[petsc-users] parallel computing error
권승리 / 학생 / 항공우주공학과
ksl7912 at snu.ac.kr
Fri May 5 02:49:28 CDT 2023
Dear Barry Smith
Thanks to you, I knew the difference between MATAIJ and MATDENSE.
However, I still have some problems.
There is no problem when I run with a single core. But, MatGetFactor error
occurs when using multi-core.
Could you give me some advice?
The error message is
[0]PETSC ERROR: --------------------- Error Message
--------------------------------------------------------------
[0]PETSC ERROR: See https://petsc.org/release/overview/linear_solve_table/
for possible LU and Cholesky solvers
[0]PETSC ERROR: MatSolverType petsc does not support matrix type mpidense
[0]PETSC ERROR: See https://petsc.org/release/faq/ for trouble shooting.
[0]PETSC ERROR: Petsc Release Version 3.18.5, unknown
[0]PETSC ERROR: ./app on a arch-linux-c-opt named ubuntu by ksl Fri May 5
00:35:23 2023
[0]PETSC ERROR: Configure options --download-mpich --with-debugging=0
COPTFLAGS="-O3 -march=native -mtune=native" CXXOPTFLAGS="-O3 -march=native
-mtune=native" FOPTFLAGS="-O3 -march=native -mtune=native" --download-mumps
--download-scalapack --download-parmetis --download-metis
--download-parmetis --download-hpddm --download-slepc
[0]PETSC ERROR: #1 MatGetFactor() at
/home/ksl/petsc/src/mat/interface/matrix.c:4757
[0]PETSC ERROR: #2 main() at /home/ksl/Downloads/coding_test/coding/a1.c:66
[0]PETSC ERROR: No PETSc Option Table entries
[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, 92) - process 0
My code is below:
int main(int argc, char** args)
{
Mat A, E, A_temp, A_fac;
int n = 15;
PetscInitialize(&argc, &args, NULL, NULL);
PetscCallMPI(MPI_Comm_size(PETSC_COMM_WORLD, &size));
PetscCall(MatCreate(PETSC_COMM_WORLD, &A));
PetscCall(MatSetType(A,MATDENSE));
PetscCall(MatSetSizes(A, PETSC_DECIDE, PETSC_DECIDE, n, n));
PetscCall(MatSetFromOptions(A));
PetscCall(MatSetUp(A));
// Insert values
double val;
for (int i = 0; i < n; i++) {
for (int j = 0; j < n; j++) {
if (i == j){
val = 2.0;
}
else{
val = 1.0;
}
PetscCall(MatSetValue(A, i, j, val, INSERT_VALUES));
}
}
PetscCall(MatAssemblyBegin(A, MAT_FINAL_ASSEMBLY));
PetscCall(MatAssemblyEnd(A, MAT_FINAL_ASSEMBLY));
// Make Identity matrix
PetscCall(MatCreate(PETSC_COMM_WORLD, &E));
PetscCall(MatSetType(E,MATDENSE));
PetscCall(MatSetSizes(E, PETSC_DECIDE, PETSC_DECIDE, n, n));
PetscCall(MatSetFromOptions(E));
PetscCall(MatSetUp(E));
PetscCall(MatShift(E,1.0));
PetscCall(MatAssemblyBegin(E, MAT_FINAL_ASSEMBLY));
PetscCall(MatAssemblyEnd(E, MAT_FINAL_ASSEMBLY));
PetscCall(MatDuplicate(A, MAT_DO_NOT_COPY_VALUES, &A_temp));
PetscCall(MatGetFactor(A, MATSOLVERPETSC, MAT_FACTOR_LU, &A_fac));
IS isr, isc; MatFactorInfo info;
MatGetOrdering(A, MATORDERINGNATURAL, &isr, &isc);
PetscCall(MatLUFactorSymbolic(A_fac, A, isr, isc, &info));
PetscCall(MatLUFactorNumeric(A_fac, A, &info));
MatMatSolve(A_fac, E, A_temp);
PetscCall(MatView(A_temp, PETSC_VIEWER_STDOUT_WORLD));
MatDestroy(&A);
MatDestroy(&A_temp);
MatDestroy(&A_fac);
MatDestroy(&E);
PetscCall(PetscFinalize());
}
Best regards
Seung Lee Kwon
2023년 5월 4일 (목) 오후 10:19, Barry Smith <bsmith at petsc.dev>님이 작성:
>
> The code in ex125.c contains
>
> PetscCall(MatCreate(PETSC_COMM_WORLD, &C));
> PetscCall(MatSetOptionsPrefix(C, "rhs_"));
> PetscCall(MatSetSizes(C, m, PETSC_DECIDE, PETSC_DECIDE, nrhs));
> PetscCall(MatSetType(C, MATDENSE));
> PetscCall(MatSetFromOptions(C));
> PetscCall(MatSetUp(C));
>
> This dense parallel matrix is suitable for passing to MatMatSolve() as the
> right-hand side matrix. Note it is created with PETSC_COMM_WORLD and its
> type is set to be MATDENSE.
>
> You may need to make a sample code by stripping out all the excess code
> in ex125.c to just create an MATAIJ and MATDENSE and solves with
> MatMatSolve() to determine why you code does not work.
