[vtkusers] Generating Cells For Unstructured Grids

Thu Oct 19 19:29:43 EDT 2017

 Hi all,

I am working through some examples and trying to add my own data.

I'm running VTK-8 on ubuntu 16.04.

The original examples code adds 8 cells, the example runs fine,
my hack of the example attempts to add 49000ish cells comes out with an
error.

The following code:

    gap_data_block = get_gap_data_block()
    voxelPoints = vtk.vtkPoints()
    voxelPoints.SetNumberOfPoints(len(gap_data_block))
    voxelPoints.SetData(VN.numpy_to_vtk(gap_data_block, deep=True))

    print("len(gap_data_block))
    print(gap_data_block.shape)

    aVoxel = vtk.vtkVoxel()

    for i in range(len(gap_data_block[:, 0])):
        print(len(gap_data_block), i)
        aVoxel.GetPointIds().SetId(i, i)

Gives the following output and nasty error - what is going on here??

Output:
Length Gap Data Block: 49432
Shape Gap Data Block: (49432, 3)
0
1
2
.
.
.
1601
1602
*** Error in `/usr/local/bin/vtkpython': corrupted size vs. prev_size:
0x0000000002c884f0 ***
======= Backtrace: =========
/lib/x86_64-linux-gnu/libc.so.6(+0x777e5)[0x7f491973f7e5]
/lib/x86_64-linux-gnu/libc.so.6(+0x82aec)[0x7f491974aaec]
/lib/x86_64-linux-gnu/libc.so.6(__libc_malloc+0x54)[0x7f491974c184]
/usr/lib/x86_64-linux-gnu/libpython3.5m.so.1.0(PyDict_New+0xb)[0x7f49190f6a7b]
/usr/local/lib/libvtkWrappingPython35Core-8.0.so.1(PyVTKObject_FromPointer+0x462)[0x7f48f6425b3c]
/usr/local/lib/libvtkWrappingPython35Core-8.0.so.1(_ZN13vtkPythonUtil20GetObjectFromPointerEP13vtkObjectBase+0x4b5)[0x7f48f64140e9]
/usr/local/lib/libvtkCommonCorePython35D-8.0.so.1(_ZN13vtkPythonArgs14BuildVTKObjectEPKv+0x18)[0x7f48f677b90c]
/usr/local/lib/libvtkCommonDataModelPython35D-8.0.so.1(+0x13d6ed)[0x7f48f39296ed]
/usr/lib/x86_64-linux-gnu/libpython3.5m.so.1.0(PyCFunction_Call+0xc9)[0x7f49190ef039]
/usr/lib/x86_64-linux-gnu/libpython3.5m.so.1.0(PyEval_EvalFrameEx+0x7555)[0x7f49191fb1b5]
/usr/lib/x86_64-linux-gnu/libpython3.5m.so.1.0(PyEval_EvalFrameEx+0x79d9)[0x7f49191fb639]
/usr/lib/x86_64-linux-gnu/libpython3.5m.so.1.0(+0x24ac6c)[0x7f491928bc6c]
/usr/lib/x86_64-linux-gnu/libpython3.5m.so.1.0(PyEval_EvalCodeEx+0x23)[0x7f491928bd43]
/usr/lib/x86_64-linux-gnu/libpython3.5m.so.1.0(PyEval_EvalCode+0x1b)[0x7f49191f39cb]
/usr/lib/x86_64-linux-gnu/libpython3.5m.so.1.0(PyRun_StringFlags+0x8f)[0x7f4919210e6f]
/usr/lib/x86_64-linux-gnu/libpython3.5m.so.1.0(PyRun_SimpleStringFlags+0x3b)[0x7f4919211eab]
/usr/lib/x86_64-linux-gnu/libpython3.5m.so.1.0(Py_Main+0x7c7)[0x7f4919278d57]
/usr/local/bin/vtkpython(main+0x527)[0x40200c]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf0)[0x7f49196e8830]
/usr/local/bin/vtkpython(_start+0x29)[0x401989]
======= Memory map: ========
00400000-00404000 r-xp 00000000 08:35 32780695
/usr/local/bin/vtkpython
00603000-00604000 r--p 00003000 08:35 32780695
/usr/local/bin/vtkpython
00604000-00605000 rw-p 00004000 08:35 32780695
/usr/local/bin/vtkpython
01d85000-06252000 rw-p 00000000 00:00 0
[heap]
