ElmerGUI does not load gmsh file

[martijnb]

I have a very simple grid created in gmsh (15x15x5mm block) created in gmsh. When I load the exported .msh file, ElmerGUI does show the geometry+grid but just two lines. However, body and faces do exist as I can assign equations and boundary conditions to them.
When I run ElmgerGrid from the terminal, the Elmer mesh seems to be created correctly (output below). But when I load the converted grid in the GUI I get a hard crash.
I compiled Elmer from svn source last month (on debian jessy). A couple of years ago I successfully used Elmer for heat modelling, but now I seem to be out of luck.
Is there bug, did I make a mistake during compilation, of is there something else wrong?

I attached:
- the msh file
- screenshot of Elmer after loading the msh
- screenshot of gmsh with the grid.

I hope you can help me debugging this problem

Martijn


[cmd]
ElmerGrid 14 2 sample.msh
/usr/local/fem/bin/ElmerGrid 14 2 sample.msh

Starting program Elmergrid
Elmergrid reading in-line arguments
Output will be saved to file sample.

Elmergrid loading data:
-----------------------
Format chosen using the first line: $MeshFormat
Loading mesh in Gmsh format 2.0 from file sample.msh
Allocating for 8033 knots and 43896 elements.
Moving bulk elements to boundary elements
Leading bulk elementtype is 504
Trailing bulk elementtype is 101
There are 7794 (out of 43896) lower dimensional elements.
Node 5790 belongs to maximum of 48 elements
Found correctly 7794 side elements.
Parent elements were reordered up to indx 36102.
Moved 36102 elements (out of 43896) to new positions
Initial boundary interval [1,28]
boundary index changed 6 -> 1 in 2347 elements
boundary index changed 15 -> 2 in 696 elements
boundary index changed 19 -> 3 in 700 elements
boundary index changed 23 -> 4 in 698 elements
boundary index changed 27 -> 5 in 720 elements
boundary index changed 28 -> 6 in 2346 elements
boundary index changed 1 -> 7 in 31 elements
boundary index changed 2 -> 8 in 31 elements
boundary index changed 3 -> 9 in 31 elements
boundary index changed 4 -> 10 in 31 elements
boundary index changed 8 -> 11 in 30 elements
boundary index changed 9 -> 12 in 30 elements
boundary index changed 10 -> 13 in 31 elements
boundary index changed 11 -> 14 in 30 elements
boundary index changed 13 -> 15 in 10 elements
boundary index changed 14 -> 16 in 11 elements
boundary index changed 18 -> 17 in 10 elements
boundary index changed 22 -> 18 in 10 elements
boundary index changed 5 -> 19 in 1 elements
Mapping boundary types from [1 28] to [1 19]
Initial body interval [1,1]
Numbering of bodies is already ok
Successfully read the mesh from the Gmsh input file.

Elmergrid creating and manipulating meshes:
-------------------------------------------

Elmergrid saving data with method 2:
-------------------------------------
Saving mesh in ElmerSolver format to directory sample.
Reusing an existing directory
Saving 8033 coordinates to mesh.nodes.
Saving 36102 element topologies to mesh.elements.
Saving boundary elements to mesh.boundary.
Saving header info to mesh.header.

Thank you for using Elmergrid!
Send bug reports and feature wishes to elmeradm@csc.fi
[/cmd]

[mzenker]

Hi Martijn,

in my ElmerGUI (64 bit Windows, from binary installer), your mesh opens correctly. You can check if "View->Surface mesh" and/or "View->Volume Mesh" is checked (display volume mesh makes ElmerGUI slower). If that doesn't help, you have a problem with your ElmerGUI.

HTH,

Matthias

[martijnb]

Well, then I have a problem with the ElmerGUI, but I cannot find it. Does Elmer rely on an external library for rendering?

This is my (cleaned) ElmerGUI.pri. I changed something at the comment signs.

Code: Select all

#==============================================================================
#
#                       ElmerGUI: configuration file
#
#==============================================================================

DEFINES += EG_QWT      # Use QWT for convergence monitor?
DEFINES += EG_VTK      # Use VTK for postprocessing?
DEFINES += EG_PARAVIEW # Use ParaView for postprocessing?
DEFINES += EG_MATC     # Use MATC for internal operations in postprocessing?
#DEFINES += EG_OCC      # Use OpenCASCADE 6.3 for importing CAD files? Needs VTK.
DEFINES -= EG_PYTHONQT # Use PythonQt for scripting in post processor?

#------------------------------------------------------------------------------
# 64 bit system?
#------------------------------------------------------------------------------
BITS = 64


#------------------------------------------------------------------------------
# Installation directory:
#------------------------------------------------------------------------------
ELMERGUI_HOME = $$(ELMERGUI_HOME)
isEmpty(ELMERGUI_HOME) {
   ELMER_HOME = $$(ELMER_HOME)
   isEmpty(ELMER_HOME) {
      unix: ELMER_HOME = /usr/local
      win32: ELMER_HOME = c:/Elmer7
      macx: ELMER_HOME = /usr/local
   }
   ELMERGUI_HOME = $${ELMER_HOME}/bin
}

#------------------------------------------------------------------------------
# Python library:
#------------------------------------------------------------------------------
unix {
   PY_INCLUDEPATH = /usr/include/python2.7
   PY_LIBPATH = /usr/lib
   PY_LIBS = -lpython2.7
}

#------------------------------------------------------------------------------
# QWT library:
#------------------------------------------------------------------------------
unix {
#  QWT_INCLUDEPATH = /usr/include/qwt-qt4
  QWT_INCLUDEPATH = /usr/include/qwt
  QWT_LIBPATH = /usr/lib
#  QWT_LIBS = -lqwt-qt4
  QWT_LIBS = -lqwt
}

#------------------------------------------------------------------------------
# VTK library:
#------------------------------------------------------------------------------
unix {
   VTK_INCLUDEPATH = /usr/include/vtk-5.8
   VTK_LIBPATH = /usr/lib
   VTK_LIBS = -lQVTK \
              -lvtkCommon \
              -lvtkDICOMParser \
              -lvtkFiltering \
              -lvtkGenericFiltering \
              -lvtkGraphics \
              -lvtkHybrid \
              -lvtkIO \
              -lvtkImaging \
              -lvtkInfovis \
#              -lvtkNetCDF \
              -lnetcdf \              
              -lvtkRendering \
              -lvtkViews \
              -lvtkVolumeRendering \
              -lvtkWidgets
}

[raback]

Hi

ElmerGUI does not know how to treat the orphan nodes. Use "-autoclean" flag in ElmerGrid to remove them, for instance.

-Peter