[petsc-users] Generating xdmf from h5 file.
Matthew Knepley
knepley at gmail.com
Wed Oct 8 02:15:21 CDT 2014
On Tue, Oct 7, 2014 at 10:09 PM, Justin Chang <jychang48 at gmail.com> wrote:
> 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?
>
It should work for both. I think this is the same bug as reported yesterday
by Michael Lange, that the coordinate Vec
is sometimes missing the correct block size. I will track it down.
Thanks,
Matt
> 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
>>
>
>
--
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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