[Gmsh] Gmsh exits immediately after run, "Requesting more near neighbors than data points"

Jason C jason.cipriani at gmail.com
Tue Feb 2 20:00:52 CET 2016


Using:

  - gmsh 2.11.0 (both 32 and 64 bit attempted)
  - getdp 2.7.0 (both 32 and 64 bit attempted)
  - Windows 7 64-bit, 4GB RAM
  - The attached .pro file (source: https://github.com/Steve-OH/lap_water)

When I do the following (this is a fresh install, first time running this
software):

  1. Start gmsh.
  2. Load the .pro file.
  3. Select cutX, Y, and Z in GetDP -> Post-Processing
  4. Press Run, select path to getdp, accept.

Gmsh runs for about 2-3 seconds then silently exits (verified gmsh.exe
terminated immediately with task manager). The last message printed to the
terminal (I set message verbosity to "100" arbitrarily) is:

ANN: ERROR------->Requesting more near neighbors than data
points<-------------ERROR

Partial debug log is attached and also pasted below.

How should I proceed?

I have also posted this at https://github.com/Steve-OH/lap_water/issues/1
in case it is an issue with the author's .pro file rather than gmsh.

Thanks,
Jason

=== LOG ===

Debug   : openglWindow::draw()
Debug   : Mesh has changed: reinitializing vertex arrays
Debug   : openglWindow::draw()
Info    : -------------------------------------------------------
Info    : Gmsh version   : 2.11.0
Info    : Build OS       : Windows
Info    : Build options  : Ann Bamg Bfgs Blas Blossom Chaco DIntegration
Fltk Gmm Jpeg(Fltk) Kbipack Lapack MathEx Med Mesh Metis Mmg3d Mpeg
NativeFileChooser Netgen NoSocklenT ONELAB ONELABMetamodel OpenCascade
OpenGL OptHom PETSc Parser Plugins Png(Fltk) Post SLEPc Salome Solver
Tetgen(1.5) Voro3D Zlib(Fltk)
Info    : Build date     : 20151107
Info    : Build host     : christop-e38ece
Info    : Packager       : Administrator
Info    : Executable     : C:\Programs\woodemc\gmsh-2.11.0-Windows\gmsh.exe
Info    : Home directory : C:\Users\Jason\AppData\Roaming/
Info    : Launch date    : Tue Feb 02 13:51:13 2016
Info    : Command line   : gmsh
Info    : -------------------------------------------------------
Debug   : Deleting onelabGroup widgets (108)
Debug   : Deleting onelabGroup widgets (108)

...

