<html>
<head>
<meta content="text/html; charset=windows-1252"
http-equiv="Content-Type">
</head>
<body bgcolor="#FFFFFF" text="#000000">
<div class="moz-cite-prefix">On 06/11/2015 01:05 PM, Burlen Loring
wrote:<br>
</div>
<blockquote cite="mid:5579E9F5.4050206@gmail.com" type="cite">
<meta http-equiv="Content-Type" content="text/html;
charset=windows-1252">
you ran out of memory.<br>
<br>
You may need more than 1 node, and a parallel file format.<br>
<br>
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.<br>
</blockquote>
<br>
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):<br>
<br>
<br>
import os<br>
import numpy as np<br>
import steinmesh as mesh<br>
import itertools<br>
import vtk<br>
from vtk.util import numpy_support<br>
<br>
in_fname='/nobackupp9/pmoran/stein/mhd48-1/dat/mhd48h1new_670.8.dat'<br>
out_fname='/nobackup/jcbecker/steinBmag.vts'<br>
f = open(in_fname,"rb")<br>
bx = 6<br>
npoints = mesh.MX*mesh.MY*mesh.MZ<br>
f.seek(bx*npoints*np.dtype('f4').itemsize,os.SEEK_SET)<br>
<br>
steinbmag =
np.square(np.fromfile(f,dtype=np.dtype('f4'),count=npoints))<br>
steinbmag +=
np.square(np.fromfile(f,dtype=np.dtype('f4'),count=npoints))<br>
steinbmag +=
np.square(np.fromfile(f,dtype=np.dtype('f4'),count=npoints))<br>
steinbmag = np.sqrt(steinbmag)<br>
<br>
f.close()<br>
<br>
grid = [x for x in itertools.product(mesh.xcoords, mesh.ycoords,
mesh.zcoords)]<br>
<br>
pcoords = vtk.vtkDoubleArray()<br>
pcoords.SetNumberOfComponents(3)<br>
pcoords.SetNumberOfTuples(npoints)<br>
for i in range(npoints):<br>
pcoords.SetTuple3(*((i,) + grid[i]))<br>
pts = vtk.vtkPoints()<br>
pts.SetData(pcoords)<br>
<br>
sgrid = vtk.vtkStructuredGrid()<br>
sgrid.SetDimensions(mesh.MX,mesh.MY,mesh.MZ)<br>
sgrid.SetPoints(pts)<br>
<br>
bmagV = numpy_support.numpy_to_vtk(steinbmag,deep=True)<br>
bmagV.SetName('B field magnitude')<br>
sgrid.GetPointData().SetScalars(bmagV)<br>
<br>
writer = vtk.vtkXMLStructuredGridWriter()<br>
writer.SetFileName(out_fname)<br>
writer.SetInputData(sgrid)<br>
writer.SetDataModeToBinary()<br>
writer.Write()<br>
<br>
Can anyone see what's wrong? Thanks.<br>
<br>
-jeff<br>
<br>
<br>
Program received signal SIGSEGV, Segmentation fault.<br>
0x00002aaaafb1c327 in vtkDataArrayTemplate<long
long>::GetValue(long long) ()<br>
from
/home4/jcbecker/ParaView-4.3.1-Linux-64bit/lib/paraview-4.3/libvtkCommonCore-pv4.3.so.1<br>
(gdb) bt<br>
#0 0x00002aaaafb1c327 in vtkDataArrayTemplate<long
long>::GetValue(long long)<br>
()<br>
from
/home4/jcbecker/ParaView-4.3.1-Linux-64bit/lib/paraview-4.3/libvtkCommonCore-pv4.3.so.1<br>
#1 0x00002aaaae991d71 in vtkCellArray::GetMaxCellSize() ()<br>
from
/home4/jcbecker/ParaView-4.3.1-Linux-64bit/lib/paraview-4.3/libvtkCommonDataModel-pv4.3.so.1<br>
#2 0x00002aaaac44dde9 in
vtkCellCenterDepthSort::ComputeCellCenters() ()<br>
from
/home4/jcbecker/ParaView-4.3.1-Linux-64bit/lib/paraview-4.3/libvtkRenderingCore-pv4.3.so.1<br>
#3 0x00002aaaac44e593 in vtkCellCenterDepthSort::InitTraversal() ()<br>
from
/home4/jcbecker/ParaView-4.3.1-Linux-64bit/lib/paraview-4.3/libvtkRenderingCore-pv4.3.so.1<br>
