Merge branch 'master' into shri/feature-dm-circuit

Conflicts:
src/dm/impls/makefile

Merge branch 'master' into barry/wirth-fusion-materials
bad manual merge needs to be fixed
this is what happens when branches hang around too long

Conflicts:
src/ts/examples/tutorials/advection-dif

Merge branch 'master' into barry/wirth-fusion-materials
bad manual merge needs to be fixed
this is what happens when branches hang around too long

Conflicts:
src/ts/examples/tutorials/advection-diffusion-reaction/ex10.c

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Merge branch 'madams/gamg-destroy' into prbrune/pcgamg-classicalinterpolationstrategies

Merge branch 'master' into madams/gamg-destroy

Conflicts:
src/ksp/pc/impls/gamg/gamg.c

Merge branch 'master' into barry/reduce-dmsetup-da-memoryusage

Conflicts:
src/dm/examples/tests/ex15.c
src/dm/examples/tutorials/ex3.c
src/dm/impls/da/da2.c
src/dm/impls/da/da3.c

Merge branch 'master' into barry/xcode

Merge branch 'barry/minor-draw-improvements' into jed/chem

Merge branch 'master' into knepley/feature-dmda-section

* master: (528 commits)
Doc: Fixed configure doc
Nightly summary: Added configure section.
TSSetErrorIfStepFails: fix __FUNCT__
TS: fi

Merge branch 'master' into knepley/feature-dmda-section

* master: (528 commits)
Doc: Fixed configure doc
Nightly summary: Added configure section.
TSSetErrorIfStepFails: fix __FUNCT__
TS: fix for TSGetRHSMats_Private() in the creation of the Arhs and Brhs matrices
protect logging of objects (which uses global variables) with PETSC_USE_LOG
error handler API had been previously changed but this example was not updated to new API.
DMPlex: Fixed bug in coordinate permutation
PetscSection: Doc fix for permutation
Bib: Added Top500 and fixed entry
fun3d: update PetscMallocValidate() usage
bugfix of MatCreateSeqAIJFromTriple() contributed by Nicolas Marsic <nicolas.marsic@montefiore.ulg.ac.be>
bib: rename ref with duplicate key
Webpage: Corrected '-dm_mat_type cusp' to 'dm_mat_type aijcusp'.
completed removing server code that was not removed in previous commit
removed PETSc webserver and configure package files that supported it
Allow calling MatGetBlockSize[s]() before matrix preallocation
SNESLINESEARCHBT: Set the norms when exiting early due to negligible step.
fix outdated PetscOptionsList
SNESQN: only monitor real part of dot product (fails with C++ complex)
Fix for multiple definitions in mat/color/interface/ custom fortran bindings
...

Conflicts:
config/builder.py
include/petscdmplex.h
src/dm/impls/da/dageometry.c
src/dm/impls/plex/examples/tests/ex4.c
src/dm/impls/plex/plex.c
src/dm/impls/plex/plexinterpolate.c

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Merge remote-tracking branch 'origin/jed/check-pointer-runtime' into knepley/fix-hash-scaling

* origin/jed/check-pointer-runtime:
Sys: add PetscCheckPointerSetIntensity -check_pointer_intensity

Merge remote-tracking branch 'origin/jed/check-pointer-runtime' into knepley/fix-hash-scaling

* origin/jed/check-pointer-runtime:
Sys: add PetscCheckPointerSetIntensity -check_pointer_intensity
Sys: add PetscFunctionBeginHot to switch to cheaper pointer checks
PetscStack: use same definitions for PetscStack functions
PetscStack: declare types regardless of debug vs. optimized

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Merge branch 'barry/saws'

Merge branch 'jed/check-pointer-runtime' into barry/saws

Conflicts:
include/petscerror.h
src/sys/error/pstack.c

Sys: add PetscCheckPointerSetIntensity -check_pointer_intensity

Offers run-time control over pointer checking. Intensity levels are

0. Never use a signal handler to check pointers
1. Use a sig

Sys: add PetscCheckPointerSetIntensity -check_pointer_intensity

Offers run-time control over pointer checking. Intensity levels are

0. Never use a signal handler to check pointers
1. Use a signal handler to check pointers when not in "hot" functions
2. Always use signal handler to check pointers

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Sys: add PetscFunctionBeginHot to switch to cheaper pointer checks

Some logging and debugging operations are expensive. In particular,
applications can see order of magnitude slowdowns when PetscCh

Sys: add PetscFunctionBeginHot to switch to cheaper pointer checks

Some logging and debugging operations are expensive. In particular,
applications can see order of magnitude slowdowns when PetscCheckPointer
configures a special signal handler (debug builds only). Additionally,
high-frequency events like MAT_SetValues are disabled by default because
it can be expensive to profile.

My marking "hot" regions, we can turn off the expensive operations by
default, but still have the ability to enable them at run-time. This
commit adds PetscFunctionBeginHot, with logic in PetscCheckPointer to
skip the check while inside a "hot" function.

Reported-by: Dave May <dave.mayhem23@gmail.com>

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Merge branch 'master' into barry/wirth-fusion-materials

Conflicts:
src/ts/examples/tutorials/advection-diffusion-reaction/ex10.c

Merged petsc/petsc into rmills/petsc master

Merge branch 'jed/checkpointer-noinline'

* jed/checkpointer-noinline:
visibility: PetscSegv functions and data lack headers
PetscCheckPointer: move from inline to implementation

visibility: PetscSegv functions and data lack headers

It's inconvenient to put these in headers because header availability is
sensitive to command line parameters, thus explicitly give them matchin

visibility: PetscSegv functions and data lack headers

It's inconvenient to put these in headers because header availability is
sensitive to command line parameters, thus explicitly give them matching
visibility.

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PetscCheckPointer: move from inline to implementation

Fixes incompatibilities with nvcc and with users building using
-std=c99. This function does enough that inlining isn't helping much
anyway.