[petsc-users] Bad memory scaling with PETSc 3.10
Myriam Peyrounette
myriam.peyrounette at idris.fr
Wed Mar 20 11:05:50 CDT 2019
More precisely: something happens when upgrading the functions
MatPtAPNumeric_MPIAIJ_MPIAIJ and/or MatPtAPSymbolic_MPIAIJ_MPIAIJ.
Unfortunately, there are a lot of differences between the old and new
versions of these functions. I keep investigating but if you have any
idea, please let me know.
Best,
Myriam
Le 03/20/19 à 13:48, Myriam Peyrounette a écrit :
>
> Hi all,
>
> I used git bisect to determine when the memory need increased. I found
> that the first "bad" commit is aa690a28a7284adb519c28cb44eae20a2c131c85.
>
> Barry was right, this commit seems to be about an evolution of
> MatPtAPSymbolic_MPIAIJ_MPIAIJ. You mentioned the option "-matptap_via
> scalable" but I can't find any information about it. Can you tell me more?
>
> Thanks
>
> Myriam
>
>
> Le 03/11/19 à 14:40, Mark Adams a écrit :
>> 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 <mailto: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
>>> <mailto: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
>>>> <mailto: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
>>>>> <mailto: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
>> --
>>
>
> --
> Myriam Peyrounette
> CNRS/IDRIS - HLST
> --
--
Myriam Peyrounette
CNRS/IDRIS - HLST
--
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