[petsc-users] Generating xdmf from h5 file.
Justin Chang
jychang48 at gmail.com
Tue Oct 7 22:09:29 CDT 2014
Hi Matt,
Bumping this thread. I have a similar question. The lines you wrote for
testnum 39 have also worked perfectly for me. However, when I change a
couple parameters, namely not interpolating the mesh and using
-petscspace_order 1:
./ex12 -run_type full -refinement_limit 0.015625 -petscspace_order 1
-pc_type gamg -ksp_rtol 1.0e-10 -ksp_monitor_short -ksp_converged_reason
-snes_monitor_short -snes_converged_reason -dm_view hdf5:sol.h5
-snes_view_solution hdf5:sol.h5::append
I get the following error after I run the xdmf script:
Traceback (most recent call last):
File "./bin/pythonscripts/petsc_gen_xdmf.py", line 223, in <module>
generateXdmf(sys.argv[1])
File "./bin/pythonscripts/petsc_gen_xdmf.py", line 218, in generateXdmf
Xdmf(xdmfFilename).write(hdfFilename, topoPath, numCells, numCorners,
cellDim, geomPath, numVertices, spaceDim, time, vfields, cfields)
File "./bin/pythonscripts/petsc_gen_xdmf.py", line 176, in write
self.writeSpaceGridHeader(fp, numCells, numCorners, cellDim, spaceDim)
File "./bin/pythonscripts/petsc_gen_xdmf.py", line 75, in
writeSpaceGridHeader
''' % (self.cellMap[cellDim][numCorners], numCells, "XYZ" if spaceDim >
2 else "XY"))
Does the script so far only work for interpolated meshes/problems?
Thanks,
Justin
On Sun, Sep 28, 2014 at 11:15 AM, subramanya sadasiva <potaman at outlook.com>
wrote:
> Thanks Matt,
> That worked perfectly.
>
> Subramanya
>
> ------------------------------
> Date: Fri, 26 Sep 2014 14:52:52 -0500
> Subject: Re: [petsc-users] Generating xdmf from h5 file.
> From: knepley at gmail.com
> To: potaman at outlook.com
> CC: petsc-users at mcs.anl.gov
>
>
> On Thu, Sep 25, 2014 at 10:29 PM, subramanya sadasiva <potaman at outlook.com
> > wrote:
>
> Hi Matt,
> Sorry about that,
> I changed
> if 'time' in h5:
> time = np.array(h5['time']).flatten()
> else:
> time = np.empty(1)
>
> The code now fails in the writeSpaceGridHeader function. with the error,
>
>
> Traceback (most recent call last):
> File
> "/Users/ssadasiv/software/petsc/bin/pythonscripts/petsc_gen_xdmf.py", line
> 232, in <module>
> generateXdmf(sys.argv[1])
> File
> "/Users/ssadasiv/software/petsc/bin/pythonscripts/petsc_gen_xdmf.py", line
> 227, in generateXdmf
> Xdmf(xdmfFilename).write(hdfFilename, topoPath, numCells, numCorners,
> cellDim, geomPath, numVertices, spaceDim, time, vfields, cfields)
> File
> "/Users/ssadasiv/software/petsc/bin/pythonscripts/petsc_gen_xdmf.py", line
> 180, in write
> self.writeSpaceGridHeader(fp, numCells, numCorners, cellDim, spaceDim)
> File
> "/Users/ssadasiv/software/petsc/bin/pythonscripts/petsc_gen_xdmf.py", line
> 64, in writeSpaceGridHeader
> print self.cellMap[cellDim][numCorners]
>
> The error is due to the fact that numCorners is set to be 1 , while
> celldim=2. cellMap has the following elements.
> {1: {1: 'Polyvertex', 2: 'Polyline'}, 2: {3: 'Triangle', 4:
> 'Quadrilateral'}, 3: {8: 'Hexahedron', 4: 'Tetrahedron'}}
>
>
> I also tried
> ./ex12 -dm_view vtk:my.vtk:vtk_vtu . This doesn't seem to do anything. Is
> there any specific option I need to build petsc with to get vtk output? My
> current build has hdf5 and netcdf enabled.
