Building NGSolve with HYPRE support

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4 years 3 months ago #3017 by JanWesterdiep
Replied by JanWesterdiep on topic Building NGSolve with HYPRE support
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?
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4 years 3 months ago - 4 years 3 months ago #3018 by lkogler
Replied by lkogler on topic Building NGSolve with HYPRE support
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: 4 years 3 months ago by lkogler.
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4 years 3 months ago #3024 by JanWesterdiep
Replied by JanWesterdiep on topic Building NGSolve with HYPRE support
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
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4 years 3 months ago #3025 by lkogler
Replied by lkogler on topic Building NGSolve with HYPRE support
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
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4 years 3 months ago - 4 years 3 months ago #3026 by JanWesterdiep
Replied by JanWesterdiep on topic Building NGSolve with HYPRE support
Thanks alot :-) if you can't reproduce it with clang either, I can move to a linux machine.
Last edit: 4 years 3 months ago by JanWesterdiep.
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4 years 3 months ago #3033 by lkogler
Replied by lkogler on topic Building NGSolve with HYPRE support
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
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