[petsc-users] About recent changes in GAMG

[Ashish Patel]

Hi Jed,
VmRss is on a higher side and seems to match what PetscMallocGetMaximumUsage is reporting. HugetlbPages was 0 for me.

Mark, running without the near nullspace also gives similar results. I have attached the malloc_view and gamg info for serial and 2 core runs. Some of the standout functions on rank 0 for parallel run seems to be
5.3 GB MatSeqAIJSetPreallocation_SeqAIJ
7.7 GB MatStashSortCompress_Private
10.1 GB PetscMatStashSpaceGet
7.7 GB  PetscSegBufferAlloc_Private

malloc_view also says the following
[0] Maximum memory PetscMalloc()ed 32387548912 maximum size of entire process 8270635008
which fits the PetscMallocGetMaximumUsage > PetscMemoryGetMaximumUsage output.

Let me know if you need some other info.

Thanks,
Ashish​

________________________________
From: Jed Brown <jed at jedbrown.org>
Sent: Thursday, April 18, 2024 2:16 PM
To: Mark Adams <mfadams at lbl.gov>; Ashish Patel <ashish.patel at ansys.com>; PETSc users list <petsc-users at mcs.anl.gov>
Cc: Scott McClennan <scott.mcclennan at ansys.com>
Subject: Re: [petsc-users] About recent changes in GAMG

[External Sender]

Mark Adams <mfadams at lbl.gov> writes:

>>> Yea, my interpretation of these methods is also that "
> PetscMemoryGetMaximumUsage" should be >= "PetscMallocGetMaximumUsage".
>>> But you are seeing the opposite.
>
>
> We are using PETSc main and have found a case where memory consumption
> explodes in parallel.
> Also, we see a non-negligible difference between PetscMemoryGetMaximumUsage()
> and PetscMallocGetMaximumUsage().
> Running in serial through /usr/bin/time, the max. resident set size matches
> the PetscMallocGetMaximumUsage() result.
> I would have expected it to match PetscMemoryGetMaximumUsage() instead.

PetscMemoryGetMaximumUsage uses procfs (if PETSC_USE_PROCFS_FOR_SIZE, which should be typical on Linux anyway) in PetscHeaderDestroy to update a static variable. If you haven't destroyed an object yet, its value will be nonsense.

If your program is using huge pages, it might also be inaccurate (I don't know). You can look at /proc/<pid>/statm to see what PETSc is reading (second field, which is number of pages in RSS). You can also look at the VmRss field in /proc/<pid>/status, which reads in kB. See also the HugetlbPages field in /proc/<pid>/status.

https://urldefense.us/v3/__https://www.kernel.org/doc/Documentation/filesystems/proc.txt__;!!G_uCfscf7eWS!cjjzIqrR0_JSzQFZMrxX9GzpJEPHSN5oVeNexSd2AKNVhVFmsrJy-sKYRd0VFTzEk1LB727T1dFbrhKJ208CIzji9_k$ 

If your app is swapping, these will be inaccurate because swapped memory is not resident. We don't use the first field (VmSize) because there are reasons why programs sometimes map much more memory than they'll actually use, making such numbers irrelevant for most purposes.