Debug   : Mesh has changed: reinitializing vertex arrays
Info    : Calling '"C:\Programs\woodemc\getdp-2.7.0-Windows\getdp.exe"
"C:\Programs\woodemc\lap_water-master\models\oa
k_hole.pro"    -onelab "GetDP" 127.0.0.1:57610'
Info    : Running 'GetDP'...
Info    : GetDP - Performing ONELAB 'check'
Info    : GetDP - Running
'C:\Programs\woodemc\getdp-2.7.0-Windows\getdp.exe
C:\Programs\woodemc\lap_water-master\models
\oak_hole.pro -onelab GetDP 127.0.0.1:57610' [GetDP 2.7.0, 1 node]
Info    : GetDP - Started (Tue Feb 02 13:53:12 2016, Wall = 0.031s, CPU =
0.0468003s, Mem = 8.73047Mb)
Info    : GetDP - Got mesh name from Onelab:
'C:\Programs\woodemc\lap_water-master\models\oak_hole.msh'
Info    : GetDP - Initializing Gmsh
Info    : GetDP - Loading problem definition
'C:\Programs\woodemc\lap_water-master\models\oak_hole.pro'
Info    : GetDP - Loading problem definition
'C:\Programs\woodemc\lap_water-master\models\diffusion.pro'
Info    : GetDP - Available Resolutions
Info    : GetDP - (1) LinearAdaptive
Info    : GetDP - Available PostOperations
Info    : GetDP - (1) cutX
Info    : GetDP - (2) cutY
Info    : GetDP - (3) cutZ
Info    : GetDP - Stopped (Tue Feb 02 13:53:12 2016, Wall = 0.156s, CPU =
0.0468003s, Mem = 9.94922Mb)
Info    : Done running 'GetDP'
Info    : Done
Info    : Reading
'C:\Programs\woodemc\lap_water-master\models\oak_hole.geo'...
Debug   : Surface: 301
Debug   : SVD    : 243.853,45.7905,0 (min=2)
Debug   : Plane  : (0 x + 0 y + 1 z = 0)
Debug   : Normal : (0 , 0 , 1 )
Debug   : t1     : (0 , 1 , 0 )
Debug   : t2     : (1 , 0 , 0 )
Debug   : pt     : (0 , 0 , 0 )
Debug   : Surface: 302
Debug   : SVD    : 243.853,45.7905,0 (min=2)
Debug   : Plane  : (0 x + 0 y + 1 z = 15.24)
Debug   : Normal : (0 , 0 , 1 )
Debug   : t1     : (0 , 1 , 0 )
Debug   : t2     : (1 , 0 , 0 )
Debug   : pt     : (0 , 0 , 15.24 )
Debug   : Surface: 303
Debug   : SVD    : 243.84,15.24,0 (min=2)
Debug   : Plane  : (1 x + 0 y + 0 z = 0)
Debug   : Normal : (1 , 0 , 0 )
Debug   : t1     : (0 , 0 , 1 )
Debug   : t2     : (0 , 1 , 0 )
Debug   : pt     : (0 , 0 , 0 )
Debug   : Surface: 304
Debug   : SVD    : 45.72,15.24,0 (min=2)
Debug   : Plane  : (-0 x + -1 y + -0 z = -243.84)
Debug   : Normal : (-0 , -1 , -0 )
Debug   : t1     : (0 , 0 , 1 )
Debug   : t2     : (1 , 0 , 0 )
Debug   : pt     : (0 , 243.84 , 0 )
Debug   : Surface: 305
Debug   : SVD    : 243.84,15.24,-0 (min=2)
Debug   : Plane  : (1 x + 0 y + 0 z = 45.72)
Debug   : Normal : (1 , 0 , 0 )
Debug   : t1     : (0 , 0 , 1 )
Debug   : t2     : (0 , 1 , 0 )
Debug   : pt     : (45.72 , 0 , 0 )
Debug   : Surface: 306
Debug   : SVD    : 45.72,15.24,0 (min=2)
