[petsc-users] my code runs too slow

[Xuan YU]

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




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