#4 0x00002aaab82fc2dd in
vtkOpenGLProjectedTetrahedraMapper::ProjectTetrahedra(vtkRenderer*,
vtkVolume*) ()<br>
from
/home4/jcbecker/ParaView-4.3.1-Linux-64bit/lib/paraview-4.3/libvtkRenderingVolumeOpenGL-pv4.3.so.1<br>
#5 0x00002aaab82f7997 in
vtkOpenGLProjectedTetrahedraMapper::Render(vtkRenderer*, vtkVolume*)
()<br>
from
/home4/jcbecker/ParaView-4.3.1-Linux-64bit/lib/paraview-4.3/libvtkRenderingVolumeOpenGL-pv4.3.so.1<br>
#6 0x00002aaaac4d0118 in
vtkVolume::RenderVolumetricGeometry(vtkViewport*) ()<br>
from
/home4/jcbecker/ParaView-4.3.1-Linux-64bit/lib/paraview-4.3/libvtkRenderingCore-pv4.3.so.1<br>
#7 0x00002aaaac4e1198 in
vtkLODProp3D::RenderVolumetricGeometry(vtkViewport*)<br>
()<br>
from
/home4/jcbecker/ParaView-4.3.1-Linux-64bit/lib/paraview-4.3/libvtkRenderingCore-pv4.3.so.1<br>
#8 0x00002aaab4f3a4eb in
vtkPVLODVolume::RenderVolumetricGeometry(vtkViewport*) ()<br>
from
/home4/jcbecker/ParaView-4.3.1-Linux-64bit/lib/paraview-4.3/libvtkPVVTKExtensionsRendering-pv4.3.so.1<br>
#9 0x00002aaaac4b94ee in vtkRenderer::UpdateGeometry() ()<br>
from
/home4/jcbecker/ParaView-4.3.1-Linux-64bit/lib/paraview-4.3/libvtkRenderingCore-pv4.3.so.1<br>
#10 0x00002aaab4f2d751 in vtkPVDefaultPass::Render(vtkRenderState
const*) ()<br>
from
/home4/jcbecker/ParaView-4.3.1-Linux-64bit/lib/paraview-4.3/libvtkPVVTKExtensionsRendering-pv4.3.so.1<br>
#11 0x00002aaaba0d135b in vtkCameraPass::Render(vtkRenderState
const*) ()<br>
from
/home4/jcbecker/ParaView-4.3.1-Linux-64bit/lib/paraview-4.3/libvtkRenderingOpenGL-pv4.3.so.1<br>
#12 0x00002aaaba1436c0 in vtkOpenGLRenderer::DeviceRender() ()<br>
from
/home4/jcbecker/ParaView-4.3.1-Linux-64bit/lib/paraview-4.3/libvtkRenderingOpenGL-pv4.3.so.1<br>
#13 0x00002aaaac4bb18d in vtkRenderer::Render() ()<br>
from
/home4/jcbecker/ParaView-4.3.1-Linux-64bit/lib/paraview-4.3/libvtkRenderingCore-pv4.3.so.1<br>
#14 0x00002aaaac4b8429 in vtkRendererCollection::Render() ()<br>
from
/home4/jcbecker/ParaView-4.3.1-Linux-64bit/lib/paraview-4.3/libvtkRenderingCore-pv4.3.so.1<br>
#15 0x00002aaaac4c2202 in vtkRenderWindow::DoStereoRender() ()<br>
from
/home4/jcbecker/ParaView-4.3.1-Linux-64bit/lib/paraview-4.3/libvtkRenderingCore-pv4.3.so.1<br>
#16 0x00002aaaac4c2119 in vtkRenderWindow::DoFDRender() ()<br>
from
/home4/jcbecker/ParaView-4.3.1-Linux-64bit/lib/paraview-4.3/libvtkRenderingCore-pv4.3.so.1<br>
#17 0x00002aaaac4c31a3 in vtkRenderWindow::DoAARender() ()<br>
from
/home4/jcbecker/ParaView-4.3.1-Linux-64bit/lib/paraview-4.3/libvtkRenderingCore-pv4.3.so.1<br>
#18 0x00002aaaac4bf7fe in vtkRenderWindow::Render() ()<br>
from
/home4/jcbecker/ParaView-4.3.1-Linux-64bit/lib/paraview-4.3/libvtkRenderingCore-pv4.3.so.1<br>
#19 0x00002aaaba1d17ae in vtkXOpenGLRenderWindow::Render() ()<br>
from
/home4/jcbecker/ParaView-4.3.1-Linux-64bit/lib/paraview-4.3/libvtkRenderingOpenGL-pv4.3.so.1<br>
#20 0x00002aaab3b9897f in vtkPVRenderView::Render(bool, bool) ()<br>
from
/home4/jcbecker/ParaView-4.3.1-Linux-64bit/lib/paraview-4.3/libvtkPVClientServerCoreRendering-pv4.3.so.1<br>
