[Paraview] New HDF5 based reader

[Dave Partyka]

Hi Michael,

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.

Commit

1ea84e6b53e6290f28993f64a844ca8fadbfbae8

Include <string.h> for XdmfSetStringMacro

    We need this header for strcmp in the macro implementation.  This error
    went unnoticed previously because places that used XdmfSetStringMacro
    happened to include <string.h> for another reason.

On Tue, Aug 10, 2010 at 1:21 PM, Reuter, Michael A. <reuterma at ornl.gov>wrote:

> Hi Utkarsh,
>
>        Thanks for the pointer on the cmake option as I somehow missed that
> one. However,
> using the PARAVIEW_USE_SYSTEM_HDF5 flag, cmake pointed at the system HDF5
> information and a clean build, the following compile time error occurs:
>
> Scanning dependencies of target Xdmf
> [ 47%] Building CXX object
> Utilities/Xdmf2/libsrc/CMakeFiles/Xdmf.dir/XdmfArray.cxx.o
> In file included from
> /home/2zr/src/ParaView-3.8.0/Utilities/Xdmf2/libsrc/XdmfArray.h:28,
>                 from
> /home/2zr/src/ParaView-3.8.0/Utilities/Xdmf2/libsrc/XdmfArray.cxx:25:
> /home/2zr/src/ParaView-3.8.0/Utilities/Xdmf2/libsrc/XdmfDataDesc.h: In
> member function 'XdmfInt32 XdmfDataDesc::SetHeavyDataSetName(const char*)':
> /home/2zr/src/ParaView-3.8.0/Utilities/Xdmf2/libsrc/XdmfDataDesc.h:202:
> error: 'strcmp' was not declared in this scope
> /home/2zr/src/ParaView-3.8.0/Utilities/Xdmf2/libsrc/XdmfDataDesc.h:202:
> error: 'strlen' was not declared in this scope
> /home/2zr/src/ParaView-3.8.0/Utilities/Xdmf2/libsrc/XdmfDataDesc.h:202:
> error: 'strcpy' was not declared in this scope
> In file included from
> /home/2zr/src/ParaView-3.8.0/Utilities/Xdmf2/libsrc/XdmfArray.cxx:25:
> /home/2zr/src/ParaView-3.8.0/Utilities/Xdmf2/libsrc/XdmfArray.h: In member
> function 'void XdmfArray::SetDataFromChars(char*)':
> /home/2zr/src/ParaView-3.8.0/Utilities/Xdmf2/libsrc/XdmfArray.h:398: error:
> 'strlen' was not declared in this scope
> /home/2zr/src/ParaView-3.8.0/Utilities/Xdmf2/libsrc/XdmfArray.h:399: error:
> 'strcpy' was not declared in this scope
> make[2]: *** [Utilities/Xdmf2/libsrc/CMakeFiles/Xdmf.dir/XdmfArray.cxx.o]
> Error 1
> make[1]: *** [Utilities/Xdmf2/libsrc/CMakeFiles/Xdmf.dir/all] Error 2
> make: *** [all] Error 2
>
> 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.
>
> Michael
>
> -----Original Message-----
> From: Utkarsh Ayachit [mailto:utkarsh.ayachit at kitware.com]
> Sent: Monday, August 09, 2010 13:24
> To: Reuter, Michael A.
> Cc: paraview at paraview.org
> Subject: Re: [Paraview] New HDF5 based reader
>
> Hmm, looks like your plugin is linking against a system installed
> HDF5. Did you change the ParaView to use the same? Otherwise ParaView
> brings in its own version of HDF5 and the two can't work together. To
> ensure that ParaView and your plugin uses the same HDF5, set the cmake
> variable PARAVIEW_USE_SYSTEM_HDF5 to ON and then point CMake to the
> installed hdf5.
>
> Utkarsh
>
> On Mon, Aug 9, 2010 at 11:59 AM, Reuter, Michael A. <reuterma at ornl.gov>
> wrote:
> > Hi,
> >
> >
> >
> >                 I have been working at trying to get a NeXus
> > (www.nexusformat.org) file read into ParaView. The NeXus format is HDF5
> > based and this seems to be the source of the current problem that I'm
> > encountering.  When I try to open a NeXus file via this call:
> >
> >
> >
> > NeXus::File *fh = new NeXus::File(filename, NXACC_READ);
> >
> >
> >
> > I get the backtrace that's attached to this email. The lowest level frame
> is
> > given here:
> >
> >
> >
> > Program received signal SIGSEGV, Segmentation fault.
> >
> > 0x00007fffd7a3da8b in H5FL_reg_malloc () from /usr/lib/libhdf5.so.6
> >
> > (gdb) bt
> >
> > #0  0x00007fffd7a3da8b in H5FL_reg_malloc () from /usr/lib/libhdf5.so.6
> >
> > .
> >
> >
> >
> > At first, this looked like an issue with the system HDF5 libraries, but I
> > can put the above line into a standalone program, link it against the
> same
> > libraries and I can open a file without any errors. I have searched the
> list
> > archive for any enlightenment, but I didn't find this particular problem.
> Is
> > there anything special about using HDF5 libraries in ParaView plugins
> that I
> > missed in the documentation? I am running on Ubuntu 10.04 using the
> provided
> > HDF5 libraries and I have compiled and linked the NeXus libraries against
> > the same HDF5 libraries.
> >
> >
> >
> > I know about Xdmf and have tried that with success, but I do not want to
> go
> > down the two file route, so I'd really like to get this reader working. I
> > can provide more detailed information (like plugin source code, sample
> file
> > etc.) to anyone who can help, but I don't want to spam the entire list
> with
> > it right off the bat.
> >
> >
> >
> > Thanks,
> >
> > Michael
> >
> > -------------------------------------------
> >
> > Michael Reuter
> >
> > Scientific Data Analysis Group
> >
> > Neutron Scattering Science Division
> >
> > Oak Ridge National Laboratory
> >
> >
> >
> >
> >
> >
> >
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