[Paraview] Fortran wrapper of HDF5

[Jason Fleming]

I've read the section of the hdf5 page that Pradeep linked to (C vs
Fortran ordering) several times, and for the life of me, I can't figure
out whether the hdf5 format ordering is transparent to the application
or not. 

It seems really silly that hdf5 can take care of endianness so that app
developers don't have to worry about it, but on the other hand, app
developers now have to know whether a particular hdf5 file was written
by a C or Fortran app in order to be able to read it properly. And yet
hdf5 seems to work that way. Is that right?

Cheers
Jason



On Thu, 2013-03-14 at 00:08 +0900, Pradeep Jha wrote:
> Are you implying that if I use the HDF5 fortran wrapper to convert the
> fortran binary data in h5 format and then visualize this h5 file using
> Paraview, I am looking at the the actual data with correct dimensions?
> Or I have to make some modifications so that I see the data correctly
> in Paraview?
> 
> 
> I dont want to transpose the data. I just want to visualize what I
> wrote using Fortran without any alterations.
> 
> 
> Pradeep
> 
> 
> 
> 
> 2013/3/13 Biddiscombe, John A. <biddisco at cscs.ch>
>         “How do I write the h5 file data in exactly the same way as it
>         was written in original binary file written by Fortran?”
>         
>          
>         
>         It is writing the file the same, the problem is that fortran
>         stores arrays in column major, and C in row major order. You
>         state “it automatically transposes the matrix” – not true – it
>         transposes the dimensions so that the data is still stored the
>         same, but when you write array[z,y,x] from fortran, you want
>         to read it as array[x,y,z] from C. The actual data on disk is
>         the same as your binary fortran data, but the dimensions are
>         reversed compared to the same data from C.
>         
>          
>         
>         Does that help? – the short answer is just swap the order of
>         the dimensions in your read function in the C version and then
>         things should appear the same. (but you must declare your
>         arrays with the dimensions flipped).
>         
>          
>         
>         If you want to actually transpose the data, then I’m sure
>         google will provide a code snippet
>         
>          
>         
>         I hope I’m not remembering this wrong.
>         
>          
>         
>         JB
>         
>          
>         
>          
>         
>          
>         
>          
>         
>         From: paraview-bounces at paraview.org
>         [mailto:paraview-bounces at paraview.org] On Behalf Of Pradeep
>         Jha
>         Sent: 13 March 2013 10:58
>         To: paraview at paraview.org
>         Subject: [Paraview] Fortran wrapper of HDF5
>         
>          
>         
>         I recently noticed that when I am using the fortran wrapper of
>         HDF5 to convert a binary file written by fortran into the "h5"
>         format, it automatically transposes the matrix. Apparently,
>         this is because HDF5 uses the C convention for writing binary
>         files, as explained in section: 7.3.2.5. of this page.
>         
>          
>         
>         
>         Is anyone aware of this situation? And any solutions for this
>         problem? How do I write the h5 file data in exactly the same
>         way as it was written in original binary file written by
>         Fortran?
>         
>         
> 
> 
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-- 
Dr. Jason G. Fleming
Chief Engineer, Seahorse Coastal Consulting
3103 Mandy Ln
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Tel: (252) 726-6323
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