[Paraview] Selecting volume rendering causes output to vanish

[Jeff Becker]

On 06/13/2015 08:12 PM, Burlen Loring wrote:
> It's hard for me to say, I've never seen the stein mesh package, and 
> googling doesn't turn anything up. Perhaps you could share the dataset 
> itself? I'm sure someone here could quickly reproduce the issue and 
> perhaps suggest a fix.

I'll ask if I can share the data set, but it's half a terabyte in size! 
I only read it in a small part of it for this test, so I suppose I could 
splice that out. The stein mesh package is some python that I wrote to 
import the mesh coordinates. It's simply some data specified as follows:

MX=504
MY=500
MZ=504

xcoords = [
   0.0000000000000000e+00,   9.5238097012042999e-02, 
1.9047619402408600e-01,
#... list of x coordinates
]

ycoords = [
  -5.5000001192092896e-01,  -5.3477758169174194e-01, 
-5.1964950561523438e-01,
#... list of y coordinates
]

zcoords = [
   0.0000000000000000e+00,   9.5238097012042999e-02, 
1.9047619402408600e-01,
#... list of z coordinates
]

Hopefully, that is enough to give you the information you need. Thanks.

-jeff
>
> On 6/12/2015 3:27 PM, Jeff Becker wrote:
>> On 06/11/2015 01:05 PM, Burlen Loring wrote:
>>> you ran out of memory.
>>>
>>> You may need more than 1 node, and a parallel file format.
>>>
>>> You mentioned that you had a grid of 500 x 500 points. You could 
>>> save a lot of memory by using vtkImageData, vtkRectilinearMesh or 
>>> vtkStructuredGrid if your data is amenable to one of those.
>>
>> I switched to using vtkStructuredGrid. However, after reading the 
>> file in ParaView, and attempting to volume render I get the seg. 
>> fault in pvserver below. I am creating my grid in python as follows 
>> (steinmesh contains the grid coordinates):
>>
>>
>> import os
>> import numpy as np
>> import steinmesh as mesh
>> import itertools
>> import vtk
>> from vtk.util import numpy_support
>>
>> in_fname='/nobackupp9/pmoran/stein/mhd48-1/dat/mhd48h1new_670.8.dat'
>> out_fname='/nobackup/jcbecker/steinBmag.vts'
>> f = open(in_fname,"rb")
>> bx = 6
>> npoints = mesh.MX*mesh.MY*mesh.MZ
>> f.seek(bx*npoints*np.dtype('f4').itemsize,os.SEEK_SET)
>>
>> steinbmag = np.square(np.fromfile(f,dtype=np.dtype('f4'),count=npoints))
>> steinbmag += np.square(np.fromfile(f,dtype=np.dtype('f4'),count=npoints))
>> steinbmag += np.square(np.fromfile(f,dtype=np.dtype('f4'),count=npoints))
>> steinbmag = np.sqrt(steinbmag)
>>
>> f.close()
>>
>> grid = [x for x in itertools.product(mesh.xcoords, mesh.ycoords, 
>> mesh.zcoords)]
>>
>> pcoords = vtk.vtkDoubleArray()
>> pcoords.SetNumberOfComponents(3)
>> pcoords.SetNumberOfTuples(npoints)
>> for i in range(npoints):
>>    pcoords.SetTuple3(*((i,) + grid[i]))
>> pts = vtk.vtkPoints()
>> pts.SetData(pcoords)
>>
>> sgrid = vtk.vtkStructuredGrid()
>> sgrid.SetDimensions(mesh.MX,mesh.MY,mesh.MZ)
>> sgrid.SetPoints(pts)
>>
>> bmagV = numpy_support.numpy_to_vtk(steinbmag,deep=True)
>> bmagV.SetName('B field magnitude')
>> sgrid.GetPointData().SetScalars(bmagV)
>>
>> writer = vtk.vtkXMLStructuredGridWriter()
>> writer.SetFileName(out_fname)
>> writer.SetInputData(sgrid)
>> writer.SetDataModeToBinary()
>> writer.Write()
>>
>> Can anyone see what's wrong? Thanks.
>>
>> -jeff
>>
>>
>> Program received signal SIGSEGV, Segmentation fault.
>> 0x00002aaaafb1c327 in vtkDataArrayTemplate<long long>::GetValue(long 
>> long) ()
>>    from 
>> /home4/jcbecker/ParaView-4.3.1-Linux-64bit/lib/paraview-4.3/libvtkCommonCore-pv4.3.so.1
>> (gdb) bt