>
>
>
> On May 4, 2023, at 3:20 AM, 권승리 / 학생 / 항공우주공학과 <ksl7912 at snu.ac.kr> wrote:
>
> Dear Barry Smith
>
> Thank you for your reply.
>
> I've already installed MUMPS.
>
> And I checked the example you said (ex125.c), I don't understand why the
> RHS matrix becomes the SeqDense matrix.
>
> Could you explain in more detail?
>
> Best regards
> Seung Lee Kwon
>
> 2023년 5월 4일 (목) 오후 12:08, Barry Smith <bsmith at petsc.dev>님이 작성:
>
>>
>> You can configure with MUMPS ./configure --download-mumps
>> --download-scalapack --download-ptscotch --download-metis
>> --download-parmetis
>>
>> And then use MatMatSolve() as in src/mat/tests/ex125.c with parallel
>> MatMatSolve() using MUMPS as the solver.
>>
>> Barry
>>
>>
>> On May 3, 2023, at 10:29 PM, 권승리 / 학생 / 항공우주공학과 <ksl7912 at snu.ac.kr>
>> wrote:
>>
>> Dear developers
>>
>> Thank you for your explanation.
>>
>> But I should use the MatCreateSeqDense because I want to use the
>> MatMatSolve that B matrix must be a SeqDense matrix.
>>
>> Using MatMatSolve is an inevitable part of my code.
>>
>> Could you give me a comment to avoid this error?
>>
>> Best,
>>
>> Seung Lee Kwon
>>
>> 2023년 5월 3일 (수) 오후 7:30, Matthew Knepley <knepley at gmail.com>님이 작성:
>>
>>> On Wed, May 3, 2023 at 6:05 AM 권승리 / 학생 / 항공우주공학과 <ksl7912 at snu.ac.kr>
>>> wrote:
>>>
>>>> Dear developers
>>>>
>>>> I'm trying to use parallel computing and I ran the command 'mpirun -np
>>>> 4 ./app'
>>>>
>>>> In this case, there are two problems.
>>>>
>>>> *First,* I encountered error message
>>>> ///
>>>> [0]PETSC ERROR: [1]PETSC ERROR: --------------------- Error Message
>>>> --------------------------------------------------------------
>>>> [1]PETSC ERROR: Invalid argument
>>>> [1]PETSC ERROR: Comm must be of size 1
>>>> ///
>>>> The code on the error position is
>>>> MatCreateSeqDense(PETSC_COMM_SELF, nns, ns, NULL, &Kns));
>>>>
>>>
>>> 1) "Seq" means sequential, that is "not parallel".
>>>
>>> 2) This line should still be fine since PETSC_COMM_SELF is a serial
>>> communicator
>>>
>>> 3) You should be checking the error code for each call, maybe using the
>>> CHKERRQ() macro
>>>
>>> 4) Please always send the entire error message, not a snippet
>>>
>>> THanks
>>>
>>> Matt
>>>
>>>
>>>> Could "MatCreateSeqDense" not be used in parallel computing?
>>>>
>>>> *Second*, the same error message is repeated as many times as the
>>>> number of cores.
>>>> if I use command -np 4, then the error message is repeated 4 times.
>>>> Could you recommend some advice related to this?
>>>>
>>>> Best,
>>>> Seung Lee Kwon
>>>>
>>>> --
>>>> Seung Lee Kwon, Ph.D.Candidate
>>>> Aerospace Structures and Materials Laboratory
>>>> Department of Mechanical and Aerospace Engineering
>>>> Seoul National University
>>>> Building 300 Rm 503, Gwanak-ro 1, Gwanak-gu, Seoul, South Korea, 08826
>>>> E-mail : ksl7912 at snu.ac.kr
>>>> Office : +82-2-880-7389
>>>> C. P : +82-10-4695-1062
>>>>
>>>
>>>
>>> --
>>> 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
>>>
>>> https://www.cse.buffalo.edu/~knepley/
>>> <http://www.cse.buffalo.edu/~knepley/>
>>>
>>
>>
>> --
>> Seung Lee Kwon, Ph.D.Candidate
>> Aerospace Structures and Materials Laboratory
>> Department of Mechanical and Aerospace Engineering
>> Seoul National University
>> Building 300 Rm 503, Gwanak-ro 1, Gwanak-gu, Seoul, South Korea, 08826
>> E-mail : ksl7912 at snu.ac.kr
>> Office : +82-2-880-7389
>> C. P : +82-10-4695-1062
>>
>>
>>
>
> --
> Seung Lee Kwon, Ph.D.Candidate
> Aerospace Structures and Materials Laboratory
> Department of Mechanical and Aerospace Engineering
> Seoul National University
> Building 300 Rm 503, Gwanak-ro 1, Gwanak-gu, Seoul, South Korea, 08826
> E-mail : ksl7912 at snu.ac.kr
> Office : +82-2-880-7389
> C. P : +82-10-4695-1062
>
>
>
--
Seung Lee Kwon, Ph.D.Candidate
Aerospace Structures and Materials Laboratory
Department of Mechanical and Aerospace Engineering
Seoul National University
Building 300 Rm 503, Gwanak-ro 1, Gwanak-gu, Seoul, South Korea, 08826
E-mail : ksl7912 at snu.ac.kr
Office : +82-2-880-7389
C. P : +82-10-4695-1062
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