<html><head><style>
body {
font-family: "Helvetica Neue", Helvetica, Arial, sans-serif;
padding:1em;
margin:auto;
background:#fefefe;
}
h1, h2, h3, h4, h5, h6 {
font-weight: bold;
}
h1 {
color: #000000;
font-size: 28pt;
}
h2 {
border-bottom: 1px solid #CCCCCC;
color: #000000;
font-size: 24px;
}
h3 {
font-size: 18px;
}
h4 {
font-size: 16px;
}
h5 {
font-size: 14px;
}
h6 {
color: #777777;
background-color: inherit;
font-size: 14px;
}
hr {
height: 0.2em;
border: 0;
color: #CCCCCC;
background-color: #CCCCCC;
display: inherit;
}
p, blockquote, ul, ol, dl, li, table, pre {
margin: 15px 0;
}
a, a:visited {
color: #4183C4;
background-color: inherit;
text-decoration: none;
}
#message {
border-radius: 6px;
border: 1px solid #ccc;
display:block;
width:100%;
height:60px;
margin:6px 0px;
}
button, #ws {
font-size: 12 pt;
padding: 4px 6px;
border-radius: 5px;
border: 1px solid #bbb;
background-color: #eee;
}
code, pre, #ws, #message {
font-family: Monaco;
font-size: 10pt;
border-radius: 3px;
background-color: #F8F8F8;
color: inherit;
}
code {
border: 1px solid #EAEAEA;
margin: 0 2px;
padding: 0 5px;
}
pre {
border: 1px solid #CCCCCC;
overflow: auto;
padding: 4px 8px;
}
pre > code {
border: 0;
margin: 0;
padding: 0;
}
#ws { background-color: #f8f8f8; }
.bloop_markdown table {
border-collapse: collapse;
font-family: Helvetica, arial, freesans, clean, sans-serif;
color: rgb(51, 51, 51);
font-size: 15px; line-height: 25px;
padding: 0; }
.bloop_markdown table tr {
border-top: 1px solid #cccccc;
background-color: white;
margin: 0;
padding: 0; }
.bloop_markdown table tr:nth-child(2n) {
background-color: #f8f8f8; }
.bloop_markdown table tr th {
font-weight: bold;
border: 1px solid #cccccc;
margin: 0;
padding: 6px 13px; }
.bloop_markdown table tr td {
border: 1px solid #cccccc;
margin: 0;
padding: 6px 13px; }
.bloop_markdown table tr th :first-child, table tr td :first-child {
margin-top: 0; }
.bloop_markdown table tr th :last-child, table tr td :last-child {
margin-bottom: 0; }
.bloop_markdown blockquote{
border-left: 4px solid #dddddd;
padding: 0 15px;
color: #777777; }
blockquote > :first-child {
margin-top: 0; }
blockquote > :last-child {
margin-bottom: 0; }
code, pre, #ws, #message {
word-break: normal;
word-wrap: normal;
}
hr {
display: inherit;
}
.bloop_markdown :first-child {
-webkit-margin-before: 0;
}
code, pre, #ws, #message {
font-family: Menlo, Consolas, Liberation Mono, Courier, monospace;
}
.send { color:#77bb77; }
.server { color:#7799bb; }
.error { color:#AA0000; }</style></head><body style="word-wrap:break-word;line-break:after-white-space"><div class="bloop_markdown"><p></p></div><div class="bloop_original_html"><style>body{font-family:Helvetica,Arial;font-size:13px}</style><div id="bloop_customfont" style="font-family:Helvetica,Arial;font-size:13px;color:rgba(0,0,0,1.0);margin:0px;line-height:auto">Hello, </div><div id="bloop_customfont" style="font-family:Helvetica,Arial;font-size:13px;color:rgba(0,0,0,1.0);margin:0px;line-height:auto">I’m experiencing a crash of the vtkXDMF3Reader on OSX 10.13.5 compiled with the shipped Apple’s clang compiler. </div><div id="bloop_customfont" style="font-family:Helvetica,Arial;font-size:13px;color:rgba(0,0,0,1.0);margin:0px;line-height:auto"><br></div><div id="bloop_customfont" style="font-family:Helvetica,Arial;font-size:13px;color:rgba(0,0,0,1.0);margin:0px;line-height:auto">System Information:</div><div id="bloop_customfont" style="font-family:Helvetica,Arial;font-size:13px;color:rgba(0,0,0,1.0);margin:0px;line-height:auto">OSX 10.13.5</div><div id="bloop_customfont" style="font-family:Helvetica,Arial;font-size:13px;color:rgba(0,0,0,1.0);margin:0px;line-height:auto"><div id="bloop_customfont" style="margin:0px">Apple LLVM version 9.1.0 (clang-902.0.39.2)</div><div id="bloop_customfont" style="margin:0px">Target: x86_64-apple-darwin17.6.0</div><div