Re: [petsc-dev] VecGetArrayAndMemType

24 Jun 2021

On Thu, Jun 24, 2021 at 6:50 AM Mark Adams <[email protected]> wrote:
...
Good idea.
I have it on my laptop and I have 8 bisection steps to do (the most recent
version tag is good, yes!), but the repo seems broken at ea672e62cc.
I am looking at the code and these vars are in fact not defined. I
commented out this block and am pressing on.
However, this looks like a bug.
You should be able to reproduce this by bisection with main=good and
v3.15.1=bad.
First step fails with this:
/Users/markadams/Codes/petsc2/src/dm/dt/fe/impls/basic/febasic.c:1138:11:
error: use of undeclared identifier 'n0'
      if (n0) {
          ^
/Users/markadams/Codes/petsc2/src/dm/dt/fe/impls/basic/febasic.c:1143:11:
error: use of undeclared identifier 'n1'
      if (n1) {
          ^
/Users/markadams/Codes/petsc2/src/dm/dt/fe/impls/basic/febasic.c:1148:11:
error: use of undeclared identifier 'n2'
      if (n2) {
          ^
/Users/markadams/Codes/petsc2/src/dm/dt/fe/impls/basic/febasic.c:1153:11:
error: use of undeclared identifier 'n3'
      if (n3) {
          ^
4 errors generated.
make[3]: *** [arch-macosx-gnu-g/obj/dm/dt/fe/impls/basic/febasic.o] Error 1
make[3]: *** Waiting for unfinished jobs....
make[2]: *** [libs] Error 2
**************************ERROR*************************************
  Error during compile, check arch-macosx-gnu-g/lib/petsc/conf/make.log
  Send it and arch-macosx-gnu-g/lib/petsc/conf/configure.log to
[email protected]
********************************************************************
make[1]: *** [all] Error 1
make: *** [all] Error 2
*(base) 06:32 2 (ea672e62cc...)|BISECTING ~/Codes/petsc2$ rm -fr
arch-macosx-gnu-g/*
Can you nudge it to the next commit? It looks like I split up the sets
incorrectly for the PetscWeakForm change.

   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/>

    

Matthew Knepley

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