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XDMF write_checkpoint leads to segfault in paraview

Issue #1039 invalid
Chaffra Affouda created an issue

To reproduce,

import dolfin
from dolfin import *

mesh = UnitSquareMesh(10,10)

DG1 = FunctionSpace(mesh,'DG', 1)

class Step(UserExpression):

    def __init__(self, mesh, *args, **kwargs):
        super().__init__(*args, **kwargs)
        self.mesh = mesh

    def eval_cell(self, values, x, cell):
        c = Cell(self.mesh, cell.index)
        p = c.midpoint()
        if p[0] <= 0.5:
            values[0] = 0.0
        elif p[0] >= 0.5:
            values[0] = 1.0


step = Step(mesh, domain=mesh, element=DG1.ufl_element())

f = Function(DG1)
f.interpolate(step)

file = XDMFFile("step_DG.xdmf")
file.write_checkpoint(f,"f")

Open xdmf file in paraview leads to segfault. Can @michalhabera look into this?

Comments (9)

  1. Chaffra Affouda reporter

    Error is

    HDF5-DIAG: Error detected in HDF5 (1.10.1) thread 0:
  #000: /home/chaffra/Projects/FEniCS/src/paraview/VTK/ThirdParty/hdf5/vtkhdf5/src/H5F.c line 586 in vtkhdf5_H5Fopen(): unable to open file
    major: File accessibilty
    minor: Unable to open file
  #001: /home/chaffra/Projects/FEniCS/src/paraview/VTK/ThirdParty/hdf5/vtkhdf5/src/H5Fint.c line 1305 in vtkhdf5_H5F_open(): unable to lock the file
    major: File accessibilty
    minor: Unable to open file
  #002: /home/chaffra/Projects/FEniCS/src/paraview/VTK/ThirdParty/hdf5/vtkhdf5/src/H5FD.c line 1839 in vtkhdf5_H5FD_lock(): driver lock request failed
    major: Virtual File Layer
    minor: Can't update object
  #003: /home/chaffra/Projects/FEniCS/src/paraview/VTK/ThirdParty/hdf5/vtkhdf5/src/H5FDsec2.c line 940 in H5FD_sec2_lock(): unable to lock file, errno = 11, error message = 'Resource temporarily unavailable'
    major: File accessibilty
    minor: Bad file ID accessed
HDF5-DIAG: Error detected in HDF5 (1.10.1) thread 0:
  #000: /home/chaffra/Projects/FEniCS/src/paraview/VTK/ThirdParty/hdf5/vtkhdf5/src/H5D.c line 284 in vtkhdf5_H5Dopen2(): not a location
    major: Invalid arguments to routine
    minor: Inappropriate type
  #001: /home/chaffra/Projects/FEniCS/src/paraview/VTK/ThirdParty/hdf5/vtkhdf5/src/H5Gloc.c line 251 in vtkhdf5_H5G_loc(): invalid object ID
    major: Invalid arguments to routine
    minor: Bad value
HDF5-DIAG: Error detected in HDF5 (1.10.1) thread 0:
  #000: /home/chaffra/Projects/FEniCS/src/paraview/VTK/ThirdParty/hdf5/vtkhdf5/src/H5D.c line 373 in vtkhdf5_H5Dget_space(): not a dataset
    major: Invalid arguments to routine
    minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.10.1) thread 0:
  #000: /home/chaffra/Projects/FEniCS/src/paraview/VTK/ThirdParty/hdf5/vtkhdf5/src/H5S.c line 863 in vtkhdf5_H5Sget_simple_extent_ndims(): not a dataspace
    major: Invalid arguments to routine
    minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.10.1) thread 0:
  #000: /home/chaffra/Projects/FEniCS/src/paraview/VTK/ThirdParty/hdf5/vtkhdf5/src/H5Sselect.c line 312 in vtkhdf5_H5Sget_select_npoints(): not a dataspace
    major: Invalid arguments to routine
    minor: Inappropriate type
Number of dimensions in light data description in Xdmf does not match number of dimensions in hdf5 file.
  4. Chaffra Affouda reporter

    Thanks, that was easy. Now it's the fe-filter.py that's not working. The (cell) datasets are not being populated in paraview. Here's my fe_fliter.py script. 

