[Paraview] Selecting volume rendering causes output to vanish

Sat Jun 13 23:12:08 EDT 2015

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.

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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