7f4896b0a000-7f4898205000 rw-p 00000000 00:00 0
7f489f640000-7f489f680000 rw-p 00000000 00:00 0
7f489fb00000-7f489fb40000 rw-p 00000000 00:00 0
7f48a4000000-7f48a4229000 rw-p 00000000 00:00 0
7f48a4229000-7f48a8000000 ---p 00000000 00:00 0
7f48a8000000-7f48a9ce4000 rw-p 00000000 00:00 0
7f48a9ce4000-7f48ac000000 ---p 00000000 00:00 0
7f48ac000000-7f48adca1000 rw-p 00000000 00:00 0
7f48adca1000-7f48b0000000 ---p 00000000 00:00 0
7f48b2365000-7f48b23a5000 rw-p 00000000 00:00 0
7f48b23a5000-7f48b23a8000 r-xp 00000000 08:35 32510071
/usr/lib/python3.5/lib-dynload/_
multiprocessing.cpython-35m-x86_64-linux-gnu.so
7f48b23a8000-7f48b25a7000 ---p 00003000 08:35 32510071
/usr/lib/python3.5/lib-dynload/_
multiprocessing.cpython-35m-x86_64-linux-gnu.so
7f48b25a7000-7f48b25a8000 r--p 00002000 08:35 32510071
/usr/lib/python3.5/lib-dynload/_
multiprocessing.cpython-35m-x86_64-linux-gnu.so
7f48b25a8000-7f48b25a9000 rw-p 00003000 08:35 32510071
/usr/lib/python3.5/lib-dynload/_
multiprocessing.cpython-35m-x86_64-linux-gnu.so
7f48b25a9000-7f48b2629000 rw-p 00000000 00:00 0
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7f48b661f000-7f48b6649000 r-xp 00000000 08:35 32514684
/usr/lib/python3/dist-packages/matplotlib/_
path.cpython-35m-x86_64-linux-gnu.so
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7f48b6849000-7f48b684a000 r--p 0002a000 08:35 32514684
/usr/lib/python3/dist-packages/matplotlib/_
path.cpython-35m-x86_64-linux-gnu.so
7f48b684a000-7f48b684b000 rw-p 0002b000 08:35 32514684
/usr/lib/python3/dist-packages/matplotlib/_
path.cpython-35m-x86_64-linux-gnu.so
7f48b684b000-7f48b68cc000 rw-p 00000000 00:00 0
7f48b68cc000-7f48b68dd000 r-xp 00000000 08:35 32510070
/usr/lib/python3.5/lib-dynload/_json.cpython-35m-x86_64-linux-gnu.so
7f48b68dd000-7f48b6adc000 ---p 00011000 08:35 32510070
/usr/lib/python3.5/lib-dynload/_json.cpython-35m-x86_64-linux-gnu.so
7f48b6adc000-7f48b6add000 r--p 00010000 08:35 32510070
/usr/lib/python3.5/lib-dynload/_json.cpython-35m-x86_64-linux-gnu.so
7f48b6add000-7f48b6ade000 rw-p 00011000 08:35 32510070
/usr/lib/python3.5/lib-dynload/_json.cpython-35m-x86_64-linux-gnu.so
7f48b6ade000-7f48b6b3c000 r-xp 00000000 08:35 2101571
/lib/x86_64-linux-gnu/libssl.so.1.0.0
7f48b6b3c000-7f48b6d3c000 ---p 0005e000 08:35 2101571
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7f48b6d3c000-7f48b6d40000 r--p 0005e000 08:35 2101571
/lib/x86_64-linux-gnu/libssl.so.1.0.0
7f48b6d40000-7f48b6d47000 rw-p 00062000 08:35 2101571
/lib/x86_64-linux-gnu/libssl.so.1.0.0
7f48b6d47000-7f48b6d5e000 r-xp 00000000 08:35 32507025
/usr/lib/python3.5/lib-dynload/_ssl.cpython-35m-x86_64-linux-gnu.so
7f48b6d5e000-7f48b6f5e000 ---p 00017000 08:35 32507025
/usr/lib/python3.5/lib-dynload/_ssl.cpython-35m-x86_64-linux-gnu.so
7f48b6f5e000-7f48b6f5f000 r--p 00017000 08:35 32507025
/usr/lib/python3.5/lib-dynload/_ssl.cpython-35m-x86_64-linux-gnu.so
7f48b6f5f000-7f48b6f64000 rw-p 00018000 08:35 32507025
/usr/lib/python3.5/lib-dynload/_ssl.cpython-35m-x86_64-linux-gnu.so
