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Re: Slow speed after changing from serial to parallel

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.

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@xxxxxxxxx> 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@xxxxxxxxx> 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.