Building NGSolve with HYPRE support

More
2 years 1 week ago #3017 by JanWesterdiep
Hiya,

I shelved the MPI project for a while, but am back again experimenting. I cloned the latest NGSolve build, compiled with `-DUSE_MPI=ON -DUSE_HYPRE=ON` and ran Lukas' attached `precond_test_2020-02-05.py` as `mpirun -np 4 ngspy precond_test_2020-02-05.py`. I get a segfault, but this time it does give me a backtrace:
Code:
#1 at std::__1::basic_stringbuf<char, std::__1::char_traits<char>, std::__1::allocator<char> >::str() const (in libngcore.dylib) (/Library/Developer/CommandLineTools/usr/include/c++/v1/new:252) #2 at 0x0000a3ac (in libsystem_platform.dylib) #3 #4 at HYPRE_IJMatrixGetValues (in libngcomp.dylib) + 125 #5 at HYPRE_IJMatrixAddToValues2 (in libngcomp.dylib) + 131 #6 at ngcomp::HyprePreconditioner::Mult(ngla::BaseVector const&, ngla::BaseVector&) const (in libngcomp.dylib) (/Applications/Netgen.app/Contents/Resources/include/core/profiler.hpp:157) #7 at ngcomp::HyprePreconditioner::Mult(ngla::BaseVector const&, ngla::BaseVector&) const (in libngcomp.dylib) (/Applications/Netgen.app/Contents/Resources/include/core/mpi_wrapper.hpp:72) #8 at ngcomp::S_BilinearForm<std::__1::complex<double> >::AddMatrixTP(std::__1::complex<double>, ngla::BaseVector const&, ngla::BaseVector&, ngcore::LocalHeap&) const (in libngcomp.dylib) (/Library/Developer/CommandLineTools/usr/include/c++/v1/memory:2153) #9 at ngcomp::BilinearForm::Assemble(ngcore::LocalHeap&) (in libngcomp.dylib) (/Library/Developer/CommandLineTools/usr/include/c++/v1/__locale:234) #10 #11 at std::__1::vector<bool, std::__1::allocator<bool> >::resize(unsigned long, bool) (in libngcomp.dylib) (/Library/Developer/CommandLineTools/usr/include/c++/v1/__bit_reference:0) #12 at _PyObject_CallFunctionVa (in Python) + 0 #13 at _PyFunction_FastCallKeywords (in Python) + 267 #14 at call_function (in Python) + 1051 #15 at convertitem (in Python) + 8476 #16 at compiler_enter_scope (in Python) + 242 #17 at PyObject_Call (in Python) + 114 #18 at _PyEval_EvalCodeWithName (in Python) + 675 #19 at convertitem (in Python) + 9379 #20 at compiler_enter_scope (in Python) + 242 #21 at PyEval_EvalFrame (in Python) + 11 #22 at PyRun_StringFlags (in Python) + 100 #23 at PyRun_InteractiveOneObject (in Python) + 11 #24 at ScandirIterator_exit (in Python) + 0 #25 at Py_GetArgcArgv (in Python) + 19 #26 at dyld3::OverflowSafeArray<dyld3::closure::Image::BindPattern, 4294967295ul>::growTo(unsigned long) (in libdyld.dylib) + 56

Any ideas?

Please Log in or Create an account to join the conversation.

More
2 years 1 week ago - 2 years 1 week ago #3018 by lkogler
I cannot reproduce this issue on any machine I tried it on.

Can you tell me what OS and compiler (+version) you are using?


Best,
Lukas
Last edit: 2 years 1 week ago by lkogler.

Please Log in or Create an account to join the conversation.

More
2 years 1 week ago #3024 by JanWesterdiep
Code:
$ g++ --version Configured with: --prefix=/Applications/Xcode.app/Contents/Developer/usr --with-gxx-include-dir=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.15.sdk/usr/include/c++/4.2.1 Apple clang version 11.0.0 (clang-1100.0.33.17) Target: x86_64-apple-darwin18.5.0 Thread model: posix InstalledDir: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin $ sw_vers -productVersion 10.14.4

What is kind of strange, though, is that `nsgpy` (and the entirety of the Netgen.app`) seems to be linked with python 3.7,
Code:
$ ngspy Python 3.7.4 (v3.7.4:e09359112e, Jul 8 2019, 14:54:52) $ python3 Python 3.8.5 (v3.8.5:580fbb018f, Jul 20 2020, 12:11:27)
even though I followed the website to install python 3.8 (the two versions now live side-by-side, though). Could this be a source of problems?

BTW, when I run `mpirun -np 4 ngspy mpi_poisson.py` with "hypre", I get the same problem. When I use the "bddc" preconditioner (and masterinverse), it runs OK. When I substitute `ngspy` with `python3.7`, things also run fine, but with `python3` (so `python3.8`), I again get a segfault, though at a much earlier stage. The stack trace is
Code:
$ mpirun -np 4 python3.8 mpi_poisson.py Caught SIGSEGV: segmentation fault Collecting backtrace... Caught SIGSEGV: segmentation fault Collecting backtrace... Caught SIGSEGV: segmentation fault Collecting backtrace... Caught SIGSEGV: segmentation fault Collecting backtrace... #1 at std::__1::basic_stringbuf<char, std::__1::char_traits<char>, std::__1::allocator<char> >::str() const (in libngcore.dylib ) (/Library/Developer/CommandLineTools/usr/include/c++/v1/new:252) #2 at 0x0000a3ac (in libsystem_platform.dylib) #3 at we_askshell.cmd (in libsystem_c.dylib) + 974 #4 at 0x00005ede (in libngpy.so) #5 at PyInit_libngpy (in libngpy.so) (<ngsolve dir>/ngsolve-src/external_dependencies/netgen/ng/netgenp y.cpp:33) #6 at _PyWideStringList_Copy (in Python) + 47 #7 at _imp__fix_co_filename (in Python) + 64 #8 at cfunction_vectorcall_FASTCALL_KEYWORDS (in Python) + 112 #9 at PyVectorcall_Call (in Python) + 260 #10 at PyErr_SetFromErrnoWithFilenameObjects (in Python) + 100 #11 at PyCodec_ReplaceErrors (in Python) + 559 #12 at _PyMethodDef_RawFastCallDict (in Python) + 331 #13 at call_function (in Python) + 1087 #14 at context_tp_new (in Python) + 19 #15 at _PyFunction_Vectorcall (in Python) + 19 #16 at call_function (in Python) + 1087 #17 at context_tp_richcompare (in Python) + 93 #18 at _PyFunction_Vectorcall (in Python) + 19 ..... #88 at Py_BytesMain (in Python) + 62

Please Log in or Create an account to join the conversation.

More
2 years 1 week ago #3025 by lkogler
In principle python3.7 also works. However, compiling ngsolve with python3.7 and then running with 3.8 can absolutely lead to problems.

I will try it with clang and get back to you.

Best,
Lukas

Please Log in or Create an account to join the conversation.

More
2 years 1 week ago - 2 years 1 week ago #3026 by JanWesterdiep
Thanks alot :-) if you can't reproduce it with clang either, I can move to a linux machine.
Last edit: 2 years 1 week ago by JanWesterdiep.

Please Log in or Create an account to join the conversation.

More
2 years 5 days ago #3033 by lkogler
I tried it with clang-11 now, still no problem here.

I am now thinking that it might be connected to the fortran compiler (MUMPS is a fortran library). What are you using there?

Best,
Lukas

Please Log in or Create an account to join the conversation.

Time to create page: 0.141 seconds