id="bloop_customfont" style="margin:0px">Thread model: posix</div><div id="bloop_customfont" style="margin:0px">InstalledDir: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin</div><div id="bloop_customfont" style="margin:0px">Boost: 1.66.0</div><div id="bloop_customfont" style="margin:0px">HDF5: 1.10.2</div><div id="bloop_customfont" style="margin:0px">Stuff installed with Macports</div></div><div id="bloop_customfont" style="font-family:Helvetica,Arial;font-size:13px;color:rgba(0,0,0,1.0);margin:0px;line-height:auto"><br></div><div id="bloop_customfont" style="font-family:Helvetica,Arial;font-size:13px;color:rgba(0,0,0,1.0);margin:0px;line-height:auto">Basically when I read a xdmf that stores actual data in HDF5, the program crashes.</div><div id="bloop_customfont" style="font-family:Helvetica,Arial;font-size:13px;color:rgba(0,0,0,1.0);margin:0px;line-height:auto"><br></div><div id="bloop_customfont" style="font-family:Helvetica,Arial;font-size:13px;color:rgba(0,0,0,1.0);margin:0px;line-height:auto">Here’s a MWE:</div><div id="bloop_customfont" style="font-family:Helvetica,Arial;font-size:13px;color:rgba(0,0,0,1.0);margin:0px;line-height:auto"><br></div><div id="bloop_customfont" style="font-family:Helvetica,Arial;font-size:13px;color:rgba(0,0,0,1.0);margin:0px;line-height:auto">```</div><div id="bloop_customfont" style="font-family:Helvetica,Arial;font-size:13px;color:rgba(0,0,0,1.0);margin:0px;line-height:auto"><div id="bloop_customfont" style="margin:0px">#include "vtkNew.h"</div><div id="bloop_customfont" style="margin:0px">#include "vtkXdmf3Reader.h"</div><div id="bloop_customfont" style="margin:0px"><br></div><div id="bloop_customfont" style="margin:0px">int main(int argc, char** argv) {</div><div id="bloop_customfont" style="margin:0px"><br></div><div id="bloop_customfont" style="margin:0px"> vtkNew<vtkXdmf3Reader> reader;</div><div id="bloop_customfont" style="margin:0px"><br></div><div id="bloop_customfont" style="margin:0px"> reader->SetFileName("scalar-data/scalar.xmf");</div><div id="bloop_customfont" style="margin:0px"> reader->DebugOn();</div><div id="bloop_customfont" style="margin:0px"> reader->Update();</div><div id="bloop_customfont" style="margin:0px"><br></div><div id="bloop_customfont" style="margin:0px">}</div><div>```</div><div><a href="https://github.com/macports/macports-ports/files/2160224/scalar-data.tar.gz" style="box-sizing:border-box;background-color:rgb(255,255,255);color:rgb(3,102,214);text-decoration:underline;outline-width:0px;font-family:-apple-system,system-ui,"Segoe UI",Helvetica,Arial,sans-serif,"Apple Color Emoji","Segoe UI Emoji","Segoe UI Symbol";font-size:14px;font-variant-ligatures:normal">here’s</a> the sample data file that you can use with it to test.</div><div><br></div><div>I tried to use the debugger, (below the output), It looks like a problem with the Xdmf3Reader destructor. I’m not able to understand if it’s because of Boost or a VTK’s bug with Apple Clang. Can you please give me help?</div><div><br></div><div><b>NB: </b>For further details see <a href="https://github.com/macports/macports-ports/pull/2123">this PR</a> on macports issue tracker.</div><div><br></div><div>Thanks in advance, </div><div><br></div><div>```</div><div><div>(lldb) run</div><div>Process 10472 launched: *** (x86_64)</div><div>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</div><div>vtkXdmf3Reader (0x109218d80): Registered by vtkCompositeDataPipeline (0x109219ff0), ReferenceCount = 2</div><div><br></div><div>Process 10472 stopped</div><div>* thread #1, queue = 'com.apple.main-thread', stop reason = EXC_BAD_INSTRUCTION (code=EXC_I386_INVOP, subcode=0x0)</div><div> frame #0: 0x00000001044f383b libvtkxdmf3.dylib`XdmfRectilinearGrid::~XdmfRectilinearGrid() + 47</div><div>libvtkxdmf3.dylib`XdmfRectilinearGrid::~XdmfRectilinearGrid:</div><div>-> 0x1044f383b <+47>: ud2</div><div> 0x1044f383d <+49>: nop</div><div> 0x1044f383e <+0>: pushq %rbp</div><div> 0x1044f383f <+1>: movq %rsp, %rbp</div><div>Target 0: (rayleigh) stopped.