[MacPorts] #56773: vtk 7.1.1 +hdf5: Illegal hardware instruction when using Xdmf3Reader

MacPorts

2018-07-04 18:28:14 UTC

#56773: vtk 7.1.1 +hdf5: Illegal hardware instruction when using Xdmf3Reader
-----------------------------+--------------------
Reporter: rubendibattista | Owner: (none)
Type: defect | Status: new
Priority: Normal | Milestone:
Component: ports | Version: 2.5.2
Keywords: | Port: vtk
-----------------------------+--------------------
System Information:
OSX 10.13.5
Apple Clang 9.1.0

Hello,
I opened a PR on Github [https://github.com/macports/macports-
ports/pull/2123] providing +hdf5 variant to vtk in order to have the Xdmf3
file readers. The compilation proceeds as expected, no errors are raised
(you can see the log attached in the Pull Request).

The problem is that when I try to use one of the Xdm3Readers, I receive a
"Illegal Hardware Instruction" error that seems to trace back to the
Xdm3RectilinearGrid destructor in VTK, but I don't know if it's a VTK bug
w/ Apple Clang or else...

Here a MWE to reproduce:

{{{
#include "vtkNew.h"
#include "vtkXdmf3Reader.h"

int main(int argc, char** argv) {

vtkNew<vtkXdmf3Reader> reader;

reader->SetFileName("scalar.xmf");
reader->DebugOn();
reader->Update();

}
}}}

The scalar.xmf data can be retrieved from: [https://github.com/macports
/macports-ports/files/2160224/scalar-data.tar.gz].

This is the Backtrace from lldb:

{{{
(lldb) run
Process 10472 launched:
'/Users/***/git/x/HG/examples/c++/rayleigh/build/rayleigh' (x86_64)
Debug: In /opt/local/var/macports/build/_Users_***_git_macports-
ports_graphics_vtk/vtk/work/VTK-7.1.1/Common/Core/vtkObject.cxx, line 861
vtkXdmf3Reader (0x109218d80): Registered by vtkCompositeDataPipeline
(0x109219ff0), ReferenceCount = 2

Process 10472 stopped
* thread #1, queue = 'com.apple.main-thread', stop reason =
EXC_BAD_INSTRUCTION (code=EXC_I386_INVOP, subcode=0x0)
frame #0: 0x00000001044f383b
libvtkxdmf3.dylib`XdmfRectilinearGrid::~XdmfRectilinearGrid() + 47
libvtkxdmf3.dylib`XdmfRectilinearGrid::~XdmfRectilinearGrid:
-> 0x1044f383b <+47>: ud2
0x1044f383d <+49>: nop
0x1044f383e <+0>: pushq %rbp
0x1044f383f <+1>: movq %rsp, %rbp
Target 0: (rayleigh) stopped.
(lldb) bt
* thread #1, queue = 'com.apple.main-thread', stop reason =
EXC_BAD_INSTRUCTION (code=EXC_I386_INVOP, subcode=0x0)
* frame #0: 0x00000001044f383b
libvtkxdmf3.dylib`XdmfRectilinearGrid::~XdmfRectilinearGrid() + 47
frame #1: 0x00007ffeefbfef20
frame #2: 0x00000001044f3854
libvtkxdmf3.dylib`XdmfRectilinearGrid::~XdmfRectilinearGrid() + 22
frame #3: 0x00000001044f38ab
libvtkxdmf3.dylib`XdmfRectilinearGrid::~XdmfRectilinearGrid() + 15
frame #4: 0x0000000104f1c2ed
libXdmfCore.dylib`boost::detail::shared_count::~shared_count() + 45
frame #5: 0x0000000104eeac46
libXdmfCore.dylib`std::__1::__tree<std::__1::__value_type<_xmlNode*,
boost::shared_ptr<XdmfItem> >, std::__1::__map_value_compare<_xmlNode*,
std::__1::__value_type<_xmlNode*, boost::shared_ptr<XdmfItem> >,
std::__1::less<_xmlNode*>, true>,
std::__1::allocator<std::__1::__value_type<_xmlNode*,
boost::shared_ptr<XdmfItem> > >

