[CIG-SEISMO] Post-Processing mesh2vtu can not make
Peter Danecek
Peter.Danecek at bo.ingv.it
Thu May 23 10:19:53 PDT 2013
Hi Steven,
actually it's all here:
[root at mesh2vtu mesh2vtu]# ./mesh2vtu -i velocity_E_it030000.mesh -o
velocity_E_it030000.vtu
./mesh2vtu: Reading mesh file ...
Error opening file: -i.
* no. of points: 0
* no. of cells: 0
[...]
You are trying to open a file "-i", which you won't find. I could
imagine it is the correct syntax for the perl or python driver script
(but I actually never used it, so I would need to look this up).
Anyway, if you want to use the binary directly just use something like:
./mesh2vtu <input mesh file> <output vtu file>
Your example:
velocity_E_it030000.mesh velocity_E_it030000.vtu
Calling just ./mesh2vtu should give you some usage notification as well.
Hope that helps!
~petr
On 23 May 2013, at 15:38, 胡喆骞 wrote:
> Dear Peter:
>
> Thank you for your previous mail, with your help I can use the
> mesh2vtu.
>
> Today mesh2vtu make error. I did not make changes to the system,
> but I do not know why mesh2vtu can not be used.
> Attached is my error message.
>
> Would you help me find out answer?
>
> Look forward to your reply.
>
>
> --------------
> steven
>
>
> 2012/12/6 Peter Danecek <Peter.Danecek at bo.ingv.it>
>
> Hi,
>
> for the scope of compiling and linking mesh2vtu against VTK, you
> need only a relative small part of the whole VTK. For example the
> Python wrapper or the whole Rendering and Visualization staff is not
> needed. Anyway, I guess the easiest way to install VTK is through
> the package manager of your system. I am not very familiar with
> Redhat, but you should find tutorials on the web.
>
> When you are done with the VTK installations, check where it was
> put. My first guess would be something like /usr/local/... (<prefix>)
>
> There you should find something the following ...
> NOTE: The version can be different, mesh2vtu will work also with
> other 5.x versions.
>
> <prefix>/include/vtk-5.10
> .. this is the path to put with -I flag (include) during compilation
> Here you should find quite some header files ( *.h), on my
> installation there are nearly 2000
> <prefix>/lib/vtk-5.10
> .. this is the path to put with -L flag (library) during linking
> Here you file the libraries (the extension depends on the platform,
> *.a or *.so are common)
>
> I send you my somewhat modified version of mesh2vtu. It should be
> sufficient to change the VTK_PREFIX & VER_VTK variables in the
> Makefile and type make. Note, that this version requires an extra
> parameter (to name the scalar variable) so do not expect the Perl
> wrapper to work as is. I will submit an extended version to the
> repository, when I find time to do some cleanup.
>
>
>
>
>
> --- snip ---
> [urquell:Utils/VTK-util/mesh2vtu.petr.2012-12-06] petr% make
> g++ -c -O2 -Wno-deprecated -I/opt/local/include/vtk-5.10 -o
> mesh2vtu.o mesh2vtu.cxx
> g++ mesh2vtu.o -o mesh2vtu -L/opt/local/lib/vtk-5.10 -lvtkCommon -
> lvtkIO -lvtkFiltering -lvtkRendering -lvtkGraphics
> rm mesh2vtu.o
> [urquell:Utils/VTK-util/mesh2vtu.petr.2012-12-06] petr% ls -la
> total 40
> drwxr-xr-x 5 petr petr 170 6 Dec 10:37 .
> drwxr-xr-x 22 petr petr 748 6 Dec 10:35 ..
> -rw-r--r-- 1 petr petr 1191 6 Dec 10:33 Makefile
> -rwxr-xr-x 1 petr petr 18136 6 Dec 10:37 mesh2vtu
> -rw-r--r-- 1 petr petr 13321 29 Oct 16:30 mesh2vtu.cxx
> --- snap ---
>
> Good luck!
> ~petr
>
>
>
>
>
> On 6 Dec 2012, at 03:16, 赵芳 wrote:
>
>
>
> Hello peter:
>
> 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?
> ---------------------------------------------
> fang zhao
>
>
>
>
> _______________________________________________
> CIG-SEISMO mailing list
> CIG-SEISMO at geodynamics.org
> http://geodynamics.org/cgi-bin/mailman/listinfo/cig-seismo
>
>
>
> --
> ---------------------------------------------
> Steven Hu
>
> <mesh2vtu-error.txt>
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