[petsc-users] Code speedup after upgrading

[Mohammad Gohardoust]

That's right, these loops also take roughly half time as well. If I am not
mistaken, petsc (MatSetValue) is called after doing some calculations over
each tetrahedral element.
Thanks for your suggestion. I will try that and will post the results.

Mohammad

On Wed, Mar 24, 2021 at 3:23 PM Junchao Zhang <junchao.zhang at gmail.com>
wrote:

>
>
>
> On Wed, Mar 24, 2021 at 2:17 AM Mohammad Gohardoust <gohardoust at gmail.com>
> wrote:
>
>> 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.
>>
> So these expensive loops must also take half time with newer petsc?  And
> these loops do not call petsc routines?
> I think you can build two PETSc versions with the same configuration
> options, then run your code with one MPI rank to see if there is a
> difference.
> If they give the same performance, then scale to 2, 4, ... ranks and see
> what happens.
>
>
>
>>
>> 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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