[petsc-dev] VecGetArrayAndMemType

Matthew Knepley knepley at gmail.com
Thu Jun 24 06:04:02 CDT 2021 

On Thu, Jun 24, 2021 at 7:00 AM Mark Adams <mfadams at lbl.gov> wrote:

> OK, this is what I get with bisect:
>
> (base) 06:54 (c3b2925bfb...)|BISECTING ~/Codes/petsc2$ git bisect good
> The merge base c3b2925bfbe1c0a0b3a69c9a76295d0747e33d47 is bad.
> This means the bug has been fixed between
> c3b2925bfbe1c0a0b3a69c9a76295d0747e33d47 and
> [09da24df01e50defd94bc4f7396f866a808ecea5
> c3b2925bfbe1c0a0b3a69c9a76295d0747e33d47].
>
> (base) 06:56 (v3.15.1) ~/Codes/petsc2$ git checkout
> c3b2925bfbe1c0a0b3a69c9a76295d0747e33d47
> Previous HEAD position was 09da24df01 Increase patchlevel to 3.15.1
> HEAD is now at c3b2925bfb Merge branch 'knepley-main-patch-78504' into
> 'release'
> (base) 06:56 (c3b2925bfb...) ~/Codes/petsc2$
>

I do not understand. Neither of those commits do anything.