Debug   : Plane  : (-0 x + -1 y + -0 z = -0)
Debug   : Normal : (-0 , -1 , -0 )
Debug   : t1     : (0 , 0 , 1 )
Debug   : t2     : (1 , 0 , 0 )
Debug   : pt     : (0 , 0 , 0 )
Debug   : Surface: 307
Debug   : SVD    : 15.24,2.54,0 (min=2)
Debug   : Plane  : (1 x + 0 y + 0 z = 21.59)
Debug   : Normal : (1 , 0 , 0 )
Debug   : t1     : (0 , 0 , 1 )
Debug   : t2     : (0 , 1 , 0 )
Debug   : pt     : (21.59 , 0 , 0 )
Debug   : Surface: 308
Debug   : SVD    : 15.24,2.54,0 (min=2)
Debug   : Plane  : (-0 x + -1 y + -0 z = -123.19)
Debug   : Normal : (-0 , -1 , -0 )
Debug   : t1     : (0 , 0 , 1 )
Debug   : t2     : (1 , 0 , 0 )
Debug   : pt     : (0 , 123.19 , 0 )
Debug   : Surface: 309
Debug   : SVD    : 15.24,2.54,-0 (min=2)
Debug   : Plane  : (1 x + 0 y + 0 z = 24.13)
Debug   : Normal : (1 , 0 , 0 )
Debug   : t1     : (0 , 0 , 1 )
Debug   : t2     : (0 , 1 , 0 )
Debug   : pt     : (24.13 , 0 , 0 )
Debug   : Surface: 310
Debug   : SVD    : 15.24,2.54,0 (min=2)
Debug   : Plane  : (-0 x + -1 y + -0 z = -120.65)
Debug   : Normal : (-0 , -1 , -0 )
Debug   : t1     : (0 , 0 , 1 )
Debug   : t2     : (1 , 0 , 0 )
Debug   : pt     : (0 , 120.65 , 0 )
Debug   : Gmsh model (GModel) imported:
Debug   : 24 Vertices
Debug   : 28 Edges
Debug   : 10 Faces
Debug   : 1 Regions
Info    : Done reading
'C:\Programs\woodemc\lap_water-master\models\oak_hole.geo'
Info    : Meshing 1D...
Info    : Meshing curve 101 (Line)
ANN: ERROR------->Requesting more near neighbors than data
points<-------------ERROR
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Debug   : openglWindow::draw()
Debug   : Mesh has changed: reinitializing vertex arrays
Debug   : openglWindow::draw()
Info    : -------------------------------------------------------
Info    : Gmsh version   : 2.11.0
Info    : Build OS       : Windows
Info    : Build options  : Ann Bamg Bfgs Blas Blossom Chaco DIntegration Fltk Gmm Jpeg(Fltk) Kbipack Lapack MathEx Med Mesh Metis Mmg3d Mpeg NativeFileChooser Netgen NoSocklenT ONELAB ONELABMetamodel OpenCascade OpenGL OptHom PETSc Parser Plugins Png(Fltk) Post SLEPc Salome Solver Tetgen(1.5) Voro3D Zlib(Fltk)
Info    : Build date     : 20151107
Info    : Build host     : christop-e38ece
Info    : Packager       : Administrator
Info    : Executable     : C:\Programs\woodemc\gmsh-2.11.0-Windows\gmsh.exe
Info    : Home directory : C:\Users\Jason\AppData\Roaming/
Info    : Launch date    : Tue Feb 02 13:51:13 2016
Info    : Command line   : gmsh
Info    : -------------------------------------------------------
Debug   : Deleting onelabGroup widgets (108)
Debug   : Deleting onelabGroup widgets (108)

