[Paraview] New HDF5 based reader

Fri Aug 20 11:11:41 EDT 2010

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.

Michael

From: Dave Partyka [mailto:dave.partyka at kitware.com]
Sent: Tuesday, August 10, 2010 15:09
To: Reuter, Michael A.
Cc: Utkarsh Ayachit; paraview at paraview.org
Subject: Re: [Paraview] New HDF5 based reader

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<mailto: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<mailto:utkarsh.ayachit at kitware.com>]
Sent: Monday, August 09, 2010 13:24
To: Reuter, Michael A.
Cc: paraview at paraview.org<mailto: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<mailto:reuterma at ornl.gov>> wrote:
> Hi,
>
>
>
>                 I have been working at trying to get a NeXus
> (www.nexusformat.org<http://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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