</div><div>(lldb) bt</div><div>* thread #1, queue = 'com.apple.main-thread', stop reason = EXC_BAD_INSTRUCTION (code=EXC_I386_INVOP, subcode=0x0)</div><div> * frame #0: 0x00000001044f383b libvtkxdmf3.dylib`XdmfRectilinearGrid::~XdmfRectilinearGrid() + 47</div><div> frame #1: 0x00007ffeefbfef20</div><div> frame #2: 0x00000001044f3854 libvtkxdmf3.dylib`XdmfRectilinearGrid::~XdmfRectilinearGrid() + 22</div><div> frame #3: 0x00000001044f38ab libvtkxdmf3.dylib`XdmfRectilinearGrid::~XdmfRectilinearGrid() + 15</div><div> frame #4: 0x0000000104f1c2ed libXdmfCore.dylib`boost::detail::shared_count::~shared_count() + 45</div><div> 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</div><div> 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</div><div> 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</div><div> frame #8: 0x0000000104eea377 libXdmfCore.dylib`XdmfCoreReader::XdmfCoreReaderImpl::closeFile() + 31</div><div> frame #9: 0x0000000104eea44b libXdmfCore.dylib`XdmfCoreReader::readItems(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&) const + 65</div><div> frame #10: 0x0000000104eea777 libXdmfCore.dylib`XdmfCoreReader::read(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&) const + 27</div><div> frame #11: 0x00000001044f2912 libvtkxdmf3.dylib`XdmfReader::read(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&) const + 14</div><div> frame #12: 0x000000010444aa32 libvtkIOXdmf3-7.1.1.dylib`vtkXdmf3Reader::Internals::Init(char const*, bool) + 2224</div><div> frame #13: 0x0000000104443ffe libvtkIOXdmf3-7.1.1.dylib`vtkXdmf3Reader::Internals::PrepareDocument(vtkXdmf3Reader*, char const*, bool) + 96</div><div> frame #14: 0x0000000104443ecf libvtkIOXdmf3-7.1.1.dylib`vtkXdmf3Reader::RequestDataObject(vtkInformationVector*) + 57</div><div> frame #15: 0x0000000107cdf00f libvtkCommonExecutionModel-7.1.1.dylib`vtkExecutive::CallAlgorithm(vtkInformation*, int, vtkInformationVector**, vtkInformationVector*) + 69</div><div> frame #16: 0x0000000107cd49fe libvtkCommonExecutionModel-7.1.1.dylib`vtkCompositeDataPipeline::ExecuteDataObject(vtkInformation*, vtkInformationVector**, vtkInformationVector*) + 304</div><div> frame #17: 0x0000000107cd944e libvtkCommonExecutionModel-7.1.1.dylib`vtkDemandDrivenPipeline::ProcessRequest(vtkInformation*, vtkInformationVector**, vtkInformationVector*) + 166</div><div> frame #18: 0x0000000107cf601d libvtkCommonExecutionModel-7.1.1.dylib`vtkStreamingDemandDrivenPipeline::ProcessRequest(vtkInformation*, vtkInformationVector**, vtkInformationVector*) + 543</div><div> frame #19: 0x0000000107cd9968 libvtkCommonExecutionModel-7.1.1.dylib`vtkDemandDrivenPipeline::UpdateInformation() + 48</div><div> frame #20: 0x0000000107cf6438 libvtkCommonExecutionModel-7.1.1.dylib`vtkStreamingDemandDrivenPipeline::Update(int, vtkInformationVector*) + 36</div><div> frame #21: 0x0000000100021d1f rayleigh`main(argc=1, argv=0x00007ffeefbff4e8) at rayleigh.cpp:10</div><div> frame #22: 0x00007fff7c908015 libdyld.dylib`start + 1</div><div> frame #23: 0x00007fff7c908015 libdyld.dylib`start + 1</div></div><div><br></div><div>```</div></div><div id="bloop_customfont" style="font-family:Helvetica,Arial;font-size:13px;color:rgba(0,0,0,1.0);margin:0px;line-height:auto"><br></div><div id="bloop_customfont" style="font-family:Helvetica,Arial;font-size:13px;color:rgba(0,0,0,1.0);margin:0px;line-height:auto"><br></div><br><div class="bloop_sign" id="bloop_sign_1530676429289867008">
<title></title>
<pre> _
-. .´ |∞∞∞∞
', ; |∞∞∞∞∞∞
˜˜ |∞∞∞∞∞∞∞∞∞ RdB
,., |∞∞∞∞∞∞
.' '. |∞∞∞∞
-' `’
<a href="http://rdb.is">http://rdb.is</a>
</pre>
</div></div><div class="bloop_markdown"><p></p></div></body></html>