7f48b6f64000-7f48b71a4000 rw-p 00000000 00:00 0
7f48b71a4000-7f48b71a5000 r-xp 00000000 08:35 32507023
/usr/lib/python3.5/lib-dynload/_opcode.cpython-35m-x86_64-linux-gnu.so
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7f48b73a4000-7f48b73a5000 r--p 00000000 08:35 32507023
/usr/lib/python3.5/lib-dynload/_opcode.cpython-35m-x86_64-linux-gnu.so
7f48b73a5000-7f48b73a6000 rw-p 00001000 08:35 32507023
/usr/lib/python3.5/lib-dynload/_opcode.cpython-35m-x86_64-linux-gnu.so
7f48b73a6000-7f48b74e6000 rw-p 00000000 00:00 0
7f48b74e6000-7f48b74f5000 r-xp 00000000 08:35 38939108
/usr/lib/python3/dist-packages/h5py/h5l.cpython-35m-x86_64-linux-gnu.so
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7f48b76f6000-7f48b76f9000 rw-p 00010000 08:35 38939108
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7f48b76f9000-7f48b770a000 r-xp 00000000 08:35 38939111
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/usr/lib/python3/dist-packages/h5py/h5o.cpython-35m-x86_64-linux-gnu.so
7f48b790a000-7f48b790d000 rw-p 00011000 08:35 38939111
/usr/lib/python3/dist-packages/h5py/h5o.cpython-35m-x86_64-linux-gnu.so
7f48b790d000-7f48b794e000 rw-p 00000000 00:00 0
7f48b794e000-7f48b7952000 r-xp 00000000 08:35 38939144
/usr/lib/python3/dist-packages/h5py/h5fd.cpython-35m-x86_64-linux-gnu.so
7f48b7952000-7f48b7b51000 ---p 00004000 08:35 38939144
/usr/lib/python3/dist-packages/h5py/h5fd.cpython-35m-x86_64-linux-gnu.so
7f48b7b51000-7f48b7b52000 r--p 00003000 08:35 38939144
/usr/lib/python3/dist-packages/h5py/h5fd.cpython-35m-x86_64-linux-gnu.so
7f48b7b52000-7f48b7b53000 rw-p 00004000 08:35 38939144
/usr/lib/python3/dist-packages/h5py/h5fd.cpython-35m-x86_64-linux-gnu.so
7f48b7b53000-7f48b7b5e000 r-xp 00000000 08:35 38939143
/usr/lib/python3/dist-packages/h5py/h5i.cpython-35m-x86_64-linux-gnu.so
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7f48b7d5d000-7f48b7d5e000 r--p 0000a000 08:35 38939143
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7f48b85b4000-7f48b85b5000 r--p 00013000 08:35 38939149
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7f48b85b8000-7f48b85bf000 r-xp 00000000 08:35 38939102
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/usr/lib/python3/dist-packages/h5py/_proxy.cpython-35m-x86_64-linux-gnu.so
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/usr/lib/python3/dist-packages/h5py/_proxy.cpython-35m-x86_64-linux-gnu.so
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7f48b89ca000-7f48b89cb000 r--p 00009000 08:35 38939164
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7f48b8bfd000-7f48b8c11000 r-xp 00000000 08:35 38939099
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7f48b8e11000-7f48b8e15000 rw-p 00014000 08:35 38939099
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7f48b8e15000-7f48b8e2b000 r-xp 00000000 08:35 38939165
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7f48b8e2b000-7f48b902a000 ---p 00016000 08:35 38939165
