titan3 2]# find /app/ -name psi4 -type f\r\n/app/miniconda/pkgs/psi4-0.2.54-py27_gf997694/bin/psi4\r\n/app/miniconda/bin/psi4\r\n[root@titan3 2]# /app/miniconda/bin/psi4 --version\r\n0.2.54\r\n"},"comment":{"url":"https://api.github.com/repos/psi4/psi4public/issues/comments/126342063","html_url":"https://github.com/psi4/psi4public/issues/153#issuecomment-126342063","issue_url":"https://api.github.com/repos/psi4/psi4public/issues/153","id":126342063,"user":{"login":"loriab","id":2314730,"avatar_url":"https://avatars.githubusercontent.com/u/2314730?v=3","gravatar_id":"","url":"https://api.github.com/users/loriab","html_url":"https://github.com/loriab","followers_url":"https://api.github.com/users/loriab/followers","following_url":"https://api.github.com/users/loriab/following{/other_user}","gists_url":"https://api.github.com/users/loriab/gists{/gist_id}","starred_url":"https://api.github.com/users/loriab/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/loriab/subscriptions","organizations_url":"https://api.github.com/users/loriab/orgs","repos_url":"https://api.github.com/users/loriab/repos","events_url":"https://api.github.com/users/loriab/events{/privacy}","received_events_url":"https://api.github.com/users/loriab/received_events","type":"User","site_admin":false},"created_at":"2015-07-30T14:11:25Z","updated_at":"2015-07-30T14:11:25Z","body":"Yes, I agree it looks messed up. Added the further info in last post for @psi-rking "}}