[petsc-users] Trying to run https://petsc.org/release/src/ksp/ksp/tutorials/ex72.c.html

Tue Jul 30 13:51:11 CDT 2024

Hi, Stefano,

I am trying to understand the example there you mentioned. I have a
question,
the example always use DMDA there. Does BDDC also work for DMPLEX?

Thanks ,

On Tue, Jul 30, 2024 at 1:47 PM neil liu <liufield at gmail.com> wrote:

> Thanks,  Stefano,
>
> I am trying to modify the code as follows,
> MatCreate(PETSC_COMM_WORLD, &A);
> MatSetSizes(A, PETSC_DECIDE, PETSC_DECIDE, numberDof_global,
> numberDof_global);
> MatSetType(A, MATIS);
> MatSetUp(A);
> MatZeroEntries(A);
> VecCreate(PETSC_COMM_WORLD, &b);
> VecSetSizes(b, PETSC_DECIDE, numberDof_global);
> VecSetUp(b);
> VecSet(b,0.0);
> VecDuplicate(b, &x);
>
> const PetscInt *g_idx;
> ISLocalToGlobalMapping ltogm;
> DMGetLocalToGlobalMapping(dm, &ltogm);
> ISLocalToGlobalMappingGetIndices(ltogm, &g_idx);
>
> //Build idxm_global and Set LHS
> idxm_Global[ idxDofLocal ] = g_idx[ numdofPerFace*idxm[idxDofLocal]];
> MatSetValues(A, numberDof_local, idxm_Global.data(), numberDof_local,
> idxm_Global.data(), MatrixLocal.data(), ADD_VALUES);
>
> //Set RHS
> PetscScalar valueDiag = 1.0 ;
> MatZeroRows(A, objGeometryInfo.numberDof_Dirichlet, (objGeometryInfo.
> arrayDofSeqGlobal_Dirichlet).data(), valueDiag, 0, 0);
>
> VecSetValues(b, objGeometryInfo.numberDof_Dirichlet, (objGeometryInfo.
> arrayDofSeqGlobal_Dirichlet).data(), (objGeometryInfo.dof_Dirichlet).data(),
> INSERT_VALUES);
> VecSetValues(x, objGeometryInfo.numberDof_Dirichlet, (objGeometryInfo.
> arrayDofSeqGlobal_Dirichlet).data(), (objGeometryInfo.dof_Dirichlet).data(),
> INSERT_VALUES);
> ISLocalToGlobalMappingRestoreIndices(ltogm, &g_idx);
> VecAssemblyBegin(b);
> VecAssemblyEnd(b);
> VecAssemblyBegin(x);
> VecAssemblyEnd(x);
> It shows the attached error when I run the code. It seems something wrong
> is with setting RHS.
> Could you please help me double check my above code to setup the RHS?
> Thanks,
>
> On Tue, Jul 30, 2024 at 11:56 AM Stefano Zampini <
> stefano.zampini at gmail.com> wrote:
>
>> BDDC needs the matrix in MATIS format. Using MatConvert will give you
>> back the right format, but the subdomain matrices are wrong. You need to
>> assemble directly in MATIS format, something like
>>
>> MatCreate(comm,&A)
>> MatSetType(A,MATIS)
>> MatSetLocalToGlobalMapping(A,l2gmap, l2gmap)
>> for e in local_elements:
>>    E = compute_element_matrix(e)
>>    MatSetValues(A,local_element_dofs,local_element_dofs,....)
>>
>> l2gmap is an ISLocalToGlobalMapping that stores the global dof number of
>> the dofs that are local to the mesh
>>
>> See e.g.
>> https://urldefense.us/v3/__https://gitlab.com/petsc/petsc/-/blob/main/src/ksp/ksp/tutorials/ex59.c?ref_type=heads__;!!G_uCfscf7eWS!YZTeegRXq8o-IIT2OMXi5DW9t-AcAW7uZK8sHK5c9smyhbUNh3uZuwx305oWSbpKrkFCmCE_9yKGjm8EhI7eHA$ 
>> or
>> https://urldefense.us/v3/__https://gitlab.com/petsc/petsc/-/blob/main/src/ksp/ksp/tutorials/ex71.c?ref_type=heads__;!!G_uCfscf7eWS!YZTeegRXq8o-IIT2OMXi5DW9t-AcAW7uZK8sHK5c9smyhbUNh3uZuwx305oWSbpKrkFCmCE_9yKGjm_k5lEofA$ 
>>
>> Il giorno mar 30 lug 2024 alle ore 17:50 neil liu <liufield at gmail.com>
>> ha scritto:
>>
>>> Hi,
>>> I am trying to use PCBDDC for the vector based FEM. (Complex system,
>>> double precision )
