SubDomain.mark hangs when called from Python
Issue #1035
new
try to run demos/documented/subdomains/demo_subdomains.py.
I've traced the problem to the Python class not being called from C++:
# Sub domain for no-slip (mark whole boundary, inflow and outflow will overwrite)
class Noslip(SubDomain):
def inside(self, x, on_boundary):
return on_boundary
The C++ code executed up until
bool SubDomain::inside(const Array<double>& x, bool on_boundary) const
{
const Eigen::Map<const Eigen::VectorXd> _x(x.data(), x.size());
return inside(_x, on_boundary);
}
but stalls after this. My guess is the reverse communication somehow doesn't work. Does this have to do with the transition from SWIG to pybind11 ?
Comments (7)
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reporter
I compiled from source on macos 10.13 with 2018.1.0 with GCC 8.2.
The output is:
❯ cd python/demo/documented/subdomains ❯ python3 demo_subdomains.py Computing mesh entities of dimension 1 Elapsed wall, usr, sys time: 0.00595024, 0, 0 (Compute entities dim = 1) Computing sub domain markers for sub domain 0. Requesting connectivity 1 - 2. Requesting connectivity 2 - 1. Computing mesh connectivity 1 - 2 from transpose. Elapsed wall, usr, sys time: 0.000968464, 0, 0 (Compute connectivity 1-2) -> insidethen "sleeps" forever. Also does not respond to Ctrl-C, have to kill python from another prompt.
I inserted a log output here:
dolfin/dolfin/mesh/SubDomain.cpp:51bool SubDomain::inside(const Array<double>& x, bool on_boundary) const { log(TRACE, "-> inside"); const Eigen::Map<const Eigen::VectorXd> _x(x.data(), x.size()); return inside(_x, on_boundary); } -
reporter
Should JIT have been called on
# Sub domain for no-slip (mark whole boundary, inflow and outflow will overwrite) class Noslip(SubDomain): def inside(self, x, on_boundary): return on_boundary ... noslip = Noslip() noslip.mark(sub_domains, 0)If yes, it's not being called. How else does Noslip::inside get called from the C code?
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I have reported the same issue in the afternoon on slack, installation channel. I am also on macosx.
If it can help, below a sampling of the process I got. I was unable to have a better stack trace on the hanging process.
I cannot reproduce on the docker virtual machine.
wSampling process 97978 for 3 seconds with 1 millisecond of run time between samples Sampling completed, processing symbols... Analysis of sampling Python (pid 97978) every 1 millisecond Process: Python [97978] Path: /usr/local/Cellar/python/3.7.0/Frameworks/Python.framework/Versions/3.7/Resources/Python.app/Contents/MacOS/Python Load Address: 0x102824000 Identifier: Python Version: ??? Code Type: X86-64 Parent Process: bash [95701] Date/Time: 2018-08-20 17:55:44.808 +0200 Launch Time: 2018-08-20 17:55:19.274 +0200 OS Version: Mac OS X 10.13.6 (17G65) Report Version: 7 Analysis Tool: /usr/bin/sample Physical footprint: 55.4M Physical footprint (peak): 55.4M ---- Call graph: 2560 Thread_4893417 DispatchQueue_1: com.apple.main-thread (serial) + 2560 start (in libdyld.dylib) + 1 [0x7fff6786b015] + 2560 _Py_UnixMain (in Python) + 104 [0x102919fd4] + 2560 pymain_main (in Python) + 5114 [0x102919842] + 2560 PyRun_SimpleFileExFlags (in Python) + 283 [0x102902159] + 2560 PyRun_FileExFlags (in Python) + 164 [0x102902a7a] + 2560 run_mod (in Python) + 54 [0x102903a5f] + 2560 PyEval_EvalCode (in Python) + 42 [0x1028d4851] + 2560 _PyEval_EvalCodeWithName (in Python) + 1837 [0x1028dead1] + 2560 _PyEval_EvalFrameDefault (in Python) + 4301 [0x1028d59a6] + 2560 call_function (in