>> #0  0x00002aaaafb1c327 in vtkDataArrayTemplate<long 
>> long>::GetValue(long long)
>>     ()
>>    from 
>> /home4/jcbecker/ParaView-4.3.1-Linux-64bit/lib/paraview-4.3/libvtkCommonCore-pv4.3.so.1
>> #1  0x00002aaaae991d71 in vtkCellArray::GetMaxCellSize() ()
>>    from 
>> /home4/jcbecker/ParaView-4.3.1-Linux-64bit/lib/paraview-4.3/libvtkCommonDataModel-pv4.3.so.1
>> #2  0x00002aaaac44dde9 in vtkCellCenterDepthSort::ComputeCellCenters() ()
>>    from 
>> /home4/jcbecker/ParaView-4.3.1-Linux-64bit/lib/paraview-4.3/libvtkRenderingCore-pv4.3.so.1
>> #3  0x00002aaaac44e593 in vtkCellCenterDepthSort::InitTraversal() ()
>>    from 
>> /home4/jcbecker/ParaView-4.3.1-Linux-64bit/lib/paraview-4.3/libvtkRenderingCore-pv4.3.so.1
>> #4  0x00002aaab82fc2dd in 
>> vtkOpenGLProjectedTetrahedraMapper::ProjectTetrahedra(vtkRenderer*, 
>> vtkVolume*) ()
>>    from 
>> /home4/jcbecker/ParaView-4.3.1-Linux-64bit/lib/paraview-4.3/libvtkRenderingVolumeOpenGL-pv4.3.so.1
>> #5  0x00002aaab82f7997 in 
>> vtkOpenGLProjectedTetrahedraMapper::Render(vtkRenderer*, vtkVolume*) ()
>>    from 
>> /home4/jcbecker/ParaView-4.3.1-Linux-64bit/lib/paraview-4.3/libvtkRenderingVolumeOpenGL-pv4.3.so.1
>> #6  0x00002aaaac4d0118 in 
>> vtkVolume::RenderVolumetricGeometry(vtkViewport*) ()
>>    from 
>> /home4/jcbecker/ParaView-4.3.1-Linux-64bit/lib/paraview-4.3/libvtkRenderingCore-pv4.3.so.1
>> #7  0x00002aaaac4e1198 in 
>> vtkLODProp3D::RenderVolumetricGeometry(vtkViewport*)
>>     ()
>>    from 
>> /home4/jcbecker/ParaView-4.3.1-Linux-64bit/lib/paraview-4.3/libvtkRenderingCore-pv4.3.so.1
>> #8  0x00002aaab4f3a4eb in 
>> vtkPVLODVolume::RenderVolumetricGeometry(vtkViewport*) ()
>>    from 
>> /home4/jcbecker/ParaView-4.3.1-Linux-64bit/lib/paraview-4.3/libvtkPVVTKExtensionsRendering-pv4.3.so.1
>> #9  0x00002aaaac4b94ee in vtkRenderer::UpdateGeometry() ()
>>    from 
>> /home4/jcbecker/ParaView-4.3.1-Linux-64bit/lib/paraview-4.3/libvtkRenderingCore-pv4.3.so.1
>> #10 0x00002aaab4f2d751 in vtkPVDefaultPass::Render(vtkRenderState 
>> const*) ()
>>    from 
>> /home4/jcbecker/ParaView-4.3.1-Linux-64bit/lib/paraview-4.3/libvtkPVVTKExtensionsRendering-pv4.3.so.1
>> #11 0x00002aaaba0d135b in vtkCameraPass::Render(vtkRenderState const*) ()
>>    from 
>> /home4/jcbecker/ParaView-4.3.1-Linux-64bit/lib/paraview-4.3/libvtkRenderingOpenGL-pv4.3.so.1
>> #12 0x00002aaaba1436c0 in vtkOpenGLRenderer::DeviceRender() ()
>>    from 
>> /home4/jcbecker/ParaView-4.3.1-Linux-64bit/lib/paraview-4.3/libvtkRenderingOpenGL-pv4.3.so.1
>> #13 0x00002aaaac4bb18d in vtkRenderer::Render() ()
>>    from 
>> /home4/jcbecker/ParaView-4.3.1-Linux-64bit/lib/paraview-4.3/libvtkRenderingCore-pv4.3.so.1
>> #14 0x00002aaaac4b8429 in vtkRendererCollection::Render() ()
>>    from 
>> /home4/jcbecker/ParaView-4.3.1-Linux-64bit/lib/paraview-4.3/libvtkRenderingCore-pv4.3.so.1
>> #15 0x00002aaaac4c2202 in vtkRenderWindow::DoStereoRender() ()
>>    from 
>> /home4/jcbecker/ParaView-4.3.1-Linux-64bit/lib/paraview-4.3/libvtkRenderingCore-pv4.3.so.1
>> #16 0x00002aaaac4c2119 in vtkRenderWindow::DoFDRender() ()
>>    from 
>> /home4/jcbecker/ParaView-4.3.1-Linux-64bit/lib/paraview-4.3/libvtkRenderingCore-pv4.3.so.1
>> #17 0x00002aaaac4c31a3 in vtkRenderWindow::DoAARender() ()
>>    from 
>> /home4/jcbecker/ParaView-4.3.1-Linux-64bit/lib/paraview-4.3/libvtkRenderingCore-pv4.3.so.1
>> #18 0x00002aaaac4bf7fe in vtkRenderWindow::Render() ()
>>    from 
>> /home4/jcbecker/ParaView-4.3.1-Linux-64bit/lib/paraview-4.3/libvtkRenderingCore-pv4.3.so.1
