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/> >