Segmentation fault when reading a homegrown HDF5 file

ParaView Support
1

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

2

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)

3

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,

4

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