[petsc-users] DMPlexProjectField not including BC constraints?
Justin Chang
jchang27 at uh.edu
Fri Apr 24 17:38:31 CDT 2015
I actually made a mistake in PetscFECreateDefault(...), if that's what
you're referring to, and put dm instead of user.dmVel. However the problem
remains.
Everything is a scalar (i.e., numComp is 1 for both DMs). dm and user.dmVel
should have the same chart but user.dmVel does not invoke
DMPlexAddBoundary(..). Each spatial index of u_x[] will be printed
separately. Right now I am simply working with the x component.
That said, is it possible to get this sort of mapping?
Thanks,
On Fri, Apr 24, 2015 at 8:09 AM, Matthew Knepley <knepley at gmail.com> wrote:
> On Thu, Apr 23, 2015 at 10:20 PM, Justin Chang <jchang27 at uh.edu> wrote:
>
>> Matt,
>>
>> I have attempted this but I am getting an error when trying to output the
>> vector into HDF5. This is my implementation:
>>
>> /* Initialize */
>> PetscDS prob;
>> Vec vlocal, ulocal, vglobal;
>> void (*vX[1])(....) = {velx};
>>
>> /* Create DM for velocity */
>> ierr = DMClone(dm,&user.dmVel);CHKERRQ(ierr);
>> ierr = DMPlexCopyCoordinates(dm, user.dmVel);CHKERRQ(ierr);
>> ierr = PetscFECreateDefault(dm, spatialDim, 1, PETSC_TRUE, "solution_",
>> -1, &user.feVel);CHKERRQ(ierr);
>> ierr = DMGetDS(user.dmVel, &prob);CHKERRQ(ierr);
>> ierr = PetscDSSetDiscretization(prob, 0, (PetscObject)
>> user.feVel);CHKERRQ(ierr);
>> ierr = DMCreateGlobalVector(user.dmVel,&vglobal);CHKERRQ(ierr);
>> ierr = PetscObjectSetName((PetscObject) vglobal,
>> "velocity");CHKERRQ(ierr);
>>
>> /* Obtain velocity */
>> ierr = DMGetLocalVector(dm,&ulocal);CHKERRQ(ierr);
>> ierr = VecDuplicate(ulocal,&vlocal);CHKERRQ(ierr);
>> ierr =
>> DMGlobalToLocalBegin(dm,user.u,INSERT_ALL_VALUES,ulocal);CHKERRQ(ierr);
>> ierr =
>> DMGlobalToLocalEnd(dm,user.u,INSERT_ALL_VALUES,ulocal);CHKERRQ(ierr);
>> ierr =
>> DMPlexProjectFieldLocal(dm,ulocal,vX,INSERT_ALL_VALUES,vlocal);CHKERRQ(ierr);
>> ierr =
>> DMLocalToGlobalBegin(dm,vlocal,INSERT_ALL_VALUES,vglobal);CHKERRQ(ierr);
>> ierr =
>> DMLocalToGlobalEnd(dm,vlocal,INSERT_ALL_VALUES,vglobal);CHKERRQ(ierr);
>>
>
> 1) Shouldn't that be user.dmVel above, not dm?
>
> 2) Are you changing from vector to scalar here? I think so, and so you
> would need an extra step
> since that projection assumes that the layout is the same as the
> input.
>
> I do not currently have anything that maps between different layouts like
> you want. It will have to
> be written. THEN we can use the above code.
>
> Matt
>
>
>> ierr = VecViewFromOptions(vglobal,NULL,"-vec_view_x");CHKERRQ(ierr);
>>
>> And as soon as I get to the last line, it gives me this error:
>>
>>
>> [0]PETSC ERROR: PetscMallocValidate: error detected at
>> PetscViewerFileSetName_HDF5() line 251 in
>> /home/justin/petsc-dev/src/sys/classes/viewer/impls/hdf5/hdf5v.c
>> [0]PETSC ERROR: Memory at address 0x3077ac0 is corrupted
>> [0]PETSC ERROR: Probably write past beginning or end of array
>> [0]PETSC ERROR: Last intact block allocated in VecCreate_Seq() line 38 in
>> /home/justin/petsc-dev/src/vec/vec/impls/seq/bvec3.c
>> [0]PETSC ERROR: --------------------- Error Message
>> --------------------------------------------------------------
>> [0]PETSC ERROR: Memory corruption:
>> http://www.mcs.anl.gov/petsc/documentation/installation.html#valgrind
>> [0]PETSC ERROR:
>> [0]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html
>> for trouble shooting.
