[petsc-users] Bad memory scaling with PETSc 3.10

Mon Mar 11 08:40:40 CDT 2019

Is there a difference in memory usage on your tiny problem? I assume no.

I don't see anything that could come from GAMG other than the RAP stuff
that you have discussed already.

On Mon, Mar 11, 2019 at 9:32 AM Myriam Peyrounette <
myriam.peyrounette at idris.fr> wrote:

> The code I am using here is the example 42 of PETSc (
> https://www.mcs.anl.gov/petsc/petsc-3.9/src/ksp/ksp/examples/tutorials/ex42.c.html).
> Indeed it solves the Stokes equation. I thought it was a good idea to use
> an example you might know (and didn't find any that uses GAMG functions). I
> just changed the PCMG setup so that the memory problem appears. And it
> appears when adding PCGAMG.
>
> I don't care about the performance or even the result rightness here, but
> only about the difference in memory use between 3.6 and 3.10. Do you think
> finding a more adapted script would help?
>
> I used the threshold of 0.1 only once, at the beginning, to test its
> influence. I used the default threshold (of 0, I guess) for all the other
> runs.
>
> Myriam
>
> Le 03/11/19 à 13:52, Mark Adams a écrit :
>
> In looking at this larger scale run ...
>
> * Your eigen estimates are much lower than your tiny test problem.  But
> this is Stokes apparently and it should not work anyway. Maybe you have a
> small time step that adds a lot of mass that brings the eigen estimates
> down. And your min eigenvalue (not used) is positive. I would expect
> negative for Stokes ...
>
> * You seem to be setting a threshold value of 0.1 -- that is very high
>
> * v3.6 says "using nonzero initial guess" but this is not in v3.10. Maybe
> we just stopped printing that.
>
> * There were some changes to coasening parameters in going from v3.6 but
> it does not look like your problem was effected. (The coarsening algo is
> non-deterministic by default and you can see small difference on different
> runs)
>
> * We may have also added a "noisy" RHS for eigen estimates by default from
> v3.6.
>
> * And for non-symetric problems you can try -pc_gamg_agg_nsmooths 0, but
> again GAMG is not built for Stokes anyway.
>
>
> On Tue, Mar 5, 2019 at 11:53 AM Myriam Peyrounette <
> myriam.peyrounette at idris.fr> wrote:
>
>> I used PCView to display the size of the linear system in each level of
>> the MG. You'll find the outputs attached to this mail (zip file) for both
>> the default threshold value and a value of 0.1, and for both 3.6 and 3.10
>> PETSc versions.
>>
>> For convenience, I summarized the information in a graph, also attached
>> (png file).
>>
>> As you can see, there are slight differences between the two versions but
>> none is critical, in my opinion. Do you see anything suspicious in the
>> outputs?
>>
>> + I can't find the default threshold value. Do you know where I can find
>> it?
>>
>> Thanks for the follow-up
>>
>> Myriam
>>
>> Le 03/05/19 à 14:06, Matthew Knepley a écrit :
>>
>> On Tue, Mar 5, 2019 at 7:14 AM Myriam Peyrounette <
>> myriam.peyrounette at idris.fr> wrote:
>>
>>> Hi Matt,
>>>
>>> I plotted the memory scalings using different threshold values. The two
>>> scalings are slightly translated (from -22 to -88 mB) but this gain is
>>> neglectable. The 3.6-scaling keeps being robust while the 3.10-scaling
>>> deteriorates.
>>>
>>> Do you have any other suggestion?
>>>
>> Mark, what is the option she can give to output all the GAMG data?
>>
>> Also, run using -ksp_view. GAMG will report all the sizes of its grids,
>> so it should be easy to see
>> if the coarse grid sizes are increasing, and also what the effect of the
>> threshold value is.
>>
>>   Thanks,
>>
>>      Matt
>>
>>> Thanks
>>> Myriam
>>>
>>> Le 03/02/19 à 02:27, Matthew Knepley a écrit :
>>>
>>> On Fri, Mar 1, 2019 at 10:53 AM Myriam Peyrounette via petsc-users <
>>> petsc-users at mcs.anl.gov> wrote:
>>>
>>>> Hi,
>>>>
>>>> I used to run my code with PETSc 3.6. Since I upgraded the PETSc version
>>>> to 3.10, this code has a bad memory scaling.
>>>>
>>>> To report this issue, I took the PETSc script ex42.c and slightly
>>>> modified it so that the KSP and PC configurations are the same as in my
>>>> code. In particular, I use a "personnalised" multi-grid method. The
>>>> modifications are indicated by the keyword "TopBridge" in the attached
>>>> scripts.
>>>>
>>>> To plot the memory (weak) scaling, I ran four calculations for each
>>>> script with increasing problem sizes and computations cores:
>>>>
>>>> 1. 100,000 elts on 4 cores
>>>> 2. 1 million elts on 40 cores
>>>> 3. 10 millions elts on 400 cores
>>>> 4. 100 millions elts on 4,000 cores
>>>>
>>>> The resulting graph is also attached. The scaling using PETSc 3.10
>>>> clearly deteriorates for large cases, while the one using PETSc 3.6 is
>>>> robust.
>>>>
>>>> After a few tests, I found that the scaling is mostly sensitive to the
>>>> use of the AMG method for the coarse grid (line 1780 in
>>>> main_ex42_petsc36.cc). In particular, the performance strongly
>>>> deteriorates when commenting lines 1777 to 1790 (in
>>>> main_ex42_petsc36.cc).
>>>>
>>>> Do you have any idea of what changed between version 3.6 and version
>>>> 3.10 that may imply such degradation?
>>>>
>>>
>>> I believe the default values for PCGAMG changed between versions. It
>>> sounds like the coarsening rate
>>> is not great enough, so that these grids are too large. This can be set
>>> using:
>>>
>>>
>>> https://www.mcs.anl.gov/petsc/petsc-current/docs/manualpages/PC/PCGAMGSetThreshold.html
>>>
>>> There is some explanation of this effect on that page. Let us know if
>>> setting this does not correct the situation.
>>>
>>>   Thanks,
>>>
>>>      Matt
>>>
>>>
>>>> Let me know if you need further information.
>>>>
>>>> Best,
>>>>
>>>> Myriam Peyrounette
>>>>
>>>>
>>>> --
>>>> Myriam Peyrounette
>>>> CNRS/IDRIS - HLST
>>>> --
>>>>
>>>>
>>>
>>> --
>>> 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
>>>
>>> https://www.cse.buffalo.edu/~knepley/
>>> <http://www.cse.buffalo.edu/%7Eknepley/>
>>>
>>>
>>> --
>>> Myriam Peyrounette
>>> CNRS/IDRIS - HLST
>>> --
>>>
>>>
>>
>> --
>> 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
>>
>> https://www.cse.buffalo.edu/~knepley/
>> <http://www.cse.buffalo.edu/%7Eknepley/>
>>
>>
>> --
>> Myriam Peyrounette
>> CNRS/IDRIS - HLST
>> --
>>
>>
> --
> Myriam Peyrounette
> CNRS/IDRIS - HLST
> --
>
>
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