   Matt


> On Wed, Jun 23, 2021 at 11:14 PM Junchao Zhang <junchao.zhang at gmail.com>
> wrote:
>
>> Mark,
>>   I am not sure what your problem is.  If it is a regression, can you
>> bisect it?
>> --Junchao Zhang
>>
>>
>> On Wed, Jun 23, 2021 at 4:04 PM Mark Adams <mfadams at lbl.gov> wrote:
>>
>>> I also tried commenting out the second VecView, so there is just one
>>> step in the file, and the .h5 file is only 8 bytes smaller and the .xmf
>>> file goes from 5373  bytes to 3090 bytes.
>>>
>>> On Wed, Jun 23, 2021 at 4:01 PM Mark Adams <mfadams at lbl.gov> wrote:
>>>
>>>> It is not a device issue but it is a regression.
>>>>
>>>> Landau ex1 is tiny and just calls VecView before and after the TSsolve,
>>>> which is one time step. If you add "*-dm_view hdf5:f.h5 -vec_view
>>>> hdf5:f.h5::append -dm_landau_Ez 10.*" to landau/ex1 (see below), you
>>>> get an h5 file with two time steps, as it should be.
>>>> This is a huge electric field, Ez=10, which makes the electron
>>>> distribution (u_e) get visibly pulled off center.
>>>> In Visit, both time steps have identical data that is clearly after the
>>>> solve and not the initial condition (see attached).
>>>>
>>>> I ran this again with -ex1_ts_max_steps 0 and get the expected result
>>>> of two steps/frames with the symmetric initial condition in both. THis is
>>>> correct behavior.
>>>>
>>>> Any ideas?
>>>> Thanks
>>>>
>>>> diff --git a/src/ts/utils/dmplexlandau/tutorials/ex1.c
>>>> b/src/ts/utils/dmplexlandau/tutorials/ex1.c
>>>> index 9e4c8f1b61..31dfda2fad 100644
>>>> --- a/src/ts/utils/dmplexlandau/tutorials/ex1.c
>>>> +++ b/src/ts/utils/dmplexlandau/tutorials/ex1.c
>>>> @@ -66,6 +66,6 @@ int main(int argc, char **argv)
>>>>    test:
>>>>      suffix: 0
>>>>      requires: p4est !complex
>>>> -    args: -petscspace_degree 3 -petscspace_poly_tensor 1
>>>> -dm_landau_type p4est -dm_landau_ion_masses 2,4 -dm_landau_ion_charges 1,18
>>>> -dm_landau_thermal_temps 5,5,.5 -dm_landau_n 1.00018,1,1e-5 -dm_landau_n_0
>>>> 1e20 -ex1_ts_monitor -ex1_snes_rtol 1.e-14 -ex1_snes_stol 1.e-14
>>>> -ex1_snes_monitor -ex1_snes_converged_reason -ex1_ts_type arkimex
>>>> -ex1_ts_arkimex_type 1bee -ex1_ts_max_snes_failures -1 -ex1_ts_rtol 1e-1
>>>> -ex1_ts_dt 1.e-1 -ex1_ts_max_time 1 -ex1_ts_adapt_clip .5,1.25
>>>> -ex1_ts_adapt_scale_solve_failed 0.75
>>>> -ex1_ts_adapt_time_step_increase_delay 5 -ex1_ts_max_steps 1 -ex1_pc_type
>>>> lu -ex1_ksp_type preonly -dm_landau_amr_levels_max 7
>>>> -dm_landau_domain_radius 5 -dm_landau_amr_re_levels 0 -dm_landau_re_radius
>>>> 1 -dm_landau_amr_z_refine1 1 -dm_landau_amr_z_refine2 0
>>>> -dm_landau_amr_post_refine 0 -dm_landau_z_radius1 .1 -dm_landau_z_radius2
>>>> .1 -dm_refine 1 -dm_landau_gpu_assembly false
>>>> +    args: -petscspace_degree 3 -petscspace_poly_tensor 1
>>>> -dm_landau_type p4est -dm_landau_ion_masses 2,4 -dm_landau_ion_charges 1,18
>>>> -dm_landau_thermal_temps 5,5,.5 -dm_landau_n 1.00018,1,1e-5 -dm_landau_n_0
>>>> 1e20 -ex1_ts_monitor -ex1_snes_rtol 1.e-14 -ex1_snes_stol 1.e-14
>>>> -ex1_snes_monitor -ex1_snes_converged_reason -ex1_ts_type arkimex
>>>> -ex1_ts_arkimex_type 1bee -ex1_ts_max_snes_failures -1 -ex1_ts_rtol 1e-1
>>>> -ex1_ts_dt 1.e-1 -ex1_ts_max_time 1 -ex1_ts_adapt_clip .5,1.25
>>>> -ex1_ts_adapt_scale_solve_failed 0.75
>>>> -ex1_ts_adapt_time_step_increase_delay 5 -ex1_ts_max_steps 1 -ex1_pc_type
>>>> lu -ex1_ksp_type preonly -dm_landau_amr_levels_max 7
>>>> -dm_landau_domain_radius 5 -dm_landau_amr_re_levels 0 -dm_landau_re_radius
>>>> 1 -dm_landau_amr_z_refine1 1 -dm_landau_amr_z_refine2 0
>>>> -dm_landau_amr_post_refine 0 -dm_landau_z_radius1 .1 -dm_landau_z_radius2
>>>> .1 -dm_refine 1 -dm_landau_gpu_assembly false *-dm_view hdf5:f.h5
>>>> -vec_view hdf5:f.h5::append -dm_landau_Ez 10.*
>>>>
>>>>  TEST*/
>>>>
>>>> On Wed, Jun 23, 2021 at 1:38 PM Mark Adams <mfadams at lbl.gov> wrote:
>>>>
>>>>> Landau ex1 should work. I will test.
>>>>>
>>>>> On Wed, Jun 23, 2021 at 10:47 AM Matthew Knepley <knepley at gmail.com>
>>>>> wrote:
>>>>>
>>>>>> On Wed, Jun 23, 2021 at 10:44 AM Junchao Zhang <
>>>>>> junchao.zhang at gmail.com> wrote:
>>>>>>
>>>>>>> Use VecGetArrayRead/Write() to get up-to-date host pointers to the
>>>>>>> vector array.
>>>>>>>
>>>>>>
>>>>>> I think Mark is saying that those are not working. We do call
>>>>>> VecGetArrayRead() in the HDF5 code.
>>>>>>
>>>>>> Mark, it seem like a small broken code is necessary.
>>>>>>
>>>>>>   Thanks,
>>>>>>
>>>>>>     Matt
>>>>>>
>>>>>>
>>>>>>> --Junchao Zhang
>>>>>>>
>>>>>>>
>>>>>>> On Wed, Jun 23, 2021 at 9:15 AM Mark Adams <mfadams at lbl.gov> wrote:
>>>>>>>
>>>>>>>> First, there seem to be two pages for VecGetArrayAndMemType (one
>>>>>>>> has a pointer to the other).
>>>>>>>>
>>>>>>>> So I need to get a CPU array for HDF5 viewing. Totally broken for
>>>>>>>> devices.
>>>>>>>>
>>>>>>>> I don't find a VecGetArrayCpu[HOST] that does the right thing.
>>>>>>>>
>>>>>>>> Perhaps have VecGetArrayAndMemType return a valid CPU pointer when
>>>>>>>> "mtype==NULL"?
>>>>>>>>
>>>>>>>> Mark
>>>>>>>>
>>>>>>>
>>>>>>
>>>>>> --
>>>>>> 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/~knepley/>
>>>>>>
>>>>>

-- 
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/~knepley/>
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