#21 0x00002aaab3b9369c in vtkPVRenderView::StillRender() ()<br>
from
/home4/jcbecker/ParaView-4.3.1-Linux-64bit/lib/paraview-4.3/libvtkPVClientServerCoreRendering-pv4.3.so.1<br>
#22 0x00002aaaab493665 in
vtkPVRenderViewCommand(vtkClientServerInterpreter*, vtkObjectBase*,
char const*, vtkClientServerStream const&,
vtkClientServerStream&, void*) ()<br>
from
/home4/jcbecker/ParaView-4.3.1-Linux-64bit/lib/paraview-4.3/libvtkPVServerManagerApplication-pv4.3.so.1<br>
#23 0x00002aaaadb005e0 in
vtkClientServerInterpreter::CallCommandFunction(char const*,
vtkObjectBase*, char const*, vtkClientServerStream const&,
vtkClientServerStream&) ()<br>
from
/home4/jcbecker/ParaView-4.3.1-Linux-64bit/lib/paraview-4.3/libvtkClientServer-pv4.3.so.1<br>
#24 0x00002aaaadb05393 in
vtkClientServerInterpreter::ProcessCommandInvoke(vtkClientServerStream
const&, int) ()<br>
from
/home4/jcbecker/ParaView-4.3.1-Linux-64bit/lib/paraview-4.3/libvtkClientServer-pv4.3.so.1<br>
#25 0x00002aaaadb03832 in
vtkClientServerInterpreter::ProcessOneMessage(vtkClientServerStream
const&, int) ()<br>
from
/home4/jcbecker/ParaView-4.3.1-Linux-64bit/lib/paraview-4.3/libvtkClientServer-pv4.3.so.1<br>
#26 0x00002aaaadb03ced in
vtkClientServerInterpreter::ProcessStream(vtkClientServerStream
const&) ()<br>
from
/home4/jcbecker/ParaView-4.3.1-Linux-64bit/lib/paraview-4.3/libvtkClientServer-pv4.3.so.1<br>
#27 0x00002aaaabd8dcec in
vtkPVSessionCore::ExecuteStreamInternal(vtkClientServerStream
const&, bool) ()<br>
from
/home4/jcbecker/ParaView-4.3.1-Linux-64bit/lib/paraview-4.3/libvtkPVServerImplementationCore-pv4.3.so.1<br>
#28 0x00002aaaabd8d958 in vtkPVSessionCore::ExecuteStream(unsigned
int, vtkClientServerStream const&, bool) ()<br>
from
/home4/jcbecker/ParaView-4.3.1-Linux-64bit/lib/paraview-4.3/libvtkPVServerImplementationCore-pv4.3.so.1<br>
#29 0x00002aaaabd8c203 in vtkPVSessionBase::ExecuteStream(unsigned
int, vtkClientServerStream const&, bool) ()<br>
from
/home4/jcbecker/ParaView-4.3.1-Linux-64bit/lib/paraview-4.3/libvtkPVServerImplementationCore-pv4.3.so.1<br>
#30 0x00002aaaabd98591 in
vtkPVSessionServer::OnClientServerMessageRMI(void*, int) ()<br>
from
/home4/jcbecker/ParaView-4.3.1-Linux-64bit/lib/paraview-4.3/libvtkPVServerImplementationCore-pv4.3.so.1<br>
#31 0x00002aaaae2cc463 in vtkMultiProcessController::ProcessRMI(int,
void*, int, int) ()<br>
from
/home4/jcbecker/ParaView-4.3.1-Linux-64bit/lib/paraview-4.3/libvtkParallelCore-pv4.3.so.1<br>
#32 0x00002aaaae2cc7df in
vtkMultiProcessController::ProcessRMIs(int, int) ()<br>
from
/home4/jcbecker/ParaView-4.3.1-Linux-64bit/lib/paraview-4.3/libvtkParallelCore-pv4.3.so.1<br>
#33 0x00002aaaabfa5ec6 in
vtkTCPNetworkAccessManager::ProcessEventsInternal(unsigned long,
bool) ()<br>
from
/home4/jcbecker/ParaView-4.3.1-Linux-64bit/lib/paraview-4.3/libvtkPVClientServerCoreCore-pv4.3.so.1<br>
#34 0x00000000004019f6 in RealMain(int, char**,
vtkProcessModule::ProcessTypes)<br>
()<br>
#35 0x0000000000401a3e in main ()<br>
<br>
<br>
</body>
</html>