[petsc-users] my code runs too slow

[Xuan YU]

  ierr = MatCreateSeqAIJ(PETSC_COMM_SELF,N,N, 
10,PETSC_NULL,&J);CHKERRQ(ierr);
  ierr = MatAssemblyBegin(J,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
  ierr = MatAssemblyEnd(J,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
  ierr = SNESComputeJacobian(ts_snes,CV_Y,&J,&J,&flag);CHKERRQ(ierr);
  ierr = MatGetColoring(J,MATCOLORINGSL,&iscoloring);CHKERRQ(ierr);
  ierr = MatFDColoringCreate(J,iscoloring,&matfdcoloring);CHKERRQ(ierr);
  ierr = MatFDColoringSetFunction(matfdcoloring,(PetscErrorCode (*) 
(void))f,(void*)&appctx);CHKERRQ(ierr);
  ierr = MatFDColoringSetFromOptions(matfdcoloring);CHKERRQ(ierr);
  ierr =  
TSSetRHSJacobian(ts,J,J,TSDefaultComputeJacobianColor,matfdcoloring);

These are the Jacobian related codes.




On Jul 7, 2010, at 1:51 PM, Satish Balay wrote:

>> total: nonzeros=1830
>> mallocs used during MatSetValues calls =1830
>
> Looks like you are zero-ing out the non-zero structure - before
> assembling the matrix.
>
> Are you calling MatZeroRows() or MatZeroEntries() or something else -
> before assembling the matrix?
>
> Satish
>
> On Wed, 7 Jul 2010, Xuan YU wrote:
>
>> I made a change: ierr =
>> MatCreateSeqAIJ(PETSC_COMM_SELF,N,N,5,PETSC_NULL,&J);CHKERRQ(ierr);
>>
>> Time of the code did not change much, and got the info:
>> Matrix Object:
>>       type=seqaij, rows=1830, cols=1830
>>       total: nonzeros=1830, allocated nonzeros=36600
>>       total number of mallocs used during MatSetValues calls =1830
>>         not using I-node routines
>>
>>
>>
>> On Jul 7, 2010, at 12:51 PM, Satish Balay wrote:
>>
>>>>     total: nonzeros=1830, allocated nonzeros=29280
>>>>     total number of mallocs used during MatSetValues calls =1830
>>>
>>> There is something wrong with your preallocation or matrix
>>> assembly. You should see zero mallocs for efficient assembly.
>>>
>>> http://www.mcs.anl.gov/petsc/petsc-as/documentation/faq.html#efficient-assembly
>>>
>>> satish
>>>
>>>
>>> On Wed, 7 Jul 2010, Xuan YU wrote:
>>>
>>>> Hi,
>>>>
>>>> I finite difference Jacobian approximation for my TS model. The  
>>>> size of
>>>> the
>>>> vector is 1830. I got the following info with(-ts_view):
>>>>
>>>> type: beuler
>>>> maximum steps=50
>>>> maximum time=50
>>>> total number of nonlinear solver iterations=647
>>>> total number of linear solver iterations=647
>>>> SNES Object:
>>>> type: ls
>>>>   line search variant: SNESLineSearchCubic
>>>>   alpha=0.0001, maxstep=1e+08, minlambda=1e-12
>>>> maximum iterations=50, maximum function evaluations=10000
>>>> tolerances: relative=1e-08, absolute=1e-50, solution=1e-08
>>>> total number of linear solver iterations=50
>>>> total number of function evaluations=51
>>>> KSP Object:
>>>>   type: gmres
>>>>     GMRES: restart=30, using Classical (unmodified) Gram-Schmidt
>>>> Orthogonalization with no iterative refinement
>>>>     GMRES: happy breakdown tolerance 1e-30
>>>>   maximum iterations=10000, initial guess is zero
>>>>   tolerances:  relative=1e-05, absolute=1e-50, divergence=10000
>>>>   left preconditioning
>>>>   using PRECONDITIONED norm type for convergence test
>>>> PC Object:
>>>>   type: ilu
>>>>     ILU: out-of-place factorization
>>>>     0 levels of fill
>>>>     tolerance for zero pivot 1e-12
>>>>     using diagonal shift to prevent zero pivot
>>>>     matrix ordering: natural
>>>>     factor fill ratio given 1, needed 1
>>>>       Factored matrix follows:
>>>>         Matrix Object:
>>>>           type=seqaij, rows=1830, cols=1830
>>>>           package used to perform factorization: petsc
>>>>           total: nonzeros=1830, allocated nonzeros=1830
>>>>           total number of mallocs used during MatSetValues calls =0
>>>>             not using I-node routines
>>>>   linear system matrix = precond matrix:
>>>>   Matrix Object:
>>>>     type=seqaij, rows=1830, cols=1830
>>>>     total: nonzeros=1830, allocated nonzeros=29280
>>>>     total number of mallocs used during MatSetValues calls =1830
>>>>       not using I-node routines
>>>>
>>>>
>>>> 50 output time step takes me 11.877s. So I guess there is  
>>>> something not
>>>> appropriate with my Jacobian Matrix. Could you please tell me how  
>>>> to speed
>>>> up
>>>> my code?
>>>>
>>>> Thanks!
>>>>
>>>> Xuan YU
>>>> xxy113 at psu.edu
>>>>
>>>>
>>>>
>>>>
>>>
>>>
>>
>> Xuan YU (俞烜)
>> xxy113 at psu.edu
>>
>>
>>
>>

Xuan YU (俞烜)
xxy113 at psu.edu




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