[petsc-dev] VecGetArrayAndMemType

Mark Adams mfadams at lbl.gov
Thu Jun 24 08:58:25 CDT 2021 

OK, I tried again and deleted the arch directory every time:

(base) 09:56 (84933e400a...)|BISECTING ~/Codes/petsc2$ git bisect good
d7dd068b66a8daa3a37c9e1556b34bd8def54922 is the first bad commit
commit d7dd068b66a8daa3a37c9e1556b34bd8def54922
Author: Vaclav Hapla <vaclav.hapla at erdw.ethz.ch>
Date:   Wed Apr 14 21:22:37 2021 +0200

    HDF5: Improve timestepping.

    * add PetscViewerHDF5{Push,Pop,Is}Timestepping to control timestepping
mode
    * write timestepping attribute for datasets and check it on reading
    * fail gracefully if trying to read non-timestepped dataset in
timestepping mode and vice-versa (fix #425)
    * rewrite src/vec/vec/tutorials/ex19.c to improve coverage for
timestepping testing

 doc/documentation/changes/dev.rst         |  19 ++-
 include/petsc/private/viewerhdf5impl.h    |   2 +
 include/petscviewerhdf5.h                 |   4 +
 src/dm/impls/da/gr2.c                     |  21 ++--
 src/dm/impls/plex/plexhdf5.c              |  25 +++-
 src/sys/classes/viewer/impls/hdf5/hdf5v.c | 124 ++++++++++++++++++--
 src/vec/is/is/impls/general/general.c     |  10 +-
 src/vec/is/utils/hdf5io.c                 |  45 +++++---
 src/vec/vec/impls/mpi/pdvec.c             |  14 ++-
 src/vec/vec/tutorials/ex19.c              | 186
+++++++++++++++++-------------
 src/vec/vec/tutorials/output/ex19_2.out   |   0
 src/vec/vec/tutorials/output/ex19_3.out   |   0
 src/vec/vec/tutorials/output/ex19_4.out   |   0
 13 files changed, 320 insertions(+), 130 deletions(-)
 delete mode 100644 src/vec/vec/tutorials/output/ex19_2.out
 delete mode 100644 src/vec/vec/tutorials/output/ex19_3.out
 delete mode 100644 src/vec/vec/tutorials/output/ex19_4.out

On Thu, Jun 24, 2021 at 7:04 AM Matthew Knepley <knepley at gmail.com> wrote:

> 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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