[CIG-SEISMO] Post-Processing mesh2vtu can not make
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huzheqian at gmail.com
Sun Dec 2 08:00:43 PST 2012
Hello all:
This is Steven. I don't known how to fix it. I need your help. Thank you
very much!
There are some publise with SPECFEM3D about Post-Processing.
There is a error about mesh2vtu.pl as below:
[root at Redhat mesh2vtu]# ./mesh2vtu.pl -i velocity_Z_it000400.mesh -o
velocity_Z_it000400.vtu
env: /SPECFEM3D/utils/Visualization/Paraview/mesh2vtu: Permission denied
For that, VTK has been installed as below:
[root at Redhat vtk]# ls -lF
total 101156
drwxr-xr-x 25 root root 4096 Dec 1 16:04 bin/
drwxr-xr-x 23 503 503 4096 Aug 24 2011 VTK/
-rw-r--r-- 1 root root 23745803 Sep 7 20:32 vtk-5.8.0.tar.gz
drwxr-xr-x 4 503 503 4096 Aug 24 2011 VTKData/
-rw-r--r-- 1 root root 79709318 Sep 7 21:23 vtkdata-5.8.0.tar.gz
I installed VTK in /opt/vtk/bin.
When 'ccmake' I set BUILD_SHARED_LIBS to ON, and PYTHON_WRAPPING to ON.
After 'make' and 'make install', I edit .bashrc add path as blow:
export LD_LIBRARY_PATH=$LD_LIBRATY_PATH:/opt/vtk/bin/bin/
export DYLD_FALLBACK_LIBRARY_PATH=/opt/vtk/bin/bin/
export PYTHONPATH=/opt/vtk/bin/bin/
export PYTHONPATH=$PYTHONPATH:/opt/vtk/VTK/Wrapping/Python/
But I can't run setup.pl.in which is in /opt/vtk/VTK/Wrapping/Python
[root at Redhat Python]# python setup.py.in install
File "setup.py.in", line 36
vtk_use_rendering = @VTK_PYTHON_USE_RENDERING@
^
SyntaxError: invalid syntax
I tested python scripts in /opt/vtk/VTK/Examples/GUI/Python.
[root at Redhat Python]# ./BoxWidget.py
Useing Python script to run the examply of the VTK is ok. I can see the
pop-up dialog box.
[root at Redhat Python]# python
Python 2.7.3 (default, Dec 1 2012, 15:04:54)
[GCC 4.1.2 20080704 (Red Hat 4.1.2-50)] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> import vtk
>>>
Python looks good with VTK.But I'm not sure that VTK installed properly.
After that I can not run mesh2vtu.pl too, I get the same error.
[root at Redhat mesh2vtu]# ./mesh2vtu.pl -i velocity_Z_it000400.mesh -o
velocity_Z_it000400.vtu
env: /SPECFEM3D/utils/Visualization/Paraview/mesh2vtu: Permission denied
I change files owner to root, and give all competence.
[root at Redhat mesh2vtu]# chown root:root *
[root at Redhat mesh2vtu]# chmod 777 *
[root at Redhat mesh2vtu]# ll
total 1100
-rwxrwxrwx 1 root root 4150 Apr 18 2010 cell2vtu.cxx
-rwxrwxrwx 1 root root 1385 Apr 18 2010 cell2vtu.pl
-rwxrwxrwx 1 root root 736 Apr 18 2010 century2xyz.pl
-rwxrwxrwx 1 root root 943 Dec 2 12:13 Makefile
-rwxrwxrwx 1 root root 943 Dec 2 12:13 Makefile~
-rwxrwxrwx 1 root root 1000 Nov 26 11:44 Makefile (copy)
-rwxrwxrwx 1 root root 3988 Apr 18 2010 mesh2vtu.cxx
-rwxrwxrwx 1 root root 1330 Nov 18 13:57 mesh2vtu.pl
-rwxrwxrwx 1 root root 1346 Nov 18 13:44 mesh2vtu.pl~
-rwxrwxrwx 1 root root 2046 Apr 18 2010 points2vtu.pl
-rwxrwxrwx 1 root root 4195 Apr 18 2010 surf2vtu.cxx
-rwxrwxrwx 1 root root 1399 Apr 18 2010 surf2vtu.pl
-rwxrwxrwx 1 root root 3001 Apr 18 2010 ugrid.cxx
-rwxrwxrwx 1 root root 1967 Apr 18 2010 ugrid_pts.cxx
-rwxrwxrwx 1 root root 1056328 Sep 7 14:43 velocity_Z_it000400.mesh
But the error as before.
