Segmentation fault when reading a homegrown HDF5 file

Hello,

Paraview first-timer here. Our app creates HDF5 files with a very simple structure:

h5dump -A cart_cr2130.h5 
HDF5 "cart_cr2130.h5" {
GROUP "/" {
   DATASET "Bp" {
      DATATYPE  H5T_IEEE_F64LE
      DATASPACE  SIMPLE { ( 151, 151, 151 ) / ( 151, 151, 151 ) }
   }
   DATASET "Br" {
      DATATYPE  H5T_IEEE_F64LE
      DATASPACE  SIMPLE { ( 151, 151, 151 ) / ( 151, 151, 151 ) }
   }
   [...]

I just installed ParaView 5.6.0 in my workstation (ArchLinux), and I tried to open that file, but I get a Segmentation Fault as can be seen below:

[angelv@comer ~]$ paraview 
ERROR: In /home/angelv/spack/var/spack/stage/paraview-5.6.0-rj74wdfmntjmqhcxelyksaagllsxrw2z/spack-src/VTK/IO/VeraOut/vtkVeraOutReader.cxx, line 253
vtkVeraOutReader (0x55eeaed90200): Can't open group /CORE

[comer:22212] *** Process received signal ***
[comer:22212] Signal: Segmentation fault (11)
[comer:22212] Signal code: Address not mapped (1)
[comer:22212] Failing at address: (nil)
[comer:22212] [ 0] /usr/lib/libpthread.so.0(+0x13d00)[0x7fe96bd62d00]

In VisIt I use the Pixie reader for this type of files. Is this (or equivalent) available in ParaView to read basic HDF5 files like this one?

I also tried with a .xmf file which provides a better description of the data in the .h5 file (dimension coordinates). This one doesn’t crash anymore, but I don’t seem to be able to get any meaningful plot out of it either. I don’t know if I’m doing something wrong or there is something wrong with the files (as a reference, with VisIt, which I’ve been using lately, I can read without problems the .h5 directly, or the .xmf file).

Just trying to see if ParaView will fit our needs. Any help appreciated. Many thanks,
AdV

ParaView is indeed able to read different HDF5 based format, but very flexible, so sometimes it is hard to know how to use it in ParaView. XMF is a good choice for structure.

In any case, here is a working .xmf file : Scenario1_p1.tgz (499 Bytes)
and a working TRUCHAS .h5 file : viscoplastic-ring.h5 (1.5 MB)

Hi Mathieu,

“Mathieu Westphal (Kitware) via ParaView”
noreply@discourse.paraview.org writes:

ParaView is indeed able to read different HDF5 based format, but very
flexible, so sometimes it is hard to know how to use it in
ParaView. XMF is a good choice for structure.

Our files together with a .xmf file are fine, but trying to read the
HDF5 directly (which has a home-grown structure) results in a
segmentation fault.

I guess ParaView should warn that the file cannot be opened rather than
crashing, but at least together with the .xmf file I can read the data
OK.

Thanks,

Absolutely ! Please open an issue on our gitlab
https://gitlab.kitware.com/paraview/paraview/issues