Python) + 575 [0x1028de17a] + 2560 _PyFunction_FastCallKeywords (in Python) + 225 [0x102847474] + 2560 _PyEval_EvalCodeWithName (in Python) + 1837 [0x1028dead1] + 2560 _PyEval_EvalFrameDefault (in Python) + 4981 [0x1028d5c4e] + 2560 _PyFunction_FastCallDict (in Python) + 441 [0x1028470dd] + 2560 _PyEval_EvalCodeWithName (in Python) + 1837 [0x1028dead1] + 2560 _PyEval_EvalFrameDefault (in Python) + 2604 [0x1028d5305] + 2560 call_function (in Python) + 568 [0x1028de173] + 2560 _PyCFunction_FastCallKeywords (in Python) + 44 [0x1028474af] + 2560 _PyMethodDef_RawFastCallKeywords (in Python) + 577 [0x102847f76] + 2560 ??? (in cpp.cpython-37m-darwin.so) load address 0x1030c4000 + 0xc65f [0x1030d065f] + 2560 ??? (in cpp.cpython-37m-darwin.so) load address 0x1030c4000 + 0x90e69 [0x103154e69] + 2560 dolfin::LinearVariationalSolver::solve() (in libdolfin.2018.1.dylib) + 2273 [0x1034b15e1] LinearVariationalSolver.cpp:112 + 2560 dolfin::DirichletBC::apply(dolfin::GenericMatrix*, dolfin::GenericVector*, dolfin::GenericVector const*) const (in libdolfin.2018.1.dylib) + 262 [0x103482aa6] DirichletBC.cpp:460 + 2560 dolfin::DirichletBC::compute_bc(std::__1::unordered_map<unsigned long, double, std::__1::hash<unsigned long>, std::__1::equal_to<unsigned long>, std::__1::allocator<std::__1::pair<unsigned long const, double> > >&, dolfin::DirichletBC::LocalData&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >) const (in libdolfin.2018.1.dylib) + 755 [0x103485313] DirichletBC.cpp:711 + 2560 dolfin::DirichletBC::compute_bc_topological(std::__1::unordered_map<unsigned long, double, std::__1::hash<unsigned long>, std::__1::equal_to<unsigned long>, std::__1::allocator<std::__1::pair<unsigned long const, double> > >&, dolfin::DirichletBC::LocalData&) const (in libdolfin.2018.1.dylib) + 130 [0x103488a72] DirichletBC.cpp:735 + 2560 dolfin::DirichletBC::init_facets(ompi_communicator_t*) const (in libdolfin.2018.1.dylib) + 295 [0x1034880f7] DirichletBC.cpp:619 + 2560 dolfin::DirichletBC::init_from_sub_domain(std::__1::shared_ptr<dolfin::SubDomain const>) const (in libdolfin.2018.1.dylib) + 275 [0x1034882c3] DirichletBC.cpp:650 + 2560 dolfin::SubDomain::mark(dolfin::MeshFunction<unsigned long>&, unsigned long, bool) const (in libdolfin.2018.1.dylib) + 43 [0x10379cc5b] SubDomain.cpp:109 + 2560 void dolfin::SubDomain::apply_markers<dolfin::MeshFunction<unsigned long>, unsigned long>(dolfin::MeshFunction<unsigned long>&, unsigned long, dolfin::Mesh const&, bool) const (in libdolfin.2018.1.dylib) + 1913 [0x10379d439] SubDomain.cpp:251 + 2560 dolfin::SubDomain::inside(dolfin::Array<double> const&, bool) const (in libdolfin.2018.1.dylib) + 56 [0x10379bb18] SubDomain.cpp:54 + 2560 ??? (in cpp.cpython-37m-darwin.so) load address 0x1030c4000 + 0x16e7d3 [0x1032327d3] + 2560 ??? (in cpp.cpython-37m-darwin.so) load address 0x1030c4000 + 0x1393c [0x1030d793c] + 2560 PyEval_AcquireThread (in Python) + 22 [0x1028d43a9] + 2554 take_gil (in Python) + 229 [0x1028d3fbd] + ! 2525 _pthread_cond_wait (in libsystem_pthread.dylib) + 732 [0x7fff67b84589] + ! : 2497 __psynch_cvwait (in libsystem_kernel.dylib) + 10 [0x7fff679bba16] + ! : 28 cerror_nocancel (in libsystem_kernel.dylib) + 0,20,... [0x7fff679b2ae9,0x7fff679b2afd,...] + ! 19 _pthread_cond_wait (in libsystem_pthread.dylib) + 750,663,... [0x7fff67b8459b,0x7fff67b84544,...] + ! 6 _pthread_cond_wait (in libsystem_pthread.dylib) + 458 [0x7fff67b84477] + ! : 6 __gettimeofday (in libsystem_kernel.dylib) + 17 [0x7fff679bb35e] + ! 2 _pthread_cond_wait (in libsystem_pthread.dylib) + 866 [0x7fff67b8460f] + ! : 2 _pthread_cond_updateval (in libsystem_pthread.dylib) + 40 [0x7fff67b84b12] + ! 