>
> I made the change in a branch, and merged to 'next', so it will work if
> you pull. Here is a test from ex12 (testnum 39 in builder.py):
>
> ./ex12 -run_type full -refinement_limit 0.015625 -interpolate 1
> -petscspace_order 2 -pc_type gamg -ksp_rtol 1.0e-10 -ksp_monitor_short
> -ksp_converged_reason -snes_monitor_short -snes_converged_reason -dm_view
> hdf5:sol.h5 -snes_view_solution hdf5:sol.h5::append
>
> which makes sol.h5. Then I run
>
> ./bin/pythonscripts/petsc_gen_xdmf.py sol.h5
>
> which makes sol.xmf. I load it up in Paraview and it makes the attached
> picture.
>
> Thanks,
>
> Matt
>
>
> Thanks,
> Subramanya
>
> Date: Wed, 24 Sep 2014 17:36:52 -0500
> Subject: Re: [petsc-users] Generating xdmf from h5 file.
> From: knepley at gmail.com
> To: potaman at outlook.com; petsc-maint at mcs.anl.gov; petsc-users at mcs.anl.gov
>
> On Wed, Sep 24, 2014 at 5:29 PM, subramanya sadasiva <potaman at outlook.com>
> wrote:
>
> Hi Matt,
> That did not help.
>
>
> That's not enough description to fix anything, and fixing it will require
> programming.
>
>
> Is there any other way to output the mesh to something that paraview can
> view? I tried outputting the file to a vtk file using
> ex12 -dm_view vtk:my.vtk:ascii_vtk
>
> which, I saw in another post on the forums, but that did not give me any
> output.
>
>
> This is mixing two different things. PETSc has a diagnostic ASCII vtk
> output, so the type would be ascii, not vtk,
> and format ascii_vtk . It also has a production VTU output, which is type
> vtk with format vtk_vtu.
>
> Thanks,
>
> Matt
>
>
>
> Subramanya
>
> ------------------------------
> Date: Wed, 24 Sep 2014 17:19:51 -0500
> Subject: Re: [petsc-users] Generating xdmf from h5 file.
> From: knepley at gmail.com
> To: potaman at outlook.com
> CC: petsc-users at mcs.anl.gov
>
> On Wed, Sep 24, 2014 at 5:08 PM, subramanya sadasiva <potaman at outlook.com>
> wrote:
>
> Hi,
> i was trying to use petsc_gen_xdmf.py to convert a h5 file to a xdmf file.
> The h5 file was generated by snes/ex12 which was run as,
>
> ex12 -dm_view hdf5:my.h5
>
> When I do,
> petsc_gen_xdmf.py my.h5
>
> I get the following error,
>
> File "/home/ssadasiv/software/petsc/bin/pythonscripts/petsc_gen_xdmf.py",
> line 220, in <module>
> generateXdmf(sys.argv[1])
> File
> "/home/ssadasiv/software/petsc/bin/pythonscripts/petsc_gen_xdmf.py", line
> 208, in generateXdmf
> time = np.array(h5['time']).flatten()
> File "/usr/lib/python2.7/dist-packages/h5py/_hl/group.py", line 153, in
> __getitem__
> oid = h5o.open(self.id, self._e(name), lapl=self._lapl)
> File "h5o.pyx", line 173, in h5py.h5o.open (h5py/h5o.c:3403)
> KeyError: "unable to open object (Symbol table: Can't open object)"
>
> I am not sure if the error is on my end. This is on Ubuntu 14.04 with the
> serial version of hdf5. I built petsc with --download-hdf5, is it necessary
> to use the same version of hdf5 to generate the xdmf file?
>
>
> That code is alpha, and mainly built for me to experiment with an
> application here, so it is not user-friendly. In your
> HDF5 file, there is no 'time' since you are not running a TS. This access
> to h5['time'] should just be protected, and
> an empty array should be put in if its not there.
>
> Matt
>
>
> Thanks
> Subramanya
>
>
>
>
> --
> What most experimenters take for granted before they begin their
> experiments is infinitely more interesting than any results to which their
> experiments lead.
> -- Norbert Wiener
>
>
>
>
> --
> What most experimenters take for granted before they begin their
> experiments is infinitely more interesting than any results to which their
> experiments lead.
> -- Norbert Wiener
>
>
>
>
> --
> What most experimenters take for granted before they begin their
> experiments is infinitely more interesting than any results to which their
> experiments lead.
> -- Norbert Wiener
>
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