::destroy(std::__1::__tree_node<std::__1::__value_type<_xmlNode*,

boost::shared_ptr<XdmfItem> >, void*>*) + 50
frame #6: 0x0000000104eeac3d
libXdmfCore.dylib`std::__1::__tree<std::__1::__value_type<_xmlNode*,
boost::shared_ptr<XdmfItem> >, std::__1::__map_value_compare<_xmlNode*,
std::__1::__value_type<_xmlNode*, boost::shared_ptr<XdmfItem> >,
std::__1::less<_xmlNode*>, true>,
std::__1::allocator<std::__1::__value_type<_xmlNode*,
boost::shared_ptr<XdmfItem> > >

::destroy(std::__1::__tree_node<std::__1::__value_type<_xmlNode*,

boost::shared_ptr<XdmfItem> >, void*>*) + 41
frame #7: 0x0000000104eeac31
libXdmfCore.dylib`std::__1::__tree<std::__1::__value_type<_xmlNode*,
boost::shared_ptr<XdmfItem> >, std::__1::__map_value_compare<_xmlNode*,
std::__1::__value_type<_xmlNode*, boost::shared_ptr<XdmfItem> >,
std::__1::less<_xmlNode*>, true>,
std::__1::allocator<std::__1::__value_type<_xmlNode*,
boost::shared_ptr<XdmfItem> > >

::destroy(std::__1::__tree_node<std::__1::__value_type<_xmlNode*,

boost::shared_ptr<XdmfItem> >, void*>*) + 29
frame #8: 0x0000000104eea377
libXdmfCore.dylib`XdmfCoreReader::XdmfCoreReaderImpl::closeFile() + 31
frame #9: 0x0000000104eea44b
libXdmfCore.dylib`XdmfCoreReader::readItems(std::__1::basic_string<char,
std::__1::char_traits<char>, std::__1::allocator<char> > const&) const +
65
frame #10: 0x0000000104eea777
libXdmfCore.dylib`XdmfCoreReader::read(std::__1::basic_string<char,
std::__1::char_traits<char>, std::__1::allocator<char> > const&) const +
27
frame #11: 0x00000001044f2912
libvtkxdmf3.dylib`XdmfReader::read(std::__1::basic_string<char,
std::__1::char_traits<char>, std::__1::allocator<char> > const&) const +
14
frame #12: 0x000000010444aa32
libvtkIOXdmf3-7.1.1.dylib`vtkXdmf3Reader::Internals::Init(char const*,
bool) + 2224
frame #13: 0x0000000104443ffe
libvtkIOXdmf3-7.1.1.dylib`vtkXdmf3Reader::Internals::PrepareDocument(vtkXdmf3Reader*,
char const*, bool) + 96
frame #14: 0x0000000104443ecf
libvtkIOXdmf3-7.1.1.dylib`vtkXdmf3Reader::RequestDataObject(vtkInformationVector*)
+ 57
frame #15: 0x0000000107cdf00f
libvtkCommonExecutionModel-7.1.1.dylib`vtkExecutive::CallAlgorithm(vtkInformation*,
int, vtkInformationVector**, vtkInformationVector*) + 69
frame #16: 0x0000000107cd49fe
libvtkCommonExecutionModel-7.1.1.dylib`vtkCompositeDataPipeline::ExecuteDataObject(vtkInformation*,
vtkInformationVector**, vtkInformationVector*) + 304
frame #17: 0x0000000107cd944e
libvtkCommonExecutionModel-7.1.1.dylib`vtkDemandDrivenPipeline::ProcessRequest(vtkInformation*,
vtkInformationVector**, vtkInformationVector*) + 166
frame #18: 0x0000000107cf601d
libvtkCommonExecutionModel-7.1.1.dylib`vtkStreamingDemandDrivenPipeline::ProcessRequest(vtkInformation*,
vtkInformationVector**, vtkInformationVector*) + 543
frame #19: 0x0000000107cd9968
libvtkCommonExecutionModel-7.1.1.dylib`vtkDemandDrivenPipeline::UpdateInformation()
+ 48
frame #20: 0x0000000107cf6438
libvtkCommonExecutionModel-7.1.1.dylib`vtkStreamingDemandDrivenPipeline::Update(int,
vtkInformationVector*) + 36
frame #21: 0x0000000100021d1f rayleigh`main(argc=1,
argv=0x00007ffeefbff4e8) at rayleigh.cpp:10
frame #22: 0x00007fff7c908015 libdyld.dylib`start + 1
frame #23: 0x00007fff7c908015 libdyld.dylib`start + 1
}}}

The readers are working if the xdmf files does not include actual data via
HDF5...

--
Ticket URL: <https://trac.macports.org/ticket/56773>
MacPorts <https://www.macports.org/>
Ports system for macOS