Tao: change TaoCancelMonitors() to TaoMonitorCancel()

Merge remote-tracking branch 'origin/release'

Minor fixes to website material

Modified ex88 to test MatMultHermitianTranspose_Shell and MatMultHermitianTransposeAdd_Shell and to test with complex numbers

Merge branch 'barry/2023-06-07/optimize-multivecs-zhang' into 'main'

Optimize VecMDot_Seq as suggested by Junchao Zhang using BLAS 2 gemv

See merge request petsc/petsc!6580

GAMG: Add GAMG smoother option to create ASMs with HEM coarsening

Vec: add GEMV optimizations for VecMDot and friends for VecStandard

Remove KSPPIPEFGMRES from example with skip convergence test since very sensitive to happy ending

Appears to have a sweet spot of

Vec: add GEMV optimizations for VecMDot and friends for VecStandard

Remove KSPPIPEFGMRES from example with skip convergence test since very sensitive to happy ending

Appears to have a sweet spot of much better performance for smallish vectors then
matches unrolled code for large vectors

Sample results on Barry's Apple M2 Laptop (using Apple's BLAS)

./ex19 -da_refine 5 -pc_type none -log_view -ksp_gmres_preallocate -ksp_view

Vector length 37,636

VecMDot 1920 1.0 1.9707e-01 1.0 2.23e+09 1.0 0.0e+00 0.0e+00 0.0e+00 25 29 0 0 0 25 29 0 0 0 11291

-vec_mdot_use_gemv

VecMDot 1920 1.0 7.5098e-02 1.0 2.23e+09 1.0 0.0e+00 0.0e+00 0.0e+00 12 29 0 0 0 12 29 0 0 0 29693
VecMDot 1920 1.0 8.1523e-02 1.0 2.23e+09 1.0 0.0e+00 0.0e+00 0.0e+00 12 29 0 0 0 12 29 0 0 0 27353
VecMDot 1920 1.0 7.0889e-02 1.0 2.23e+09 1.0 0.0e+00 0.0e+00 0.0e+00 11 29 0 0 0 11 29 0 0 0 31456

-da_refine 6

Vector length 148,996

VecMDot 4340 1.0 1.7666e+00 1.0 2.00e+10 1.0 0.0e+00 0.0e+00 0.0e+00 20 29 0 0 0 20 29 0 0 0 11319

-vec_mdot_use_gemv

VecMDot 4422 1.0 1.3725e+00 1.0 2.04e+10 1.0 0.0e+00 0.0e+00 0.0e+00 15 29 0 0 0 15 29 0 0 0 14884
VecMDot 4422 1.0 1.4354e+00 1.0 2.04e+10 1.0 0.0e+00 0.0e+00 0.0e+00 16 29 0 0 0 16 29 0 0 0 14231

./ex19 -da_refine 7 -pc_type none -log_view -ksp_gmres_preallocate -ksp_view -vec_mdot_use_gemv -ksp_max_it 100 -snes_max_it 1

Vector length 592,900

VecMDot 100 1.0 1.5915e-01 1.0 1.72e+09 1.0 0.0e+00 0.0e+00 0.0e+00 14 27 0 0 0 14 27 0 0 0 10804

-vec_mdot_use_gemv

VecMDot 100 1.0 1.6854e-01 1.0 1.72e+09 1.0 0.0e+00 0.0e+00 0.0e+00 14 27 0 0 0 14 27 0 0 0 10230
VecMDot 100 1.0 1.5698e-01 1.0 1.72e+09 1.0 0.0e+00 0.0e+00 0.0e+00 14 27 0 0 0 14 27 0 0 0 10983

-da_refine 8

vector length 2,365,444

VecMDot 100 1.0 6.2499e-01 1.0 6.86e+09 1.0 0.0e+00 0.0e+00 0.0e+00 13 27 0 0 0 13 27 0 0 0 10976

-vec_mdot_use_gemv

VecMDot 100 1.0 6.8197e-01 1.0 6.88e+09 1.0 0.0e+00 0.0e+00 0.0e+00 14 27 0 0 0 14 27 0 0 0 10087

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Merge remote-tracking branch 'origin/release'

Merge branch 'stefanozampini/minsurf-local' into 'main'