2 _pthread_cond_wait (in libsystem_pthread.dylib) + 875 [0x7fff67b84618] + ! 2 pthread_mutex_lock (in libsystem_pthread.dylib) + 0,20 [0x7fff67b8134c,0x7fff67b81360] + 3 take_gil (in Python) + 152 [0x1028d3f70] + ! 2 gettimeofday (in libsystem_c.dylib) + 45 [0x7fff678ca6c3] + ! : 1 __commpage_gettimeofday (in libsystem_kernel.dylib) + 0 [0x7fff679b2414] + ! : 1 __commpage_gettimeofday_internal (in libsystem_kernel.dylib) + 31 [0x7fff679b243a] + ! 1 gettimeofday (in libsystem_c.dylib) + 193 [0x7fff678ca757] + 1 DYLD-STUB$$gettimeofday (in Python) + 0 [0x10295b0a0] + 1 DYLD-STUB$$pthread_cond_timedwait (in Python) + 0 [0x10295b208] + 1 take_gil (in Python) + 116 [0x1028d3f4c] 2560 Thread_4893446 + 2560 thread_start (in libsystem_pthread.dylib) + 13 [0x7fff67b82bf9] + 2560 _pthread_start (in libsystem_pthread.dylib) + 377 [0x7fff67b8350d] + 2560 _pthread_body (in libsystem_pthread.dylib) + 340 [0x7fff67b83661] + 2560 progress_engine (in libopen-pal.40.dylib) + 26 [0x105ab478e] + 2560 event_base_loop (in libevent-2.1.6.dylib) + 786 [0x105b5f519] + 2560 select_dispatch (in libevent-2.1.6.dylib) + 219 [0x105b67e65] + 2560 __select (in libsystem_kernel.dylib) + 10 [0x7fff679bbcf2] 2560 Thread_4893447 2560 thread_start (in libsystem_pthread.dylib) + 13 [0x7fff67b82bf9] 2560 _pthread_start (in libsystem_pthread.dylib) + 377 [0x7fff67b8350d] 2560 _pthread_body (in libsystem_pthread.dylib) + 340 [0x7fff67b83661] 2560 progress_engine (in mca_pmix_pmix2x.so) + 26 [0x10f234d3b] 2560 event_base_loop (in libevent-2.1.6.dylib) + 786 [0x105b5f519] 2560 kq_dispatch (in libevent-2.1.6.dylib) + 525 [0x105b68820] 2560 kevent (in libsystem_kernel.dylib) + 10 [0x7fff679bcbea] Total number in stack (recursive counted multiple, when >=5): Sort by top of stack, same collapsed (when >= 5): __select (in libsystem_kernel.dylib) 2560 kevent (in libsystem_kernel.dylib) 2560 __psynch_cvwait (in libsystem_kernel.dylib) 2497 cerror_nocancel (in libsystem_kernel.dylib) 28 _pthread_cond_wait (in libsystem_pthread.dylib) 19 __gettimeofday (in libsystem_kernel.dylib) 6 Binary Images: 0x102824000 - 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0x7fff67bb4ff7 libunwind.dylib (35.3) <BEF3FB49-5604-3B5F-82B5-332B80023AC3> /usr/lib/system/libunwind.dylib 0x7fff67bb5000 - 0x7fff67be2ff7 libxpc.dylib (1205.70.9) <0BC7AD67-671D-31D4-8B88-C317B8379598> /usr/lib/system/libxpc.dylib Sample analysis of process 97978 written to file /dev/stdout -
There's no JIT. Python is (should be) called from C++ thanks to pybind11.
Maybe it has something to do with changes in threads in Python 3.7: https://docs.python.org/3/whatsnew/3.7.html. Can you check you have up-to-date pybind11 version?
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Thanks @janblecha, I solved indeed installing dev version of
pybind11. Problably related to this issue inpybind11: https://github.com/pybind/pybind11/issues/1444. Everything should be fixed with the next release of pybind11.Maybe leave this issue open and update the readme here https://bitbucket.org/fenics-project/dolfin/src/master/python/README.rst about the minimal pybind version for python3.7 when the next release is out?
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reporter
Oh, thanks @blechta and @cmaurini.
I had pybind11 2.2.3 from Homebrew. That should be the release from Github.
I installed the pybind11 HEAD now and the demo works.
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How to reproduce it? I can't reproduce it neither with 2018.1.0 nor master.