>
>
> PetscMemoryGetMaximumUsage
> PetscMallocGetMaximumUsage
>  Time
> Serial + Option 1
>  4.8 GB
>  7.4 GB
> 112 sec
> 2 core + Option1
> 15.2 GB
> 45.5 GB
> 150 sec
> Serial + Option 2
> 3.1 GB
> 3.8 GB
>  167 sec
> 2 core + Option2
> 13.1 GB
> 17.4 GB
> 89 sec
> Serial + Option 3
> 4.7GB
> 5.2GB
> 693 sec
> 2 core + Option 3
> 23.2 GB
> 26.4 GB
> 411 sec
>
>
> On Thu, Apr 18, 2024 at 4:13 PM Mark Adams <mfadams at lbl.gov> wrote:
>
>> The next thing you might try is not using the null space argument.
>> Hypre does not use it, but GAMG does.
>> You could also run with -malloc_view to see some info on mallocs. It is
>> probably in the Mat objects.
>> You can also run with "-info" and grep on GAMG in the output and send that.
>>
>> Mark
>>
>> On Thu, Apr 18, 2024 at 12:03 PM Ashish Patel <ashish.patel at ansys.com>
>> wrote:
>>
>>> Hi Mark,
>>>
>>> Thanks for your response and suggestion. With hypre both memory and time
>>> looks good, here is the data for that
>>>
>>> PetscMemoryGetMaximumUsage
>>> PetscMallocGetMaximumUsage
>>>  Time
>>> Serial + Option 4
>>> 5.55 GB
>>>  5.17 GB
>>> 15.7 sec
>>> 2 core + Option 4
>>> 5.85 GB
>>> 4.69 GB
>>> 21.9 sec
>>>
>>> Option 4
>>> mpirun -n _ ./ex1 -A_name matrix.dat -b_name vector.dat -n_name
>>> _null_space.dat -num_near_nullspace 6 -ksp_type cg -pc_type hypre
>>> -pc_hypre_boomeramg_strong_threshold 0.9 -ksp_view -log_view
>>> -log_view_memory -info :pc
>>>
>>> I am also attaching a standalone program to reproduce these options and
>>> the link to matrix, rhs and near null spaces (serial.tar 2.xz
>>> <https://urldefense.us/v3/__https://ansys-my.sharepoint.com/:u:/p/ashish_patel/EbUM5Ahp-epNi4xDxR9mnN0B1dceuVzGhVXQQYJzI5Py2g__;!!G_uCfscf7eWS!ar7t_MsQ-W6SXcDyEWpSDZP_YngFSqVsz2D-8chGJHSz7IZzkLBvN4UpJ1GXrRBGyhEHqmDUQGBfqTKf5x_BPXo$ >
>>> ) if you would like to try as well. Please let me know if you have
>>> trouble accessing the link.
>>>
>>> Ashish
>>> ------------------------------
>>> *From:* Mark Adams <mfadams at lbl.gov>
>>> *Sent:* Wednesday, April 17, 2024 7:52 PM
>>> *To:* Jeremy Theler (External) <jeremy.theler-ext at ansys.com>
>>> *Cc:* Ashish Patel <ashish.patel at ansys.com>; Scott McClennan <
>>> scott.mcclennan at ansys.com>
>>> *Subject:* Re: About recent changes in GAMG
>>>
>>>
>>> *[External Sender]*
>>>
>>>
>>> On Wed, Apr 17, 2024 at 7:20 AM Jeremy Theler (External) <
>>> jeremy.theler-ext at ansys.com> wrote:
>>>
>>> Hey Mark. Long time no see! How are thing going over there?
>>>
>>> We are using PETSc main and have found a case where memory consumption
>>> explodes in parallel.
>>> Also, we see a non-negligible difference between
>>> PetscMemoryGetMaximumUsage() and PetscMallocGetMaximumUsage().
>>> Running in serial through /usr/bin/time, the max. resident set size
>>> matches the PetscMallocGetMaximumUsage() result.
>>> I would have expected it to match PetscMemoryGetMaximumUsage() instead.
>>>
>>>
>>> Yea, my interpretation of these methods is also that "Memory" should be
>>> >= "Malloc". But you are seeing the opposite.
>>>
>>> I don't have any idea what is going on with your big memory penalty going
>>> from 1 to 2 cores on this test, but the first thing to do is try other
>>> solvers and see how that behaves. Hypre in particular would be a good thing
>>> to try because it is a similar algorithm.
>>>
>>> Mark
>>>
>>>
>>>
>>> The matrix size is around 1 million. We can share it with you if you
>>> want, along with the RHS and the 6 near nullspace vectors and a modified
>>> ex1.c which will read these files and show the following behavior.
>>>
>>> Observations using latest main for elastic matrix with a block size of 3
>>> (after removing bonded glue-like DOFs with direct elimination) and near
>>> null space provided
>>>
>>>    - Big memory penalty going from serial to parallel (2 core)
>>>    - Big difference between PetscMemoryGetMaximumUsage and
>>>    PetscMallocGetMaximumUsage, why?
>>>    - The memory penalty decreases with -pc_gamg_aggressive_square_graph false
>>>    (option 2)
>>>    - The difference between PetscMemoryGetMaximumUsage and
>>>    PetscMallocGetMaximumUsage reduces when -pc_gamg_threshold is
>>>    increased from 0 to 0.01 (option 3), the solve time increase a lot though.
>>>
>>>
>>>
>>>
>>>
>>> PetscMemoryGetMaximumUsage
>>> PetscMallocGetMaximumUsage
>>>  Time
>>> Serial + Option 1
>>>  4.8 GB
>>>  7.4 GB
>>> 112 sec
>>> 2 core + Option1
>>> 15.2 GB
>>> 45.5 GB
>>> 150 sec
>>> Serial + Option 2
>>> 3.1 GB
>>> 3.8 GB
>>>  167 sec
