Re: [petsc-dev] VecGetArrayAndMemType

24 Jun 2021

On Thu, Jun 24, 2021 at 9:58 AM Mark Adams <[email protected]> wrote:
...
OK, I tried again and deleted the arch directory every time:
Okay, this changes the interface for OutputSequenceNumber. It _should_ be
backwards compatible. The likely error I would think
is that it thinks you have a timestep at first but not later, however that
should be an HDF5 error. Maybe it think the timestep is always
the same and overwrites?

  Thanks,

     Matt
...
(base) 09:56 (84933e400a...)|BISECTING ~/Codes/petsc2$ git bisect good
d7dd068b66a8daa3a37c9e1556b34bd8def54922 is the first bad commit
commit d7dd068b66a8daa3a37c9e1556b34bd8def54922
Author: Vaclav Hapla <[email protected]>
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 <[email protected]> wrote:
...
On Thu, Jun 24, 2021 at 7:00 AM Mark Adams <[email protected]> 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 <[email protected]>
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 <[email protected]> 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 <[email protected]> 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 <[email protected]> wrote:
...
Landau ex1 should work. I will test.
On Wed, Jun 23, 2021 at 10:47 AM Matthew Knepley <[email protected]>
wrote:
...
On Wed, Jun 23, 2021 at 10:44 AM Junchao Zhang <
[email protected]> 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 <[email protected]>
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/>
-- 
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/>

    

Matthew Knepley

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