>> #19 0x00002aaaba1d17ae in vtkXOpenGLRenderWindow::Render() ()
>>    from 
>> /home4/jcbecker/ParaView-4.3.1-Linux-64bit/lib/paraview-4.3/libvtkRenderingOpenGL-pv4.3.so.1
>> #20 0x00002aaab3b9897f in vtkPVRenderView::Render(bool, bool) ()
>>    from 
>> /home4/jcbecker/ParaView-4.3.1-Linux-64bit/lib/paraview-4.3/libvtkPVClientServerCoreRendering-pv4.3.so.1
>> #21 0x00002aaab3b9369c in vtkPVRenderView::StillRender() ()
>>    from 
>> /home4/jcbecker/ParaView-4.3.1-Linux-64bit/lib/paraview-4.3/libvtkPVClientServerCoreRendering-pv4.3.so.1
>> #22 0x00002aaaab493665 in 
>> vtkPVRenderViewCommand(vtkClientServerInterpreter*, vtkObjectBase*, 
>> char const*, vtkClientServerStream const&, vtkClientServerStream&, 
>> void*) ()
>>    from 
>> /home4/jcbecker/ParaView-4.3.1-Linux-64bit/lib/paraview-4.3/libvtkPVServerManagerApplication-pv4.3.so.1
>> #23 0x00002aaaadb005e0 in 
>> vtkClientServerInterpreter::CallCommandFunction(char const*, 
>> vtkObjectBase*, char const*, vtkClientServerStream const&, 
>> vtkClientServerStream&) ()
>>    from 
>> /home4/jcbecker/ParaView-4.3.1-Linux-64bit/lib/paraview-4.3/libvtkClientServer-pv4.3.so.1
>> #24 0x00002aaaadb05393 in 
>> vtkClientServerInterpreter::ProcessCommandInvoke(vtkClientServerStream const&, 
>> int) ()
>>    from 
>> /home4/jcbecker/ParaView-4.3.1-Linux-64bit/lib/paraview-4.3/libvtkClientServer-pv4.3.so.1
>> #25 0x00002aaaadb03832 in 
>> vtkClientServerInterpreter::ProcessOneMessage(vtkClientServerStream 
>> const&, int) ()
>>    from 
>> /home4/jcbecker/ParaView-4.3.1-Linux-64bit/lib/paraview-4.3/libvtkClientServer-pv4.3.so.1
>> #26 0x00002aaaadb03ced in 
>> vtkClientServerInterpreter::ProcessStream(vtkClientServerStream 
>> const&) ()
>>    from 
>> /home4/jcbecker/ParaView-4.3.1-Linux-64bit/lib/paraview-4.3/libvtkClientServer-pv4.3.so.1
>> #27 0x00002aaaabd8dcec in 
>> vtkPVSessionCore::ExecuteStreamInternal(vtkClientServerStream const&, 
>> bool) ()
>>    from 
>> /home4/jcbecker/ParaView-4.3.1-Linux-64bit/lib/paraview-4.3/libvtkPVServerImplementationCore-pv4.3.so.1
>> #28 0x00002aaaabd8d958 in vtkPVSessionCore::ExecuteStream(unsigned 
>> int, vtkClientServerStream const&, bool) ()
>>    from 
>> /home4/jcbecker/ParaView-4.3.1-Linux-64bit/lib/paraview-4.3/libvtkPVServerImplementationCore-pv4.3.so.1
>> #29 0x00002aaaabd8c203 in vtkPVSessionBase::ExecuteStream(unsigned 
>> int, vtkClientServerStream const&, bool) ()
>>    from 
>> /home4/jcbecker/ParaView-4.3.1-Linux-64bit/lib/paraview-4.3/libvtkPVServerImplementationCore-pv4.3.so.1
>> #30 0x00002aaaabd98591 in 
>> vtkPVSessionServer::OnClientServerMessageRMI(void*, int) ()
>>    from 
>> /home4/jcbecker/ParaView-4.3.1-Linux-64bit/lib/paraview-4.3/libvtkPVServerImplementationCore-pv4.3.so.1
>> #31 0x00002aaaae2cc463 in vtkMultiProcessController::ProcessRMI(int, 
>> void*, int, int) ()
>>    from 
>> /home4/jcbecker/ParaView-4.3.1-Linux-64bit/lib/paraview-4.3/libvtkParallelCore-pv4.3.so.1
>> #32 0x00002aaaae2cc7df in vtkMultiProcessController::ProcessRMIs(int, 
>> int) ()
>>    from 
>> /home4/jcbecker/ParaView-4.3.1-Linux-64bit/lib/paraview-4.3/libvtkParallelCore-pv4.3.so.1
>> #33 0x00002aaaabfa5ec6 in 
>> vtkTCPNetworkAccessManager::ProcessEventsInternal(unsigned long, bool) ()
>>    from 
>> /home4/jcbecker/ParaView-4.3.1-Linux-64bit/lib/paraview-4.3/libvtkPVClientServerCoreCore-pv4.3.so.1
>> #34 0x00000000004019f6 in RealMain(int, char**, 
>> vtkProcessModule::ProcessTypes)
>>     ()
>> #35 0x0000000000401a3e in main ()
>>
>>
>

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