>>> 2 core + Option2
>>> 13.1 GB
>>> 17.4 GB
>>> 89 sec
>>> Serial + Option 3
>>> 4.7GB
>>> 5.2GB
>>> 693 sec
>>> 2 core + Option 3
>>> 23.2 GB
>>> 26.4 GB
>>> 411 sec
>>>
>>> Option 1
>>> mpirun -n _ ./ex1 -A_name matrix.dat -b_name vector.dat -n_name
>>> _null_space.dat -num_near_nullspace 6 -ksp_type cg -pc_type gamg
>>> -pc_gamg_coarse_eq_limit 1000 -ksp_view -log_view -log_view_memory
>>> -pc_gamg_aggressive_square_graph true -pc_gamg_threshold 0.0 -info :pc
>>>
>>> Option 2
>>> mpirun -n _ ./ex1 -A_name matrix.dat -b_name vector.dat -n_name
>>> _null_space.dat -num_near_nullspace 6 -ksp_type cg -pc_type gamg
>>> -pc_gamg_coarse_eq_limit 1000 -ksp_view -log_view -log_view_memory
>>> -pc_gamg_aggressive_square_graph *false* -pc_gamg_threshold 0.0 -info :pc
>>>
>>> Option 3
>>> mpirun -n _ ./ex1 -A_name matrix.dat -b_name vector.dat -n_name
>>> _null_space.dat -num_near_nullspace 6 -ksp_type cg -pc_type gamg
>>> -pc_gamg_coarse_eq_limit 1000 -ksp_view -log_view -log_view_memory
>>> -pc_gamg_aggressive_square_graph true -pc_gamg_threshold *0.01* -info :pc
>>> ------------------------------
>>> *From:* Mark Adams <mfadams at lbl.gov>
>>> *Sent:* Tuesday, November 14, 2023 11:28 AM
>>> *To:* Jeremy Theler (External) <jeremy.theler-ext at ansys.com>
>>> *Cc:* Ashish Patel <ashish.patel at ansys.com>
>>> *Subject:* Re: About recent changes in GAMG
>>>
>>>
>>> *[External Sender]*
>>> Sounds good,
>>>
>>> I think the not-square graph "aggressive" coarsening is only issue that I
>>> see and you can fix this by using:
>>>
>>> -mat_coarsen_type mis
>>>
>>> Aside, '-pc_gamg_aggressive_square_graph' should do it also, and you can
>>> use both and they will be ignored in earlier versions.
>>>
>>> If you see a difference then the first thing to do is run with '-info
>>> :pc' and send that to me (you can grep on 'GAMG' and send that if you like
>>> to reduce the data).
>>>
>>> Thanks,
>>> Mark
>>>
>>>
>>> On Tue, Nov 14, 2023 at 8:49 AM Jeremy Theler (External) <
>>> jeremy.theler-ext at ansys.com> wrote:
>>>
>>> Hi Mark.
>>> Thanks for reaching out. For now, we are going to stick to 3.19 for our
>>> production code because the changes in 3.20 impact in our tests in
>>> different ways (some of them perform better, some perform worse).
>>> I now switched to another task about investigating structural elements in
>>> DMplex.
>>> I'll go back to analyzing the new changes in GAMG in a couple of weeks so
>>> we can then see if we upgrade to 3.20 or we wait until 3.21.
>>>
>>> Thanks for your work and your kindness.
>>> --
>>> jeremy
>>> ------------------------------
>>> *From:* Mark Adams <mfadams at lbl.gov>
>>> *Sent:* Tuesday, November 14, 2023 9:35 AM
>>> *To:* Jeremy Theler (External) <jeremy.theler-ext at ansys.com>
>>> *Cc:* Ashish Patel <ashish.patel at ansys.com>
>>> *Subject:* Re: About recent changes in GAMG
>>>
>>>
>>> *[External Sender]*
>>> Hi Jeremy,
>>>
>>> Just following up.
>>> I appreciate your digging into performance regressions in GAMG.
>>> AMG is really a pain sometimes and we want GAMG to be solid, at least for
>>> mainstream options, and your efforts are appreciated.
>>> So feel free to start this discussion up.
>>>
>>> Thanks,
>>> Mark
>>>
>>> On Wed, Oct 25, 2023 at 9:52 PM Jeremy Theler (External) <
>>> jeremy.theler-ext at ansys.com> wrote:
>>>
>>> Dear Mark
>>>
>>> Thanks for the follow up and sorry for the delay.
>>> I'm taking some days off. I'll be back to full throttle next week so can
>>> continue the discussion about these changes in GAMG.
>>>
>>> Regards,
>>> Jeremy
>>>
>>> ------------------------------
>>> *From:* Mark Adams <mfadams at lbl.gov>
>>> *Sent:* Wednesday, October 18, 2023 9:15 AM
>>> *To:* Jeremy Theler (External) <jeremy.theler-ext at ansys.com>; PETSc
>>> users list <petsc-users at mcs.anl.gov>
>>> *Cc:* Ashish Patel <ashish.patel at ansys.com>
>>> *Subject:* Re: About recent changes in GAMG
>>>
>>>
>>> *[External Sender]*
>>> Hi Jeremy,
>>>
>>> I hope you don't mind putting this on the list (w/o data), but this is
>>> documentation and you are the second user that found regressions.
>>> Sorry for the churn.
>>>
>>> There is a lot here so we can iterate, but here is a pass at your
>>> questions.
>>>
>>> *** Using MIS-2 instead of square graph was motivated by setup
>>> cost/performance but on GPUs with some recent fixes in Kokkos (in a branch)
>>> square graph seems OK.
>>> My experience was that square graph is better in terms of quality and we
>>> have a power user, like you all, that found this also.
