Slow speed after changing from serial to parallel

[Matthew Knepley]

On Mon, Apr 14, 2008 at 8:43 AM, Ben Tay <zonexo at gmail.com> wrote:
> Hi Matthew,
>
>  I think you've misunderstood what I meant. What I'm trying to say is
> initially I've got a serial code. I tried to convert to a parallel one. Then
> I tested it and it was pretty slow. Due to some work requirement, I need to
> go back to make some changes to my code. Since the parallel is not working
> well, I updated and changed the serial one.
>
>  Well, that was a while ago and now, due to the updates and changes, the
> serial code is different from the old converted parallel code. Some files
> were also deleted and I can't seem to get it working now. So I thought I
> might as well convert the new serial code to parallel. But I'm not very sure
> what I should do 1st.
>
>  Maybe I should rephrase my question in that if I just convert my poisson
> equation subroutine from a serial PETSc to a parallel PETSc version, will it
> work? Should I expect a speedup? The rest of my code is still serial.

You should, of course, only expect speedup in the parallel parts

  Matt

>  Thank you very much.
>
>
>
>  Matthew Knepley wrote:
>
> > I am not sure why you would ever have two codes. I never do this. PETSc
> > is designed to write one code to run in serial and parallel. The PETSc
> part
> > should look identical. To test, run the code yo uhave verified in serial
> and
> > output PETSc data structures (like Mat and Vec) using a binary viewer.
> > Then run in parallel with the same code, which will output the same
> > structures. Take the two files and write a small verification code that
> > loads both versions and calls MatEqual and VecEqual.
> >
> >  Matt
> >
> > On Mon, Apr 14, 2008 at 5:49 AM, Ben Tay <zonexo at gmail.com> wrote:
> >
> >
> > > Thank you Matthew. Sorry to trouble you again.
> > >
> > >  I tried to run it with -log_summary output and I found that there's
> some
> > > errors in the execution. Well, I was busy with other things and I just
> came
> > > back to this problem. Some of my files on the server has also been
> deleted.
> > > It has been a while and I  remember that  it worked before, only much
> > > slower.
> > >
> > >  Anyway, most of the serial code has been updated and maybe it's easier
> to
> > > convert the new serial code instead of debugging on the old parallel
> code
> > > now. I believe I can still reuse part of the old parallel code. However,
> I
> > > hope I can approach it better this time.
> > >
> > >  So supposed I need to start converting my new serial code to parallel.
> > > There's 2 eqns to be solved using PETSc, the momentum and poisson. I
> also
> > > need to parallelize other parts of my code. I wonder which route is the
> > > best:
> > >
> > >  1. Don't change the PETSc part ie continue using PETSC_COMM_SELF,
> modify
> > > other parts of my code to parallel e.g. looping, updating of values etc.
> > > Once the execution is fine and speedup is reasonable, then modify the
> PETSc
> > > part - poisson eqn 1st followed by the momentum eqn.
> > >
> > >  2. Reverse the above order ie modify the PETSc part - poisson eqn 1st
> > > followed by the momentum eqn. Then do other parts of my code.
> > >
> > >  I'm not sure if the above 2 mtds can work or if there will be
> conflicts. Of
> > > course, an alternative will be:
> > >
> > >  3. Do the poisson, momentum eqns and other parts of the code
> separately.
> > > That is, code a standalone parallel poisson eqn and use samples values
> to
> > > test it. Same for the momentum and other parts of the code. When each of
> > > them is working, combine them to form the full parallel code. However,
> this
> > > will be much more troublesome.
> > >
> > >  I hope someone can give me some recommendations.
> > >
> > >  Thank you once again.
> > >
> > >
> > >
> > >  Matthew Knepley wrote:
> > >
> > >
> > >
> > > > 1) There is no way to have any idea what is going on in your code
> > > >   without -log_summary output
> > > >
> > > > 2) Looking at that output, look at the percentage taken by the solver
> > > >   KSPSolve event. I suspect it is not the biggest component, because
> > > >  it is very scalable.
> > > >
> > > >  Matt
> > > >
> > > > On Sun, Apr 13, 2008 at 4:12 AM, Ben Tay <zonexo at gmail.com> wrote:
> > > >
> > > >
> > > >
> > > >
> > > > > Hi,
> > > > >
> > > > > I've a serial 2D CFD code. As my grid size requirement increases,
> the
> > > > > simulation takes longer. Also, memory requirement becomes a problem.
> > > > >
> > > > >
> > > >
> > > Grid
> > >
> > >
> > > >
> > > > > size 've reached 1200x1200. Going higher is not possible due to
> memory
> > > > > problem.
> > > > >
> > > > > I tried to convert my code to a parallel one, following the examples
> > > > >
> > > > >
> > > >
> > > given.
> > >
> > >
> > > >
> > > > > I also need to restructure parts of my code to enable parallel
> looping.
> > > > >
> > > > >
> > > >
> > > I
> > >
> > >
> > > >
> > > > > 1st changed the PETSc solver to be parallel enabled and then I
> > > > >
> > > > >
> > > >
> > > restructured
> > >
> > >
> > > >
> > > > > parts of my code. I proceed on as longer as the answer for a simple
> test
> > > > > case is correct. I thought it's not really possible to do any speed
> > > > >
> > > > >
> > > >
> > > testing
> > >
> > >
> > > >
> > > > > since the code is not fully parallelized yet. When I finished during
> > > > >
> > > > >
> > > >
> > > most of
> > >
> > >
> > > >
> > > > > the conversion, I found that in the actual run that it is much
> slower,
> > > > > although the answer is correct.
> > > > >
> > > > > So what is the remedy now? I wonder what I should do to check what's
> > > > >
> > > > >
> > > >
> > > wrong.
> > >
> > >
> > > >
> > > > > Must I restart everything again? Btw, my grid size is 1200x1200. I
> > > > >
> > > > >
> > > >
> > > believed
> > >
> > >
> > > >
> > > > > it should be suitable for parallel run of 4 processors? Is that so?
> > > > >
> > > > > Thank you.
> > > > >
> > > > >
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> > > >
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>



-- 
What most experimenters take for granted before they begin their
experiments is infinitely more interesting than any results to which
their experiments lead.
-- Norbert Wiener