>>> My code can work well with *asm*,
>>> petsc-3.21.1/petsc/arch-linux-c-opt/bin/mpirun -n 8 ./app -pc_type asm
>>> -pc_asm_overlap 6  -ksp_converged_reason -ksp_view
>>> -ksp_gmres_modifiedgramschmidt  -ksp_gmres_restart 1500 -ksp_rtol 1e-8
>>> -ksp_monitor -ksp_max_it 100000
>>>
>>> When I tried BDDC, it was stuck for solving the linear system (it can
>>> not print anything for ksp_monitor). I did the conversion for matrix,
>>>
>>> *   Mat J;*
>>> *   MatConvert(A, MATIS, MAT_INITIAL_MATRIX, &J);*
>>> *   KSPSetOperators(ksp, A, J);*
>>> *   MatDestroy(&J);*
>>> *   KSPSetInitialGuessNonzero(ksp, PETSC_TRUE);*
>>> *   KSPSetFromOptions(ksp);*
>>>
>>> petsc-3.21.1/petsc/arch-linux-c-debug/bin/mpirun -n 2 ./app -ksp_type cg
>>> -pc_type bddc -ksp_monitor  -mat_type is
>>>
>>> Do you have any suggestions?
>>>
>>> Thanks ,
>>> Xiaodong
>>>
>>>
>>> On Mon, Jul 29, 2024 at 6:19 PM neil liu <liufield at gmail.com> wrote:
>>>
>>>> When I compile with real data,
>>>> it shows the attached error.
>>>>
>>>> The data file is in binary format, right?
>>>>
>>>>
>>>>
>>>> On Mon, Jul 29, 2024 at 5:36 PM Stefano Zampini <
>>>> stefano.zampini at gmail.com> wrote:
>>>>
>>>>> Your PETSc installation is for complex,  data is for real
>>>>>
>>>>> On Mon, Jul 29, 2024, 23:14 neil liu <liufield at gmail.com> wrote:
>>>>>
>>>>>> I compiled Petsc with single precision. However, it is not converged
>>>>>> with the data. Please see the attached file. On Mon, Jul 29, 2024 at 4: 25
>>>>>> PM Barry Smith <bsmith@ petsc. dev> wrote: This can happen if the
>>>>>> data was stored in single precision
>>>>>> ZjQcmQRYFpfptBannerStart
>>>>>> This Message Is From an External Sender
>>>>>> This message came from outside your organization.
>>>>>>
>>>>>> ZjQcmQRYFpfptBannerEnd
>>>>>> I compiled Petsc with single precision. However, it is not converged
>>>>>> with the data.
>>>>>>
>>>>>> Please see the attached file.
>>>>>>
>>>>>> On Mon, Jul 29, 2024 at 4:25 PM Barry Smith <bsmith at petsc.dev> wrote:
>>>>>>
>>>>>>>
>>>>>>>    This can happen if the data was stored in single precision and
>>>>>>> PETSc was built for double.
>>>>>>>
>>>>>>>
>>>>>>> On Jul 29, 2024, at 3:55 PM, neil liu <liufield at gmail.com> wrote:
>>>>>>>
>>>>>>> This Message Is From an External Sender
>>>>>>> This message came from outside your organization.
>>>>>>> Dear Petsc developers,,
>>>>>>>
>>>>>>> I am trying to run
>>>>>>> https://urldefense.us/v3/__https://petsc.org/release/src/ksp/ksp/tutorials/ex72.c.html__;!!G_uCfscf7eWS!YZTeegRXq8o-IIT2OMXi5DW9t-AcAW7uZK8sHK5c9smyhbUNh3uZuwx305oWSbpKrkFCmCE_9yKGjm_Z20MEcA$ 
>>>>>>> <https://urldefense.us/v3/__https://petsc.org/release/src/ksp/ksp/tutorials/ex72.c.html__;!!G_uCfscf7eWS!ZG4gvmS6hQD8ymbvCUDfAatzRUJHzmWO-hOgp9m0xXuAXgIB-fxe_xspYs3WEPi_Ed0UFLMHKanYuYWrTlQGrA$>
>>>>>>> with
>>>>>>>
>>>>>>> petsc-3.21.1/petsc/arch-linux-c-opt/bin/mpirun -n 2 ./ex72  -f
>>>>>>> /Documents/PetscData/poisson_DMPLEX_32x32_16.dat -pc_type bddc -ksp_type cg
>>>>>>> -ksp_norm_type natural -ksp_error_if_not_converged -mat_type is
>>>>>>>
>>>>>>> The file was downloaded and put in the directory PetscData.
>>>>>>>
>>>>>>> The error is shown as follows,
>>>>>>>
>>>>>>> 0]PETSC ERROR: --------------------- Error Message
>>>>>>> --------------------------------------------------------------