>> [0]PETSC ERROR: Petsc Development GIT revision: v3.5.3-2766-g0d12e5d GIT
>> Date: 2015-04-21 21:32:23 -0500
>> [0]PETSC ERROR: ./main on a arch-linux2-c-debug named pacotaco by justin
>> Thu Apr 23 22:14:21 2015
>> [0]PETSC ERROR: Configure options --download-chaco --download-exodusii
>> --download-fblaslapack --download-hdf5 --download-metis --download-mpich
>> --download-mumps --download-netcdf --download-parmetis --download-scalapack
>> --download-tetgen --download-triangle --with-cc=gcc --with-clanguage=cxx
>> --with-cmake=cmake --with-ctetgen --with-cxx=g++ --with-debugging=1
>> --with-fc=gfortran --with-valgrind=1 PETSC_ARCH=arch-linux2-c-debug
>> [0]PETSC ERROR: #1 PetscMallocValidate() line 135 in
>> /home/justin/petsc-dev/src/sys/memory/mtr.c
>> [0]PETSC ERROR: #2 PetscViewerFileSetName_HDF5() line 251 in
>> /home/justin/petsc-dev/src/sys/classes/viewer/impls/hdf5/hdf5v.c
>> [0]PETSC ERROR: #3 PetscViewerFileSetName() line 623 in
>> /home/justin/petsc-dev/src/sys/classes/viewer/impls/ascii/filev.c
>> [0]PETSC ERROR: #4 PetscOptionsGetViewer() line 130 in
>> /home/justin/petsc-dev/src/sys/classes/viewer/interface/viewreg.c
>> [0]PETSC ERROR: #5 PetscObjectViewFromOptions() line 2622 in
>> /home/justin/petsc-dev/src/sys/objects/options.c
>> [0]PETSC ERROR: #6 main() line 1237 in
>> /home/justin/Dropbox/dmplex-nonneg/main.c
>> [0]PETSC ERROR: PETSc Option Table entries:
>> [0]PETSC ERROR: -al 100
>> [0]PETSC ERROR: -at 0.01
>> [0]PETSC ERROR: -bcloc
>> 496000,496000,536000,542000,0,100,503000,503000,536000,542000,0,100,496000,503000,536000,536000,0,100,496000,503000,542000,542000,0,100
>> [0]PETSC ERROR: -bcnum 4
>> [0]PETSC ERROR: -bcval 1,1,1,1
>> [0]PETSC ERROR: -dim 3
>> [0]PETSC ERROR: -dm_refine 0
>> [0]PETSC ERROR: -dt 0.01
>> [0]PETSC ERROR: -edges 3,3,3
>> [0]PETSC ERROR: -floc 499550,499600,538950,539000,0,100
>> [0]PETSC ERROR: -flow datafiles/chrom_flow.dat
>> [0]PETSC ERROR: -fnum 1
>> [0]PETSC ERROR: -ftime 0,99
>> [0]PETSC ERROR: -fval -0.1
>> [0]PETSC ERROR: -ksp_rtol 1.0e-9
>> [0]PETSC ERROR: -ksp_type cg
>> [0]PETSC ERROR: -lower 0,0,0
>> [0]PETSC ERROR: -mat_petscspace_order 0
>> [0]PETSC ERROR: -mesh datafiles/chrom_mesh.dat
>> [0]PETSC ERROR: -mu 3.95e-5
>> [0]PETSC ERROR: -nonneg 0
>> [0]PETSC ERROR: -numsteps 0
>> [0]PETSC ERROR: -options_left 0
>> [0]PETSC ERROR: -pc_type jacobi
>> [0]PETSC ERROR: -progress 1
>> [0]PETSC ERROR: -solution_petscspace_order 1
>> [0]PETSC ERROR: -tao_type tron
>> [0]PETSC ERROR: -upper 1,1,1
>> [0]PETSC ERROR: -vec_view_x hdf5:solx.h5
>> [0]PETSC ERROR: -vec_view_y hdf5:soly.h5
>> [0]PETSC ERROR: -vec_view_z hdf5:solz.h5
>> [0]PETSC ERROR: -vtuname pressure
>> [0]PETSC ERROR: -vtuprintat 1,20,80,160,320,640,999
>> [0]PETSC ERROR: -vtusteps 7
>> [0]PETSC ERROR: ----------------End of Error Message -------send entire
>> error message to petsc-maint at mcs.anl.gov----------
>>
>> Any idea what's going on here? Also, if I replace the last line with
>> VecView(vglobal,PETSC_VIEWER_STDOUT_WORLD) I get a completely wacko error:
>>
>> Vec Object:@�� ��r?������b? � jүr?�.
