[petsc-users] Code speedup after upgrading

[Mohammad Gohardoust]

So the code itself is a finite-element scheme and in stage 1 and 3 there
are expensive loops over entire mesh elements which consume a lot of time.

Mohammad

On Tue, Mar 23, 2021 at 6:08 PM Junchao Zhang <junchao.zhang at gmail.com>
wrote:

> In the new log, I saw
>
> Summary of Stages:   ----- Time ------  ----- Flop ------  --- Messages ---  -- Message Lengths --  -- Reductions --
>                         Avg     %Total     Avg     %Total    Count   %Total     Avg         %Total    Count   %Total
>  0:      Main Stage: 5.4095e+00   2.3%  4.3700e+03   0.0%  4.764e+05   3.0%  3.135e+02        1.0%  2.244e+04  12.6% 1: Solute_Assembly: 1.3977e+02  59.4%  7.3353e+09   4.6%  3.263e+06  20.7%  1.278e+03       26.9%  1.059e+04   6.0%
>
>
> But I didn't see any event in this stage had a cost close to 140s. What
> happened?
>
>  --- Event Stage 1: Solute_Assembly
>
> BuildTwoSided       3531 1.0 2.8025e+0026.3 0.00e+00 0.0 3.6e+05 4.0e+00 3.5e+03  1  0  2  0  2   1  0 11  0 33     0
> BuildTwoSidedF      3531 1.0 2.8678e+0013.2 0.00e+00 0.0 7.1e+05 3.6e+03 3.5e+03  1  0  5 17  2   1  0 22 62 33     0
> VecScatterBegin     7062 1.0 7.1911e-02 1.9 0.00e+00 0.0 7.1e+05 3.5e+02 0.0e+00  0  0  5  2  0   0  0 22  6  0     0
> VecScatterEnd       7062 1.0 2.1248e-01 3.0 1.60e+06 2.7 0.0e+00 0.0e+00 0.0e+00  0  0  0  0  0   0  0  0  0  0    73
> SFBcastOpBegin      3531 1.0 2.6516e-02 2.4 0.00e+00 0.0 3.6e+05 3.5e+02 0.0e+00  0  0  2  1  0   0  0 11  3  0     0
> SFBcastOpEnd        3531 1.0 9.5041e-02 4.7 0.00e+00 0.0 0.0e+00 0.0e+00 0.0e+00  0  0  0  0  0   0  0  0  0  0     0
> SFReduceBegin       3531 1.0 3.8955e-02 2.1 0.00e+00 0.0 3.6e+05 3.5e+02 0.0e+00  0  0  2  1  0   0  0 11  3  0     0
> SFReduceEnd         3531 1.0 1.3791e-01 3.9 1.60e+06 2.7 0.0e+00 0.0e+00 0.0e+00  0  0  0  0  0   0  0  0  0  0   112
> SFPack              7062 1.0 6.5591e-03 2.5 0.00e+00 0.0 0.0e+00 0.0e+00 0.0e+00  0  0  0  0  0   0  0  0  0  0     0
> SFUnpack            7062 1.0 7.4186e-03 2.1 1.60e+06 2.7 0.0e+00 0.0e+00 0.0e+00  0  0  0  0  0   0  0  0  0  0  2080
> MatAssemblyBegin    3531 1.0 4.7846e+00 1.1 0.00e+00 0.0 7.1e+05 3.6e+03 3.5e+03  2  0  5 17  2   3  0 22 62 33     0
> MatAssemblyEnd      3531 1.0 1.5468e+00 2.7 1.68e+07 2.7 0.0e+00 0.0e+00 0.0e+00  0  0  0  0  0   1  2  0  0  0   104
> MatZeroEntries      3531 1.0 3.0998e-02 1.2 0.00e+00 0.0 0.0e+00 0.0e+00 0.0e+00  0  0  0  0  0   0  0  0  0  0     0
>
>
> --Junchao Zhang
>
>
>
> On Tue, Mar 23, 2021 at 5:24 PM Mohammad Gohardoust <gohardoust at gmail.com>
> wrote:
>
>> Thanks Dave for your reply.
>>
>> For sure PETSc is awesome :D
>>
>> Yes, in both cases petsc was configured with --with-debugging=0 and
>> fortunately I do have the old and new -log-veiw outputs which I attached.
>>
>> Best,
>> Mohammad
>>
>> On Tue, Mar 23, 2021 at 1:37 AM Dave May <dave.mayhem23 at gmail.com> wrote:
>>
>>> Nice to hear!
>>> The answer is simple, PETSc is awesome :)
>>>
>>> Jokes aside, assuming both petsc builds were configured with
>>> —with-debugging=0, I don’t think there is a definitive answer to your
>>> question with the information you provided.
>>>
>>> It could be as simple as one specific implementation you use was
>>> improved between petsc releases. Not being an Ubuntu expert, the change
>>> might be associated with using a different compiler, and or a more
>>> efficient BLAS implementation (non threaded vs threaded). However I doubt
>>> this is the origin of your 2x performance increase.
>>>
>>> If you really want to understand where the performance improvement
>>> originated from, you’d need to send to the email list the result of
>>> -log_view from both the old and new versions, running the exact same
>>> problem.
>>>
>>> From that info, we can see what implementations in PETSc are being used
>>> and where the time reduction is occurring. Knowing that, it should be
>>> clearer to provide an explanation for it.
>>>
>>>
>>> Thanks,
>>> Dave
>>>
>>>
>>> On Tue 23. Mar 2021 at 06:24, Mohammad Gohardoust <gohardoust at gmail.com>
>>> wrote:
>>>
>>>> Hi,
>>>>
>>>> I am using a code which is based on petsc (and also parmetis). Recently
>>>> I made the following changes and now the code is running about two times
>>>> faster than before:
>>>>
>>>>    - Upgraded Ubuntu 18.04 to 20.04
>>>>    - Upgraded petsc 3.13.4 to 3.14.5
>>>>    - This time I installed parmetis and metis directly via petsc by
>>>>    --download-parmetis --download-metis flags instead of installing them
>>>>    separately and using --with-parmetis-include=... and
>>>>    --with-parmetis-lib=... (the version of installed parmetis was 4.0.3 before)
>>>>
>>>> I was wondering what can possibly explain this speedup? Does anyone
>>>> have any suggestions?
>>>>
>>>> Thanks,
>>>> Mohammad
>>>>
>>>
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