I run the RKDG constructed by transientLinearImplicitSystem
and when I use the high order (second or higher) there is the
same problem, the perf_log result of the first step is as follow:
------------------------------------------------------------------------------
| Matrix Assembly Performance: Alive time=747.555, Active time=746.16 |
------------------------------------------------------------------------------
| Event nCalls Total Avg Percent of |
| Time Time Active Time |
|------------------------------------------------------------------------------|
| |
| bounray 402 0.0045 0.000011 0.00 |
| elem init 4410 0.1852 0.000042 0.02 |
| interior 12828 0.4093 0.000032 0.05 |
| mass matrix 30870 0.1772 0.000006 0.02 |
| matrix insertion 4410 745.3840 0.169021 99.90 |
------------------------------------------------------------------------------
| Totals: 52920 746.1602 100.00 |
------------------------------------------------------------------------------
no neighbor matrix here. The CONSTANT and FIRST basis works fast
and I can get the right result for euler equation.
Thank you very much!
Luyi
John Peterson 写道:
> Hi,
>
> Could you possibly resend the timing results with the original/correct
> spacing? They're a little tough to read.
>
> It looks like you are inserting two (or more?) different element
> matrices for each element and it looks like the "neighbor matrix
> insertion" is taking the most time.
>
> This appears to be an atypical usage pattern which I don't understand
> (for example, is there only one neighbor per element?) and may be
> either a library bug or a bug in your implementation. As Roy already
> mentioned, the most likely culprit in cases where matrix assembly
> takes too long is incorrect memory pre-allocation; your symptoms
> combined with the fact that you are performing a non-standard (at
> least for LibMesh) assembly procedure leads me to think that Roy is on
> the right track. Simply saying that
>
>
>> I check the init funciton in petsc_matrix.C and it is ok, the matrix
>> size is dofs X dofs before assemble,
>>
>
> is not really meaningful, one needs to know the number of non-zeros
> per row and the coupling between the different DoFs to be sure the
> sparsity pattern is set correctly.
>
> I would say that you should post your code so that we can take a look,
> but I'm not sure anyone has enough time to give it such a detailed
> examination. What might be more helpful is a PDF describing the
> finite element method you are attempting to implement... then we could
> give a few pointers on what might be the right approach to take in
> LibMesh.
>
> Finally, slow performance aside, does your code actually produce good
> answers or are we spending time debugging something that's not
> conceptually correct?
>
> -J
>
>
>
>
> On Mon, May 12, 2008 at 12:41 AM, luyi <[EMAIL PROTECTED]> wrote:
>
>> Hello,
>>
>> I make a DG programme on libmesh, there is a problem that the first step
>> takes so long when I use
>> high order basis, the performance log is as follow:
>>
>>
>> ------------------------------------------------------------------------------
>> | Matrix Assembly Performance: Alive time=683.179, Active time=682.44 |
>>
>> ------------------------------------------------------------------------------
>> | Event nCalls Total Avg Percent of |
>> | Time Time Active Time |
>>
>> |------------------------------------------------------------------------------|
>> | |
>> | Assemble init 1 0.0001 0.000120 0.00 |
>> | bounray matrix 134 0.0041 0.000030 0.00 |
>> | elem init 1470 0.0757 0.000051 0.01 |
>> | interior matrix 4276 0.2926 0.000068 0.04 |
>> | mass matrix 5880 0.0607 0.000010 0.01 |
>> | matrix insertion 1470 173.4288 0.117979 25.41 |
>> | neighbor matrix insertion 4276 508.5776 0.118938 74.52 |
>>
>> ------------------------------------------------------------------------------
>> | Totals: 17507 682.4396 100.00 |
>>
>> ------------------------------------------------------------------------------
>>
>> Why the matrix insertion spend more than 10 minutes even there is only
>> 17460 dofs?
>> code like this:
>> perf_log.stop_event("interior matrix");
>>
>> perf_log.start_event ("neighbor matrix insertion");
>>
>> euler_system.matrix->add_matrix(Kn,dof_indices,neighbor_dof_indices);
>>
>> perf_log.stop_event ("neighbor matrix insertion");
>>
>> perf_log.start_event ("matrix insertion");
>>
>> euler_system.matrix->add_matrix(Ke, dof_indices);
>> euler_system.rhs->add_vector(Fe, dof_indices);
>>
>> perf_log.stop_event ("matrix insertion");
>>
>>
>>
>>
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>
>
>
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