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<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>Thanks for the fix. My reader can now open the NeXus file, so I
can continue to make it display the data. Thanks for all the help.<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>Michael<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'><o:p> </o:p></span></p>
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<p class=MsoNormal><b><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'>From:</span></b><span
style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'> Dave Partyka
[mailto:dave.partyka@kitware.com] <br>
<b>Sent:</b> Tuesday, August 10, 2010 15:09<br>
<b>To:</b> Reuter, Michael A.<br>
<b>Cc:</b> Utkarsh Ayachit; paraview@paraview.org<br>
<b>Subject:</b> Re: [Paraview] New HDF5 based reader<o:p></o:p></span></p>
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<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal>Hi Michael, <o:p></o:p></p>
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<p class=MsoNormal><o:p> </o:p></p>
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<p class=MsoNormal>This compile error should be fixed now. You should update
Paraview to the latest version and also do a 'git submodule update' to update
Xdmf.<o:p></o:p></p>
<div>
<p class=MsoNormal><o:p> </o:p></p>
</div>
<div>
<p class=MsoNormal>Commit<o:p></o:p></p>
</div>
<div>
<p class=MsoNormal><o:p> </o:p></p>
</div>
<div>
<p class=MsoNormal>1ea84e6b53e6290f28993f64a844ca8fadbfbae8<o:p></o:p></p>
</div>
<div>
<p class=MsoNormal><o:p> </o:p></p>
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<div>
<p class=MsoNormal>Include <string.h> for XdmfSetStringMacro<o:p></o:p></p>
</div>
<div>
<p class=MsoNormal> <o:p></o:p></p>
</div>
<div>
<p class=MsoNormal> We need this header for strcmp in the
macro implementation. This error<o:p></o:p></p>
</div>
<div>
<p class=MsoNormal> went unnoticed previously because places
that used XdmfSetStringMacro<o:p></o:p></p>
</div>
<div>
<p class=MsoNormal> happened to include <string.h> for
another reason.<o:p></o:p></p>
</div>
<p class=MsoNormal><o:p> </o:p></p>
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<p class=MsoNormal>On Tue, Aug 10, 2010 at 1:21 PM, Reuter, Michael A. <<a
href="mailto:reuterma@ornl.gov">reuterma@ornl.gov</a>> wrote:<o:p></o:p></p>
<p class=MsoNormal>Hi Utkarsh,<br>
<br>
Thanks for the pointer on the cmake option as I
somehow missed that one. However,<br>
using the PARAVIEW_USE_SYSTEM_HDF5 flag, cmake pointed at the system HDF5 information
and a clean build, the following compile time error occurs:<br>
<br>
Scanning dependencies of target Xdmf<br>
[ 47%] Building CXX object
Utilities/Xdmf2/libsrc/CMakeFiles/Xdmf.dir/XdmfArray.cxx.o<br>
In file included from /home/2zr/src/ParaView-3.8.0/Utilities/Xdmf2/libsrc/XdmfArray.h:28,<br>
from
/home/2zr/src/ParaView-3.8.0/Utilities/Xdmf2/libsrc/XdmfArray.cxx:25:<br>
/home/2zr/src/ParaView-3.8.0/Utilities/Xdmf2/libsrc/XdmfDataDesc.h: In member
function 'XdmfInt32 XdmfDataDesc::SetHeavyDataSetName(const char*)':<br>
/home/2zr/src/ParaView-3.8.0/Utilities/Xdmf2/libsrc/XdmfDataDesc.h:202: error:
'strcmp' was not declared in this scope<br>
/home/2zr/src/ParaView-3.8.0/Utilities/Xdmf2/libsrc/XdmfDataDesc.h:202: error:
'strlen' was not declared in this scope<br>
/home/2zr/src/ParaView-3.8.0/Utilities/Xdmf2/libsrc/XdmfDataDesc.h:202: error:
'strcpy' was not declared in this scope<br>
In file included from
/home/2zr/src/ParaView-3.8.0/Utilities/Xdmf2/libsrc/XdmfArray.cxx:25:<br>
/home/2zr/src/ParaView-3.8.0/Utilities/Xdmf2/libsrc/XdmfArray.h: In member
function 'void XdmfArray::SetDataFromChars(char*)':<br>
/home/2zr/src/ParaView-3.8.0/Utilities/Xdmf2/libsrc/XdmfArray.h:398: error:
'strlen' was not declared in this scope<br>
/home/2zr/src/ParaView-3.8.0/Utilities/Xdmf2/libsrc/XdmfArray.h:399: error:
'strcpy' was not declared in this scope<br>
make[2]: *** [Utilities/Xdmf2/libsrc/CMakeFiles/Xdmf.dir/XdmfArray.cxx.o] Error
1<br>
make[1]: *** [Utilities/Xdmf2/libsrc/CMakeFiles/Xdmf.dir/all] Error 2<br>
make: *** [all] Error 2<br>
<br>
I did a little poking at the source code and it looks like the correct headers
for the above functions are being included, but the compiler doesn't think so.<br>
<span style='color:#888888'><br>
Michael</span><o:p></o:p></p>
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<p class=MsoNormal><br>
-----Original Message-----<br>
From: Utkarsh Ayachit [mailto:<a href="mailto:utkarsh.ayachit@kitware.com">utkarsh.ayachit@kitware.com</a>]<br>
Sent: Monday, August 09, 2010 13:24<br>
To: Reuter, Michael A.<br>
Cc: <a href="mailto:paraview@paraview.org">paraview@paraview.org</a><br>
Subject: Re: [Paraview] New HDF5 based reader<br>
<br>
Hmm, looks like your plugin is linking against a system installed<br>
HDF5. Did you change the ParaView to use the same? Otherwise ParaView<br>
brings in its own version of HDF5 and the two can't work together. To<br>
ensure that ParaView and your plugin uses the same HDF5, set the cmake<br>
variable PARAVIEW_USE_SYSTEM_HDF5 to ON and then point CMake to the<br>
installed hdf5.<br>
<br>
Utkarsh<br>
<br>
On Mon, Aug 9, 2010 at 11:59 AM, Reuter, Michael A. <<a
href="mailto:reuterma@ornl.gov">reuterma@ornl.gov</a>> wrote:<br>
> Hi,<br>
><br>
><br>
><br>
>
I have been working at trying to get a NeXus<br>
> (<a href="http://www.nexusformat.org" target="_blank">www.nexusformat.org</a>)
file read into ParaView. The NeXus format is HDF5<br>
> based and this seems to be the source of the current problem that I'm<br>
> encountering. When I try to open a NeXus file via this call:<br>
><br>
><br>
><br>
> NeXus::File *fh = new NeXus::File(filename, NXACC_READ);<br>
><br>
><br>
><br>
> I get the backtrace that's attached to this email. The lowest level frame
is<br>
> given here:<br>
><br>
><br>
><br>
> Program received signal SIGSEGV, Segmentation fault.<br>
><br>
> 0x00007fffd7a3da8b in H5FL_reg_malloc () from /usr/lib/libhdf5.so.6<br>
><br>
> (gdb) bt<br>
><br>
> #0 0x00007fffd7a3da8b in H5FL_reg_malloc () from
/usr/lib/libhdf5.so.6<br>
><br>
> .<br>
><br>
><br>
><br>
> At first, this looked like an issue with the system HDF5 libraries, but I<br>
> can put the above line into a standalone program, link it against the same<br>
> libraries and I can open a file without any errors. I have searched the
list<br>
> archive for any enlightenment, but I didn't find this particular problem.
Is<br>
> there anything special about using HDF5 libraries in ParaView plugins that
I<br>
> missed in the documentation? I am running on Ubuntu 10.04 using the
provided<br>
> HDF5 libraries and I have compiled and linked the NeXus libraries against<br>
> the same HDF5 libraries.<br>
><br>
><br>
><br>
> I know about Xdmf and have tried that with success, but I do not want to
go<br>
> down the two file route, so I'd really like to get this reader working. I<br>
> can provide more detailed information (like plugin source code, sample
file<br>
> etc.) to anyone who can help, but I don't want to spam the entire list
with<br>
> it right off the bat.<br>
><br>
><br>
><br>
> Thanks,<br>
><br>
> Michael<br>
><br>
> -------------------------------------------<br>
><br>
> Michael Reuter<br>
><br>
> Scientific Data Analysis Group<br>
><br>
> Neutron Scattering Science Division<br>
><br>
> Oak Ridge National Laboratory<br>
><br>
><br>
><br>
><br>
><br>
><br>
><br>
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