>>
>> ~E�b?�\2p}^r?���"�.b?'xDs��q?�|n��a?`K� Lwq?�n��a?�Ψ���p?�g◻u`?!�
>>
>> |�
>>
>> p?;� :2_?��� �5n?�6/w $]?��I!}�k?! c /�Z?�s# li?�=Y�� X?I%
>> �[�f?^�u=��T?�Sx��Yc?�F �u�Q?6
>> e��_?;6��a3L? z_�R X?��
>> �l�D?X�(�(�P?= �/k�9?;z� I B?
>>
>> R�ٕp$?� j�-� ?��7��- ��H>�h�:�� ��6 5�{��2@�L��]P�I#B�<U��U�O�fV`oI�7trdj�\��\��w0P��)e���a�Kf�s�uS�K���z
>> e���� �V� ΏY�g� �3�2WY��Xëj�)�&M�[�s�!Q&+m��*�l�V^�Ӈй�uo�� ڄD`�z 1 MPI
>> processes
>> type: seq
>> [0]PETSC ERROR:
>> ------------------------------------------------------------------------
>> [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation,
>> probably memory access out of range
>> [0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
>> [0]PETSC ERROR: or see
>> http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind
>> [0]PETSC ERROR: or try http://valgrind.org on GNU/linux and Apple Mac OS
>> X to find memory corruption errors
>> [0]PETSC ERROR: PetscMallocValidate: error detected at
>> PetscSignalHandlerDefault() line 149 in
>> /home/justin/petsc-dev/src/sys/error/signal.c
>> [0]PETSC ERROR: Memory at address 0x2575ac0 is corrupted
>> [0]PETSC ERROR: Probably write past beginning or end of array
>> [0]PETSC ERROR: Last intact block allocated in VecCreate_Seq() line 38 in
>> /home/justin/petsc-dev/src/vec/vec/impls/seq/bvec3.c
>> [0]PETSC ERROR: --------------------- Error Message
>> --------------------------------------------------------------
>> [0]PETSC ERROR: Memory corruption:
>> http://www.mcs.anl.gov/petsc/documentation/installation.html#valgrind
>> [0]PETSC ERROR:
>> [0]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html
>> for trouble shooting.
>> [0]PETSC ERROR: Petsc Development GIT revision: v3.5.3-2766-g0d12e5d GIT
>> Date: 2015-04-21 21:32:23 -0500
>> [0]PETSC ERROR: ./main on a arch-linux2-c-debug named pacotaco by justin
>> Thu Apr 23 22:17:26 2015
>> [0]PETSC ERROR: Configure options --download-chaco --download-exodusii
>> --download-fblaslapack --download-hdf5 --download-metis --download-mpich
>> --download-mumps --download-netcdf --download-parmetis --download-scalapack
>> --download-tetgen --download-triangle --with-cc=gcc --with-clanguage=cxx
>> --with-cmake=cmake --with-ctetgen --with-cxx=g++ --with-debugging=1
>> --with-fc=gfortran --with-valgrind=1 PETSC_ARCH=arch-linux2-c-debug
>> [0]PETSC ERROR: #1 PetscMallocValidate() line 135 in
>> /home/justin/petsc-dev/src/sys/memory/mtr.c
>> [0]PETSC ERROR: #2 PetscSignalHandlerDefault() line 149 in
>> /home/justin/petsc-dev/src/sys/error/signal.c
>>
>>
>> However, if I run the program with debugging off (i.e.,
>> --with-debugging=0), VecView gives me an answer that seems relatively
>> correct.
>>
>> Any idea what's going on here?
