[petsc-users] DMPlexProjectField not including BC constraints?
Justin Chang
jchang27 at uh.edu
Thu Apr 23 22:20:51 CDT 2015
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);
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
$]?��I!}�k?!c/�Z?�s#li?�=Y��X?I%�[�f?^�u=��T?�Sx��Yc?�F�u�Q?6
e��_?;6��a3L?z_�RX?���l�D?X�(�(�P?=�/k�9?;z�IB?
R�ٕp$?�j�-�?��7��-��H>�h�:����6
5�{��2@�L��]P�I#B�<U��U�O�fV`oI�7trdj�\��\��w0P��)e���a�Kf�s�uS�K���ze�����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
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