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/ >>>>>>>> <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/> >> >