>>> So I switched the default back to square graph.
>>>
>>> Interesting that you found that MIS-2 (new method) could be faster, but
>>> it might be because the two methods coarsen at different rates and that can
>>> make a big difference.
>>> (the way to test would be to adjust parameters to get similar coarsen
>>> rates, but I digress)
>>> It's hard to understand the differences between these two methods in
>>> terms of aggregate quality so we need to just experiment and have options.
>>>
>>> *** As far as your thermal problem. There was a complaint that the eigen
>>> estimates for chebyshev smoother were not recomputed for nonlinear problems
>>> and I added an option to do that and turned it on by default:
>>> Use '-pc_gamg_recompute_esteig false' to get back to the original.
>>> (I should have turned it off by default)
>>>
>>> Now, if your problem is symmetric and you use CG to compute the eigen
>>> estimates there should be no difference.
>>> If you use CG to compute the eigen estimates in GAMG (and have GAMG give
>>> them to cheby, the default) that when you recompute the eigen estimates the
>>> cheby eigen estimator is used and that will use gmres by default unless you
>>> set the SPD property in your matrix.
>>> So if you set '-pc_gamg_esteig_ksp_type cg' you want to also set
>>> '-mg_levels_esteig_ksp_type cg' (verify with -ksp_view and -options_left)
>>> CG is a much better estimator for SPD.
>>>
>>> And I found that the cheby eigen estimator uses an LAPACK *eigen* method
>>> to compute the eigen bounds and GAMG uses a *singular value* method.
>>> The two give very different results on the lid driven cavity test (ex19).
>>> eigen is lower, which is safer but not optimal if it is too low.
>>> I have a branch to have cheby use the singular value method, but I don't
>>> plan on merging it (enough churn and I don't understand these differences).
>>>
>>> *** '-pc_gamg_low_memory_threshold_filter false' recovers the old
>>> filtering method.
>>> This is the default now because there is a bug in the (new) low memory
>>> filter.
>>> This bug is very rare and catastrophic.
>>> We are working on it and will turn it on by default when it's fixed.
>>> This does not affect the semantics of the solver, just work and memory
>>> complexity.
>>>
>>> *** As far as tet4 vs tet10, I would guess that tet4 wants more
>>> aggressive coarsening.
>>> The default is to do aggressive on one (1) level.
>>> You might want more levels for tet4.
>>> And the new MIS-k coarsening can use any k (default is 2) wth
>>> '-mat_coarsen_misk_distance k' (eg, k=3)
>>> I have not added hooks to have a more complex schedule to specify the
>>> method on each level.
>>>
>>> Thanks,
>>> Mark
>>>
>>> On Tue, Oct 17, 2023 at 9:33 PM Jeremy Theler (External) <
>>> jeremy.theler-ext at ansys.com> wrote:
>>>
>>> Hey Mark
>>>
>>> Regarding the changes in the coarsening algorithm in 3.20 with respect to
>>> 3.19 in general we see that for some problems the MIS strategy gives and
>>> overall performance which is slightly better and for some others it is
>>> slightly worse than the "baseline" from 3.19.
>>> We also saw that current main has switched back to the old square
>>> coarsening algorithm by default, which again, in some cases is better and
>>> in others is worse than 3.19 without any extra command-line option.
>>>
>>> Now what seems weird to us is that we have a test case which is a heat
>>> conduction problem with radiation boundary conditions (so it is non linear)
>>> using tet10 and we see
>>>
>>>    1. that in parallel v3.20 is way worse than v3.19, although the
>>>    memory usage is similar
>>>    2. that petsc main (with no extra flags, just the defaults) recover
>>>    the 3.19 performance but memory usage is significantly larger
>>>
>>>
>>> I tried using the -pc_gamg_low_memory_threshold_filter flag and the
>>> results were the same.
>>>
>>> Find attached the log and snes views of 3.19, 3.20 and main using 4 MPI
>>> ranks.
>>> Is there any explanation about these two points we are seeing?
>>> Another weird finding is that if we use tet4 instead of tet10, v3.20 is
>>> only 10% slower than the other two and main does not need more memory than
>>> the other two.
>>>
>>> BTW, I have dozens of other log view outputs comparing 3.19, 3.20 and
>>> main should you be interested.
>>>
>>> Let me know if it is better to move this discussion into the PETSc
>>> mailing list.
>>>
>>> Regards,
>>> jeremy theler
>>>
>>>
>>>
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