[petsc-users] Code speedup after upgrading

Junchao Zhang junchao.zhang at gmail.com
Wed Mar 24 17:23:33 CDT 2021 

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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