[Paraview] Selecting volume rendering causes output to vanish

Jeff Becker jeffrey.c.becker at nasa.gov
Fri Jun 12 18:27:40 EDT 2015 

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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