Hi Michael, <div><br></div><div>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.<div><br></div><div>Commit</div><div><br>
</div><div>1ea84e6b53e6290f28993f64a844ca8fadbfbae8</div><div><br></div><div><div>Include <string.h> for XdmfSetStringMacro</div><div> </div><div> We need this header for strcmp in the macro implementation. This error</div>
<div> went unnoticed previously because places that used XdmfSetStringMacro</div><div> happened to include <string.h> for another reason.</div><br><div class="gmail_quote">On Tue, Aug 10, 2010 at 1:21 PM, Reuter, Michael A. <span dir="ltr"><<a href="mailto:reuterma@ornl.gov">reuterma@ornl.gov</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">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>
<font color="#888888"><br>
Michael<br>
</font><div><div></div><div class="h5"><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>
> _______________________________________________<br>
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</div></div></blockquote></div><br></div></div>