[petsc-users] Code speedup after upgrading

[Satish Balay]

On Tue, 23 Mar 2021, Matthew Knepley wrote:

> On Tue, Mar 23, 2021 at 9:08 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?
> >
> 
> This is true, but all the PETSc operations are speeding up by a factor 2x.
> It is hard to believe these were run on the same machine.
> For example, VecScale speeds up!?!  So it is not network, or optimizations.
> I cannot explain this.

* Using C compiler: /home/mohammad/Programs/petsc/arch-linux-c-opt/bin/mpicc  -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -Ofast -march=native -mtune=native

Perhaps the CPU is new enough that '-march=native -mtune=native' makes a difference between '18.04 to 20.04'?

You can build 3.13.4 again and see if the numbers are similar to the old or new numbers you currently have..

* --download-fblaslapack --download-openblas 

You should use one or the other - but not both. Perhaps one is using openblas in thread mode [vs single thread for the other]?

Satish


> 
>    Matt
> 
>  --- 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
> >>>>
> >>>
> 
>