    Traceback (most recent call last):
  File "<string>", line 22, in <module>
  File "<string>", line 2, in RequestData
  File "<string>", line 277, in <module>
  File "<string>", line 221, in traverse
AttributeError: 'NoneType' object has no attribute 'GetNumberOfComponents'
ds_in =  vtkUnstructuredGrid (0x560309ff9e50)
  Debug: Off
  Modified Time: 9346991
  Reference Count: 2
  Registered Events: (none)
  Information: 0x5603064da7d0
  Data Released: False
  Global Release Data: Off
  UpdateTime: 9346993
  Field Data:
    Debug: Off
    Modified Time: 9346969
    Reference Count: 1
    Registered Events: (none)
    Number Of Arrays: 0
    Number Of Components: 0
    Number Of Tuples: 0
  Number Of Points: 600
  Number Of Cells: 200
  Cell Data:
    Debug: Off
    Modified Time: 9346987
    Reference Count: 1
    Registered Events: 
      Registered Observers:
        vtkObserver (0x5603087ebee0)
          Event: 33
          EventName: ModifiedEvent
          Command: 0x560306fc6f10
          Priority: 0
          Tag: 1
    Number Of Arrays: 0
    Number Of Components: 0
    Number Of Tuples: 0
    Copy Tuple Flags: ( 1 1 1 1 1 0 1 1 )
    Interpolate Flags: ( 1 1 1 1 1 0 0 1 )
    Pass Through Flags: ( 1 1 1 1 1 1 1 1 )
    Scalars: (none)
    Vectors: (none)
    Normals: (none)
    TCoords: (none)
    Tensors: (none)
    GlobalIds: (none)
    PedigreeIds: (none)
    EdgeFlag: (none)
  Point Data:
    Debug: Off
    Modified Time: 9346991
    Reference Count: 1
    Registered Events: 
      Registered Observers:
        vtkObserver (0x560308c1cce0)
          Event: 33
          EventName: ModifiedEvent
          Command: 0x560306fc6f10
          Priority: 0
          Tag: 1
    Number Of Arrays: 1
    Array 0 name = f
    Number Of Components: 1
    Number Of Tuples: 600
    Copy Tuple Flags: ( 1 1 1 1 1 0 1 1 )
    Interpolate Flags: ( 1 1 1 1 1 0 0 1 )
    Pass Through Flags: ( 1 1 1 1 1 1 1 1 )
    Scalars: 
      Debug: Off
      Modified Time: 9345604
      Reference Count: 3
      Registered Events: (none)
      Name: f
      Data type: double
      Size: 1023
      MaxId: 599
      NumberOfComponents: 1
      Information: 0x560307c67ee0
        Debug: Off
        Modified Time: 9347038
        Reference Count: 1
        Registered Events: (none)
        PER_FINITE_COMPONENT: vtkInformationVector(0x560308cd8910)
        PER_COMPONENT: vtkInformationVector(0x56030cae74b0)
      Name: f
      Number Of Components: 1
      Number Of Tuples: 600
      Size: 1023
      MaxId: 599
      LookupTable: (none)
    Vectors: (none)
    Normals: (none)
    TCoords: (none)
    Tensors: (none)
    GlobalIds: (none)
    PedigreeIds: (none)
    EdgeFlag: (none)
  Bounds: 
    Xmin,Xmax: (0, 1)
    Ymin,Ymax: (0, 1)
    Zmin,Zmax: (0, 0)
  Compute Time: 9460598
  Number Of Points: 600
  Point Coordinates: 0x560318265230
  Locator: 0
  Number Of Pieces: 1
  Piece: 0
  Ghost Level: 0
  5. Michal Habera

    That filter is not meant to work. This functionality should work in latest Paraview out of box. Do not use any external filter. Use Paraview 5.5.0+.

  7. Chaffra Affouda reporter

    OK I see. I am using paraview 5.5.2. In this case I am expecting to see a discontinuous step function but it looks like there is interpolation at the step edge. What am I doing wrong here? Paraview is still visualizing cells at the step-edge when you do a WarpByScalar.

  8. Michal Habera

    I see step as should be.

    Sorry, I don't have time to give you support on this. Ask on allanswered. This is not issue.

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–
Type
bug
Priority
major
Status
invalid
Component
io
Milestone
2019.1
Version
dev
Votes
0
Watchers
1
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