>>>>>>> [0]PETSC ERROR: Read from file failed
>>>>>>> [0]PETSC ERROR: Read past end of file
>>>>>>> [0]PETSC ERROR: WARNING! There are unused option(s) set! Could be
>>>>>>> the program crashed before usage or a spelling mistake, etc!
>>>>>>> [0]PETSC ERROR:   Option left: name:-ksp_error_if_not_converged (no
>>>>>>> value) source: command line
>>>>>>> [0]PETSC ERROR:   Option left: name:-ksp_norm_type value: natural
>>>>>>> source: command line
>>>>>>> [0]PETSC ERROR:   Option left: name:-ksp_type value: cg source:
>>>>>>> command line
>>>>>>> [0]PETSC ERROR:   Option left: name:-pc_type value: bddc source:
>>>>>>> command line
>>>>>>> [0]PETSC ERROR: See https://urldefense.us/v3/__https://petsc.org/release/faq/__;!!G_uCfscf7eWS!YZTeegRXq8o-IIT2OMXi5DW9t-AcAW7uZK8sHK5c9smyhbUNh3uZuwx305oWSbpKrkFCmCE_9yKGjm_9Texx-Q$ 
>>>>>>> <https://urldefense.us/v3/__https://petsc.org/release/faq/__;!!G_uCfscf7eWS!ZG4gvmS6hQD8ymbvCUDfAatzRUJHzmWO-hOgp9m0xXuAXgIB-fxe_xspYs3WEPi_Ed0UFLMHKanYuYVR0x14Xg$>
>>>>>>>  for trouble shooting.
>>>>>>> [0]PETSC ERROR: Petsc Release Version 3.21.1, unknown
>>>>>>> [0]PETSC ERROR: ./ex72 on a arch-linux-c-opt named
>>>>>>>  Mon Jul 29 15:50:04 2024
>>>>>>> [0]PETSC ERROR: Configure options --with-cc=gcc --with-fc=gfortran
>>>>>>> --with-cxx=g++ --download-fblaslapack --download-mpich
>>>>>>> --with-scalar-type=complex --download-triangle --with-debugging=no
>>>>>>> [0]PETSC ERROR: #1 PetscBinaryRead() at
>>>>>>> /home/xxxxxx/Documents/petsc-3.21.1/petsc/src/sys/fileio/sysio.c:327
>>>>>>> [0]PETSC ERROR: #2 PetscViewerBinaryWriteReadAll() at
>>>>>>> /home/xiaodong.liu/Documents/petsc-3.21.1/petsc/src/sys/classes/viewer/impls/binary/binv.c:1077
>>>>>>> [0]PETSC ERROR: #3 PetscViewerBinaryReadAll() at
>>>>>>> /home/xiaodong.liu/Documents/petsc-3.21.1/petsc/src/sys/classes/viewer/impls/binary/binv.c:1119
>>>>>>> [0]PETSC ERROR: #4 MatLoad_MPIAIJ_Binary() at
>>>>>>> Documents/petsc-3.21.1/petsc/src/mat/impls/aij/mpi/mpiaij.c:3093
>>>>>>> [0]PETSC ERROR: #5 MatLoad_MPIAIJ() at
>>>>>>> /Documents/petsc-3.21.1/petsc/src/mat/impls/aij/mpi/mpiaij.c:3035
>>>>>>> [0]PETSC ERROR: #6 MatLoad() at
>>>>>>> /Documents/petsc-3.21.1/petsc/src/mat/interface/matrix.c:1344
>>>>>>> [0]PETSC ERROR: #7 MatLoad_IS() at
>>>>>>> /Documents/petsc-3.21.1/petsc/src/mat/impls/is/matis.c:2575
>>>>>>> [0]PETSC ERROR: #8 MatLoad() at
>>>>>>> /home/Documents/petsc-3.21.1/petsc/src/mat/interface/matrix.c:1344
>>>>>>> [0]PETSC ERROR: #9 main() at ex72.c:105
>>>>>>> [0]PETSC ERROR: PETSc Option Table entries:
>>>>>>> [0]PETSC ERROR: -f
>>>>>>> /Documents/PetscData/poisson_DMPLEX_32x32_16.dat (source: command
>>>>>>> line)
>>>>>>> [0]PETSC ERROR: -ksp_error_if_not_converged (source: command line)
>>>>>>> [0]PETSC ERROR: -ksp_norm_type natural (source: command line)
>>>>>>> [0]PETSC ERROR: -ksp_type cg (source: command line)
>>>>>>> [0]PETSC ERROR: -mat_type is (source: command line)
>>>>>>> [0]PETSC ERROR: -pc_type bddc (source: command line)
>>>>>>> [0]PETSC ERROR: ----------------End of Error Message -------send
>>>>>>> entire error message to petsc-maint at mcs.anl.gov----------
>>>>>>> application called MPI_Abort(MPI_COMM_SELF, 66) - process 0
>>>>>>>
>>>>>>>
>>>>>>>
>>
>> --
>> Stefano
>>
>
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