I try to 'make' in /SPECFEM3D/utils/Visualization/Paraview/mesh2vtu. Then
I get error as blow:
[root at Redhat mesh2vtu]# make
g++ -O3 -I/opt/seismo-util/include -I/opt/seismo-util/include/vtk -Wno-
deprecated -c mesh2vtu.cxx -o mesh2vtu.o
mesh2vtu.cxx:39:31: error: vtk/vtkFloatArray.h: No such file or directory
mesh2vtu.cxx:40:27: error: vtk/vtkPoints.h: No such file or directory
mesh2vtu.cxx:41:30: error: vtk/vtkPointData.h: No such file or directory
mesh2vtu.cxx:42:37: error: vtk/vtkUnstructuredGrid.h: No such file or
directory
mesh2vtu.cxx:43:46: error: vtk/vtkXMLUnstructuredGridWriter.h: No such
file or directory
mesh2vtu.cxx:44:53: error: vtk/vtkUnstructuredGridToPolyDataFilter.h: No
such file or directory
mesh2vtu.cxx:45:38: error: vtk/vtkXMLPolyDataWriter.h: No such file or
directory
mesh2vtu.cxx:47:31: error: vtk/vtkDelaunay3D.h: No such file or directory
mesh2vtu.cxx:48:30: error: vtk/vtkCellArray.h: No such file or directory
mesh2vtu.cxx:49:29: error: vtk/vtkPointSet.h: No such file or directory
mesh2vtu.cxx:50:31: error: vtk/vtkHexahedron.h: No such file or directory
mesh2vtu.cxx: In function ‘int main(int, char**)’:
mesh2vtu.cxx:81: error: ‘vtkPoints’ was not declared in this scope
mesh2vtu.cxx:81: error: ‘newPts’ was not declared in this scope
mesh2vtu.cxx:81: error: ‘vtkPoints’ is not a class or namespace
mesh2vtu.cxx:82: error: ‘vtkFloatArray’ was not declared in this scope
mesh2vtu.cxx:82: error: ‘newScalars’ was not declared in this scope
mesh2vtu.cxx:82: error: ‘vtkFloatArray’ is not a class or namespace
mesh2vtu.cxx:94: error: ‘vtkCellArray’ was not declared in this scope
mesh2vtu.cxx:94: error: ‘cells’ was not declared in this scope
mesh2vtu.cxx:94: error: ‘vtkCellArray’ is not a class or namespace
mesh2vtu.cxx:102: error: ‘vtkHexahedron’ was not declared in this scope
mesh2vtu.cxx:102: error: ‘hex’ was not declared in this scope
mesh2vtu.cxx:102: error: ‘vtkHexahedron’ is not a class or namespace
mesh2vtu.cxx:118: error: ‘vtkUnstructuredGrid’ was not declared in this
scope
mesh2vtu.cxx:118: error: ‘dataSet’ was not declared in this scope
mesh2vtu.cxx:118: error: ‘vtkUnstructuredGrid’ is not a class or namespace
mesh2vtu.cxx:129: error: ‘vtkXMLUnstructuredGridWriter’ was not declared
in this scope
mesh2vtu.cxx:129: error: ‘writer’ was not declared in this scope
mesh2vtu.cxx:129: error: ‘vtkXMLUnstructuredGridWriter’ is not a class or
namespace
make: *** [mesh2vtu.o] Error 1
I edit Makefile in /SPECFEM3D/utils/Visualization/Paraview/mesh2vtu as
blow:
#############################################################
## modify to match your compiler defaults
CXX=g++
## modify to match your library paths
# VTK libraries
VTK=/opt/vtk/bin
LIBS=-L/usr/local/lib/vtk-5.8 -lvtkCommon -lvtkIO -lvtkRendering
-lvtkFiltering -lvtkGraphics
INCLUDES=-I/usr/local/include/vtk-5.8
CPPFLAGS= -O3 $(INCLUDES) -Wno-deprecated
#############################################################
When I 'make' I get the same error:
[root at Redhat mesh2vtu]# make
g++ -O3 -I/usr/local/include/vtk-5.8 -Wno- deprecated -c mesh2vtu.cxx -o
mesh2vtu.o
mesh2vtu.cxx:39:31: error: vtk/vtkFloatArray.h: No such file or directory
mesh2vtu.cxx:40:27: error: vtk/vtkPoints.h: No such file or directory
......