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7f48b9235000-7f48b9236000 r--p 00006000 08:35 38939109
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7f48b9238000-7f48b9249000 r-xp 00000000 08:35 38939098
/usr/lib/python3/dist-packages/h5py/h5.cpython-35m-x86_64-linux-gnu.so
7f48b9249000-7f48b9448000 ---p 00011000 08:35 38939098
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7f48b9448000-7f48b9449000 r--p 00010000 08:35 38939098
/usr/lib/python3/dist-packages/h5py/h5.cpython-35m-x86_64-linux-gnu.so
7f48b9449000-7f48b944b000 rw-p 00011000 08:35 38939098
/usr/lib/python3/dist-packages/h5py/h5.cpython-35m-x86_64-linux-gnu.so
7f48b944b000-7f48b944c000 rw-p 00000000 00:00 0
7f48b944c000-7f48b9455000 r-xp 00000000 08:35 38939150
/usr/lib/python3/dist-packages/h5py/utils.cpython-35m-x86_64-linux-gnu.so
7f48b9455000-7f48b9654000 ---p 00009000 08:35 38939150
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7f48b9654000-7f48b9655000 r--p 00008000 08:35 38939150
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7f48b9655000-7f48b9656000 rw-p 00009000 08:35 38939150
/usr/lib/python3/dist-packages/h5py/utils.cpython-35m-x86_64-linux-gnu.so
7f48b9656000-7f48b9696000 rw-p 00000000 00:00 0
7f48b9696000-7f48b96d9000 r-xp 00000000 08:35 38939100
/usr/lib/python3/dist-packages/h5py/h5t.cpython-35m-x86_64-linux-gnu.so
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/usr/lib/python3/dist-packages/h5py/h5t.cpython-35m-x86_64-linux-gnu.so
7f48b98d8000-7f48b98d9000 r--p 00042000 08:35 38939100
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7f48b98e3000-7f48b9901000 r-xp 00000000 08:35 32248272
/usr/lib/x86_64-linux-gnu/libhdf5_serial_hl.so.10.0.2
7f48b9901000-7f48b9b00000 ---p 0001e000 08:35 32248272
/usr/lib/x86_64-linux-gnu/libhdf5_serial_hl.so.10.0.2
7f48b9b00000-7f48b9b01000 r--p 0001d000 08:35 32248272
/usr/lib/x86_64-linux-gnu/libhdf5_serial_hl.so.10.0.2
7f48b9b01000-7f48b9b02000 rw-p 0001e000 08:35 32248272
/usr/lib/x86_64-linux-gnu/libhdf5_serial_hl.so.10.0.2
7f48b9b02000-7f48b9b03000 rw-p 00000000 00:00 0
7f48b9b03000-7f48b9b2b000 r-xp 00000000 08:35 38939110
/usr/lib/python3/dist-packages/h5py/defs.cpython-35m-x86_64-linux-gnu.so
7f48b9b2b000-7f48b9d2a000 ---p 00028000 08:35 38939110
/usr/lib/python3/dist-packages/h5py/defs.cpython-35m-x86_64-linux-gnu.so
7f48b9d2a000-7f48b9d2b000 r--p 00027000 08:35 38939110
/usr/lib/python3/dist-packages/h5py/defs.cpython-35m-x86_64-linux-gnu.so
7f48b9d2b000-7f48b9d2d000 rw-p 00028000 08:35 38939110
/usr/lib/python3/dist-packages/h5py/defs.cpython-35m-x86_64-linux-gnu.so
7f48b9d2d000-7f48b9d43000 r-xp 00000000 08:35 38939146
/usr/lib/python3/dist-packages/h5py/_objects.cpython-35m-x86_64-linux-gnu.so
7f48b9d43000-7f48b9f42000 ---p 00016000 08:35 38939146
/usr/lib/python3/dist-packages/h5py/_objects.cpython-35m-x86_64-linux-gnu.so
7f48b9f42000-7f48b9f43000 r--p 00015000 08:35 38939146
/usr/lib/python3/dist-packages/h5py/_objects.cpython-35m-x86_64-linux-gnu.soAborted
(core dumped)
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