...

Debug   : Mesh has changed: reinitializing vertex arrays
Info    : Calling '"C:\Programs\woodemc\getdp-2.7.0-Windows\getdp.exe"   "C:\Programs\woodemc\lap_water-master\models\oa
k_hole.pro"    -onelab "GetDP" 127.0.0.1:57610'
Info    : Running 'GetDP'...
Info    : GetDP - Performing ONELAB 'check'
Info    : GetDP - Running 'C:\Programs\woodemc\getdp-2.7.0-Windows\getdp.exe C:\Programs\woodemc\lap_water-master\models
\oak_hole.pro -onelab GetDP 127.0.0.1:57610' [GetDP 2.7.0, 1 node]
Info    : GetDP - Started (Tue Feb 02 13:53:12 2016, Wall = 0.031s, CPU = 0.0468003s, Mem = 8.73047Mb)
Info    : GetDP - Got mesh name from Onelab: 'C:\Programs\woodemc\lap_water-master\models\oak_hole.msh'
Info    : GetDP - Initializing Gmsh
Info    : GetDP - Loading problem definition 'C:\Programs\woodemc\lap_water-master\models\oak_hole.pro'
Info    : GetDP - Loading problem definition 'C:\Programs\woodemc\lap_water-master\models\diffusion.pro'
Info    : GetDP - Available Resolutions
Info    : GetDP - (1) LinearAdaptive
Info    : GetDP - Available PostOperations
Info    : GetDP - (1) cutX
Info    : GetDP - (2) cutY
Info    : GetDP - (3) cutZ
Info    : GetDP - Stopped (Tue Feb 02 13:53:12 2016, Wall = 0.156s, CPU = 0.0468003s, Mem = 9.94922Mb)
Info    : Done running 'GetDP'
Info    : Done
Info    : Reading 'C:\Programs\woodemc\lap_water-master\models\oak_hole.geo'...
Debug   : Surface: 301
Debug   : SVD    : 243.853,45.7905,0 (min=2)
Debug   : Plane  : (0 x + 0 y + 1 z = 0)
Debug   : Normal : (0 , 0 , 1 )
Debug   : t1     : (0 , 1 , 0 )
Debug   : t2     : (1 , 0 , 0 )
Debug   : pt     : (0 , 0 , 0 )
Debug   : Surface: 302
Debug   : SVD    : 243.853,45.7905,0 (min=2)
Debug   : Plane  : (0 x + 0 y + 1 z = 15.24)
Debug   : Normal : (0 , 0 , 1 )
Debug   : t1     : (0 , 1 , 0 )
Debug   : t2     : (1 , 0 , 0 )
Debug   : pt     : (0 , 0 , 15.24 )
Debug   : Surface: 303
Debug   : SVD    : 243.84,15.24,0 (min=2)
Debug   : Plane  : (1 x + 0 y + 0 z = 0)
Debug   : Normal : (1 , 0 , 0 )
Debug   : t1     : (0 , 0 , 1 )
Debug   : t2     : (0 , 1 , 0 )
Debug   : pt     : (0 , 0 , 0 )
Debug   : Surface: 304
Debug   : SVD    : 45.72,15.24,0 (min=2)
Debug   : Plane  : (-0 x + -1 y + -0 z = -243.84)
Debug   : Normal : (-0 , -1 , -0 )
Debug   : t1     : (0 , 0 , 1 )
Debug   : t2     : (1 , 0 , 0 )
Debug   : pt     : (0 , 243.84 , 0 )
Debug   : Surface: 305
Debug   : SVD    : 243.84,15.24,-0 (min=2)
Debug   : Plane  : (1 x + 0 y + 0 z = 45.72)
Debug   : Normal : (1 , 0 , 0 )
Debug   : t1     : (0 , 0 , 1 )
Debug   : t2     : (0 , 1 , 0 )
Debug   : pt     : (45.72 , 0 , 0 )
Debug   : Surface: 306
Debug   : SVD    : 45.72,15.24,0 (min=2)
Debug   : Plane  : (-0 x + -1 y + -0 z = -0)
Debug   : Normal : (-0 , -1 , -0 )
Debug   : t1     : (0 , 0 , 1 )
Debug   : t2     : (1 , 0 , 0 )
Debug   : pt     : (0 , 0 , 0 )
Debug   : Surface: 307
Debug   : SVD    : 15.24,2.54,0 (min=2)
Debug   : Plane  : (1 x + 0 y + 0 z = 21.59)
Debug   : Normal : (1 , 0 , 0 )
Debug   : t1     : (0 , 0 , 1 )
Debug   : t2     : (0 , 1 , 0 )
Debug   : pt     : (21.59 , 0 , 0 )
Debug   : Surface: 308
Debug   : SVD    : 15.24,2.54,0 (min=2)
Debug   : Plane  : (-0 x + -1 y + -0 z = -123.19)
Debug   : Normal : (-0 , -1 , -0 )
Debug   : t1     : (0 , 0 , 1 )
Debug   : t2     : (1 , 0 , 0 )
Debug   : pt     : (0 , 123.19 , 0 )
Debug   : Surface: 309
Debug   : SVD    : 15.24,2.54,-0 (min=2)
Debug   : Plane  : (1 x + 0 y + 0 z = 24.13)
Debug   : Normal : (1 , 0 , 0 )
Debug   : t1     : (0 , 0 , 1 )
Debug   : t2     : (0 , 1 , 0 )
Debug   : pt     : (24.13 , 0 , 0 )
Debug   : Surface: 310
Debug   : SVD    : 15.24,2.54,0 (min=2)
Debug   : Plane  : (-0 x + -1 y + -0 z = -120.65)
Debug   : Normal : (-0 , -1 , -0 )
Debug   : t1     : (0 , 0 , 1 )
Debug   : t2     : (1 , 0 , 0 )
Debug   : pt     : (0 , 120.65 , 0 )
Debug   : Gmsh model (GModel) imported:
Debug   : 24 Vertices
Debug   : 28 Edges
Debug   : 10 Faces
Debug   : 1 Regions
Info    : Done reading 'C:\Programs\woodemc\lap_water-master\models\oak_hole.geo'
Info    : Meshing 1D...
Info    : Meshing curve 101 (Line)
ANN: ERROR------->Requesting more near neighbors than data points<-------------ERROR
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