https://gitlab.com/petsc/petsc/-/commit/d7dd068b66a8daa3a37c9e1556b34bd8def54922
On Thu, Jun 24, 2021, at 11:40 AM, Mark Adams wrote:
> How does one view a commit on gitlab?
> I would like to look at d7dd068b66a8daa3a37c9e1556b34bd8def54922
>
> On Thu, Jun 24, 2021 at 9:58 AM Mark Adams <mfad...@lbl.gov> wrote:
>> 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.ha...@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 <knep...@gmail.com> wrote:
>>> On Thu, Jun 24, 2021 at 7:00 AM Mark Adams <mfad...@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.zh...@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 <mfad...@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 <mfad...@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 <mfad...@lbl.gov> wrote:
>>>>>>>> Landau ex1 should work. I will test.
>>>>>>>>
>>>>>>>> On Wed, Jun 23, 2021 at 10:47 AM Matthew Knepley <knep...@gmail.com>
>>>>>>>> wrote:
>>>>>>>>> On Wed, Jun 23, 2021 at 10:44 AM Junchao Zhang
>>>>>>>>> <junchao.zh...@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 <mfad...@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/
>>>
>>>
>>> --
>>> 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/
