[petsc-users] my code runs too slow

[Xuan YU]

On Jul 7, 2010, at 2:06 PM, Satish Balay wrote:

> On Wed, 7 Jul 2010, Xuan YU wrote:
>
>> 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);
>
> This assembly removes the unused space here. Since no values are
> inserted - it squezes out all of the allocated space. Perhaps you just
> need to remove these 2 calls as the actual matrix is assembled further
> down the code.
>

I removed these 2
But got Error Message

[0]PETSC ERROR: Object is in wrong state!
[0]PETSC ERROR: Not for unassembled matrix!





> Satish
>
>> 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
>>
>>
>>
>>

Xuan YU (俞烜)
xxy113 at psu.edu




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