>>
>> Thanks,
>>
>> On Thu, Apr 23, 2015 at 4:00 AM, Matthew Knepley <knepley at gmail.com>
>> wrote:
>>
>>> On Wed, Apr 22, 2015 at 9:57 PM, Justin Chang <jchang27 at uh.edu> wrote:
>>>
>>>> Hello,
>>>>
>>>> I am using DMPlexProjectField(...) to postprocess my final solution u
>>>> into another vector sol. I have the following pointwise functions:
>>>>
>>>> /* x-component of gradient */
>>>> void velx(const PetscScalar u[], const PetscScalar u_t[], const
>>>> PetscScalar u_x[], const PetscScalar a[], const PetscScalar a_t[], const
>>>> PetscScalar a_x[], const PetscReal x[], PetscScalar v[])
>>>> {
>>>> v[0] = -a[0]*mu*u_x[0];
>>>> }
>>>>
>>>> /* y-component of gradient */
>>>> void vely(const PetscScalar u[], const PetscScalar u_t[], const
>>>> PetscScalar u_x[], const PetscScalar a[], const PetscScalar a_t[], const
>>>> PetscScalar a_x[], const PetscReal x[], PetscScalar v[])
>>>> {
>>>> v[0] = -a[0]*mu*u_x[1];
>>>> }
>>>>
>>>> /* z-component of gradient */
>>>> void velz(const PetscScalar u[], const PetscScalar u_t[], const
>>>> PetscScalar u_x[], const PetscScalar a[], const PetscScalar a_t[], const
>>>> PetscScalar a_x[], const PetscReal x[], PetscScalar v[])
>>>> {
>>>> v[0] = -a[0]*mu*u_x[2];
>>>> }
>>>>
>>>> Where a[0] is the cell-wise permeability and mu is the (inverse of)
>>>> viscosity. I am solving the diffusion equation (P1 elements). At the end of
>>>> my simulation I have these lines:
>>>>
>>>> ierr = VecDuplicate(user.u,&user.sol);CHKERRQ(ierr);
>>>> ierr = PetscObjectSetName((PetscObject) user.sol,
>>>> "velocity");CHKERRQ(ierr);
>>>> void (*vX[1])(const PetscScalar *, const PetscScalar *, const
>>>> PetscScalar *, const PetscScalar *, const PetscScalar *, const PetscScalar
>>>> *, const PetscReal *, PetscScalar *) = {velx};
>>>> ierr =
>>>> DMPlexProjectField(dm,user.u,vX,INSERT_ALL_VALUES,user.sol);CHKERRQ(ierr);
>>>> ierr = VecViewFromOptions(user.sol,NULL,"-vec_view_x");CHKERRQ(ierr);
>>>>
>>>> void (*vY[1])(const PetscScalar *, const PetscScalar *, const
>>>> PetscScalar *, const PetscScalar *, const PetscScalar *, const PetscScalar
>>>> *, const PetscReal *, PetscScalar *) = {vely};
>>>> ierr =
>>>> DMPlexProjectField(dm,user.u,vY,INSERT_ALL_VALUES,user.sol);CHKERRQ(ierr);
>>>> ierr = VecViewFromOptions(user.sol,NULL,"-vec_view_y");CHKERRQ(ierr);
>>>>
>>>> if (spatialDim == 3) {
>>>> void (*vZ[1])(const PetscScalar *, const PetscScalar *, const
>>>> PetscScalar *, const PetscScalar *, const PetscScalar *, const PetscScalar
>>>> *, const PetscReal *, PetscScalar *) = {velz};
>>>> ierr =
>>>> DMPlexProjectField(dm,user.u,vZ,INSERT_ALL_VALUES,user.sol);CHKERRQ(ierr);
>>>> ierr = VecViewFromOptions(user.sol,NULL,"-vec_view_z");CHKERRQ(ierr);
>>>> }
>>>> ierr = VecDestroy(&user.sol);CHKERRQ(ierr);
>>>>
>>>> But when i look at the results, the dirichlet constrained values of u
>>>> were projected into the respective locations in sol. I thought putting
>>>> INSERT_ALL_VALUES would insert the pointwise functions into all locations
>>>> including the constrained ones. How can I project the above pointwise
>>>> functions into the constrained fields? Or what am I potentially missing
>>>> here?
>>>>
>>>
>>> There are no Dirichlet constrained values in the global vector user.sol.
>>> When you call VecView() it gets projected to
>>> an enlarged vector including the BC and output. What you want is to
>>> project that vector into a space with no constraints,
>>> so you really need another DM/Section combination.
>>>
>>> I think this will work:
>>>
>>> 1) Get a local vector from dm
>>>
>>> 2) Use DMPlexProjectFieldLocal(INSERT_ALL_VALUES) to fill it up
>>>
>>> 3) DMClone(dm) and give it a Section with no constraints
>>>
>>> 4) Use DMLocalToGlobal() into the new DM
>>>
>>> 5) VecView() that new global vector
>>>
>>> Thanks,
>>>
>>> Matt
>>>
>>>
>>>> Thanks,
>>>>
>>>>
>>>> --
>>>> Justin Chang
>>>> PhD Candidate, Civil Engineering - Computational Sciences
>>>> University of Houston, Department of Civil and Environmental Engineering
>>>> Houston, TX 77004
>>>> (512) 963-3262
>>>>
>>>
>>>
>>>
>>> --
>>> 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
>>>
>>
>>
>>
>> --
>> Justin Chang
>> PhD Candidate, Civil Engineering - Computational Sciences
>> University of Houston, Department of Civil and Environmental Engineering
>> Houston, TX 77004
>> (512) 963-3262
>>
>
>
>
> --
> 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
>
--
Justin Chang
PhD Candidate, Civil Engineering - Computational Sciences
University of Houston, Department of Civil and Environmental Engineering
Houston, TX 77004
(512) 963-3262
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