I copy /opt/VTK-build/include/vtk-5.8 to /opt/VTK-build/include/vtk
[root at Redhat mesh2vtu]# cp /opt/VTK-build/include/vtk-5.8
/opt/VTK-build/include/vtk
[root at Redhat include]# ll
total 204
drwxr-xr-x 2 root root 4096 Nov 18 12:49 GL
drwxr-xr-x 2 root root 4096 Dec 1 15:06 python2.7
drwxr-xr-x 20 root root 73728 Dec 2 09:39 vtk
drwxr-xr-x 20 root root 118784 Dec 2 09:39 vtk-5.8
After that I try to edit Makefile again in
/SPECFEM3D/utils/Visualization/Paraview/mesh2vtu.
#############################################################
## modify to match your compiler defaults
CXX=g++
## modify to match your library paths
# VTK libraries
VTK=/opt/vtk/bin
LIBS=-L/usr/local/lib/vtk-5.8 -lvtkCommon -lvtkIO -lvtkRendering
-lvtkFiltering -lvtkGraphics
INCLUDES=-I/usr/local/include/
CPPFLAGS= -O3 $(INCLUDES) -Wno-deprecated
#############################################################
When I 'make', I get new error as blow:
[root at Redhat mesh2vtu]# make
c++ -O3 -I/usr/local/include/ -Wno-deprecated -c mesh2vtu.cxx -o mesh2vtu.o
In file included from /usr/local/include/vtk/vtkVariant.h:35,
from /usr/local/include/vtk/vtkAbstractArray.h:45,
from /usr/local/include/vtk/vtkDataArray.h:37,
from /usr/local/include/vtk/vtkFloatArray.h:29,
from mesh2vtu.cxx:39:
/usr/local/include/vtk/vtkStdString.h:25:54: error: vtkstd/string: No such
file or directory
In file included from /usr/local/include/vtk/vtkVariant.h:36,
from /usr/local/include/vtk/vtkAbstractArray.h:45,
from /usr/local/include/vtk/vtkDataArray.h:37,
from /usr/local/include/vtk/vtkFloatArray.h:29,
from mesh2vtu.cxx:39:
/usr/local/include/vtk/vtkUnicodeString.h:47:31: error:
vtkSystemIncludes.h: No such file or directory
/usr/local/include/vtk/vtkUnicodeString.h:49:25: error: vtkstd/vector: No
such file or directory
/usr/local/include/vtk/vtkUnicodeString.h:156: error: invalid use of ‘::’
/usr/local/include/vtk/vtkUnicodeString.h:156: error: expected ‘;’ before
‘<’ token
/usr/local/include/vtk/vtkUnicodeString.h:160: error: ‘std::vector’ has not
been declared
/usr/local/include/vtk/vtkUnicodeString.h:160: error: expected ‘,’ or ‘...’
before ‘<’ token
make: *** [mesh2vtu.o] Error 1
All of *.h file is in /usr/local/include/vtk/.
What should I do for this?
---------------------------------------------
Steven Hu
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