Improve support for nonlinear domain decomposition solvers

See merge request petsc/petsc!7084

DMPLEXSNES: support objective functions

SNESNASM: some fixes

- let subsneses inherit the communicators from the local dms
- need to inject boundary values if boundarylocal is present
- fix missing convergence error for max_its == 0
- remo

SNESNASM: some fixes

- let subsneses inherit the communicators from the local dms
- need to inject boundary values if boundarylocal is present
- fix missing convergence error for max_its == 0
- remove PCLU defaults

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Update references in the manual pages to use Sphinx citation processing

Merge branch 'ilya-fursov/ts-fixevent2' into 'main'

TSEvent: refactor and fix bugs, add TSSetPostEventStep()

See merge request petsc/petsc!6752

Implement setting two distinct post-event steps

The two post-event steps are managed by:
TSSetPostEventStep(), -ts_event_post_event_step,
TSSetPostEventSecondStep(), -ts_event_post_event_second_step

Implement setting two distinct post-event steps

The two post-event steps are managed by:
TSSetPostEventStep(), -ts_event_post_event_step,
TSSetPostEventSecondStep(), -ts_event_post_event_second_step.

(The latter function and option are replacement for the original PETSc
TSSetPostEventIntervalStep(), -ts_event_post_eventinterval_step,
with some change of overall behaviour of 1st + 2nd steps).

Also, reduce the number of tests ~ 4 times.

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TSEvent: refactor and fix bugs, add TSSetPostEventStep()

Refactor the core algorithm for resolution of events: TSEventHandler()
and the helper functions, fixing the existing bugs.

Chang

TSEvent: refactor and fix bugs, add TSSetPostEventStep()

Refactor the core algorithm for resolution of events: TSEventHandler()
and the helper functions, fixing the existing bugs.

Change event indicator functions from PetscScalar to PetscReal.
Change the API of TSSetEventHandler(): in the user `indicator()` callback,
the 'fvalue' argument type changed from PetscScalar[] to PetscReal[].

Add TSSetPostEventStep(), deprecate TSSetPostEventIntervalStep().
Deprecate option -ts_event_post_eventinterval_step.

Fix bugs in interaction of TSEvent with tspan.
Add six new test examples.

Below are the examples of bugs fixed by this patch.
The source codes (ex3.c, ex3span.c, ex4.c, ex5.c) can be found
in src/ts/event/tests. To run them with the older Petsc versions,
one would need to comment out "#define NEW_VERSION".
Behaviour for three library versions is reported below:
* ORIG: current Petsc version, before the proposed patch.
* 6688: independently of the proposed patch, Merge Request 6688 was
developed, which fixed some bugs with zero-crossing directions.
* NEW : the proposed patch.

./ex3 -ts_monitor -ts_event_monitor -ts_view -ts_type beuler \
-ts_adapt_type basic -flg -V 1e9 -ts_adapt_dt_min 1e-6 -change5 1 -dir 1
* ORIG: fails to resolve 5 out of 6 events, and resolves 23 incorrect events.
* 6688: fails to exit the TSEvent iteration via the step size (bracket size)
criterion.
* NEW : ok, resolves all 6 events.

./ex4 -ts_adapt_type basic -ts_type rk -ts_dt 0.25 -ts_event_tol 1e-8 \
-dir 0 -ts_adapt_dt_min 1e-10 -ts_view -ts_monitor -ts_event_monitor
* ORIG: only reaches t = 0.0300236 after 10000 TS steps.
* 6688: only reaches t = 0.0300236 after 10000 TS steps.
* NEW : ok, reaches the final time t = 4.0 after 96 TS steps, resolving
all 16 events.

./ex5 -ts_monitor -ts_event_monitor -ts_type rk -ts_adapt_type basic \
-ts_view -ts_dt 0.25 -flg -dir 0
* ORIG: only reaches t = 4.0 after 10000 TS steps, erroneously reports
event at t = 4.0 around 5000 times.
* 6688: only reaches t = 4.0 after 10000 TS steps.
* NEW : ok, reaches the final time t = 10.0 after 99 TS steps, resolving
all 34 events.

./ex5 -ts_monitor -ts_event_monitor -ts_type rk -ts_adapt_type basic \
-ts_view -ts_dt 0.25 -flg -dir 1
* ORIG: fails, starts taking negative time steps, no events are correctly
resolved.
* 6688: ok, but slower: 90 TS steps to resolve all 17 events.
* NEW : ok, and faster: 48 TS steps to resolve all 17 events.

./ex5 -ts_monitor -ts_event_monitor -ts_type rk -ts_adapt_type basic \
-ts_view -ts_dt 0.25 -flg -dir -1
* ORIG: fails, starts taking 'nan' time steps.
* 6688: mostly fails, only reaches t = 4.99993 after 10000 TS steps.
* NEW : ok, reaches the final time t = 10.0 after 74 TS steps, resolving
all 17 events.

The same run in parallel:
mpirun -n 2 ./ex5 -ts_monitor -ts_event_monitor -ts_type rk \
-ts_adapt_type basic -ts_view -ts_dt 0.25 -flg -dir -1
* ORIG: fails, starts taking negative time steps, exits with runtime error.
* 6688: mostly fails, only reaches t = 3, besides, the parallel run is not
consistent with the serial run (see above).
* NEW : ok, reaches the final time t = 10.0 after 74 TS steps, resolving
all 17 events.

./ex3span -ts_monitor -ts_event_monitor
* ORIG: (confused by events) misses tspan points: 4.02, 4.21, 4.98, 5.01,
5.21, 5.98, 6, 6.01, 6.02, 6.21, 6.99, 7.21, 8.01, 8.21, 9.01.
* 6688: (confused by events) misses tspan points: 4.02, 4.21, 4.98, 5.01,
5.21, 5.98, 6, 6.01, 6.02, 6.21, 6.99, 7.21, 8.01, 8.21, 9.01.
* NEW : ok.

./ex3span -ts_monitor -ts_event_monitor -ts_event_post_event_step 0.5
* ORIG: misses the majority of tspan points (except 0.01 and 0.21),
and also resolves the last event location at wrong time t = 9.21.
* 6688: misses the majority of tspan points (except 0.01 and 0.21),
and also resolves the last event location at wrong time t = 9.21.
* NEW : ok.

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PetscFE: Add Jacobian type argument to PetscFEIntegrateBdJacobian()

DMDASNES: support using user context if operation context is not provided

Add MPI_Allreduce inside the main objective driver

SNESNEWTONTR: code improvements

support QN models

accepts Cauchy point if it is on the boundary

Enlarge trust region only if direction is on the boundary

Use previously estimated largest eigenval

SNESNEWTONTR: code improvements

support QN models

accepts Cauchy point if it is on the boundary

Enlarge trust region only if direction is on the boundary

Use previously estimated largest eigenvalue of hessian in minimum decrease

Customize trust region norm

Fix dogleg path computation

Update output files and add tests

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MATLMVM: must call reset if history size changes

PCLMVM: support automatic updates and operators of type MATLMVM

Merge branch 'hdf5-1.14.0' into 'main'

HDF5 1.14.3

See merge request petsc/petsc!6116

drop support for MED files

Fix PetscOptionsGetViewer() so it works in a thread-safe way

When PetscOptionsGetViewer() returns, for example, PETSC_VIEWER_STDOUT_SELF the same object is shared
by all threads that call PetscOptio

Fix PetscOptionsGetViewer() so it works in a thread-safe way

When PetscOptionsGetViewer() returns, for example, PETSC_VIEWER_STDOUT_SELF the same object is shared
by all threads that call PetscOptionsGetViewer(). In the previous code PetscObjectReference() and
dereference (via PetscViewerDestroy() where called on the viewer by multiple threads after the viewer
was accessed thus corrupting the object.

This branch introduces a PetscOptionsRestoreViewer() that allows not doing the referencing and dereferencing
on persistant viewers, thus removing the specific race condition above.

Other possible solutions include

Use a lock on each PetscObjectReference/Dereference() just in case they are shared. Could be time consuming so one
could mark each object as either threadshared or independent and only do the locks on threadshared objects. This lowers
the cost but would require more extensive changes to PETSc infrastructure. And I do not know if this shared/not shared model
is what we need in the long run, though it might be.

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Fix bugs in handling PetscViewerGetSubViewer() and tabing in ASCII viewers

Reported-by: Pierre Jolivet

Merge branch 'stefanozampini/pc-housekeeping' into 'main'

Some housekeeping on default PC

See merge request petsc/petsc!6997