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fix outdated PetscOptionsList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 'master' into knepley/feature-fem-dgspace

* master: (593 commits)
Bib: Added Top500 and fixed entry
fun3d: update PetscMallocValidate() usage
bib: rename ref with duplicate key

Merge branch 'master' into knepley/feature-fem-dgspace

* master: (593 commits)
Bib: Added Top500 and fixed entry
fun3d: update PetscMallocValidate() usage
bib: rename ref with duplicate key
Webpage: Corrected '-dm_mat_type cusp' to 'dm_mat_type aijcusp'.
Allow calling MatGetBlockSize[s]() before matrix preallocation
SNESLINESEARCHBT: Set the norms when exiting early due to negligible step.
SNESQN: only monitor real part of dot product (fails with C++ complex)
Corrected the #include statement in the man pages for the PetscObjectComposedDataSet/Getwhatever routines.
DMPlex: Added doc for DMPlexGetHybridBounds()
winzip: detect if winzip is used to extract petsc.tar.gz and error out.
configure: remove self.archIndependent as its not being used. [it is used to create externalpackages/package/arch dir which is unused]
configure: fix packages using package-dir/PETSC_ARCH as out-of-source-build location Perhaps this should be changed to package-dir/build?
configure: remove dead code previously used to download BuildSystem
configure: check if compilerDefines [and compilerFixes] exist in framework before using them
configure: save/restore reconfigure.py when --with-clean is used
configure: add --with-clean option to delete buildfiles/externalpackages in PETSC_DIR/PETSC_ARCH and potential externalpackages in --with-external-package-dir/PETSC_ARCH
configure: With --with-externalpackages-dir=dir store/build packages in dir/PETSC_ARCH
Add MatSeqSBAIJSetPreallocationCSR()
configure: switch to using PETSC_DIR/PETSC_ARCH/externalpackages by updating package.py to use externalpackages.py as the externalPackagesDirProvider
configure: move dead code configureExternalPackagesDir() from petscdir.py to externalpackagesdir.py Also set PETSC_DIR/PETSC_ARCH/externalpackages as the externalpackagesdir
...

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manually remove old AMS code that got sucked in from master

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

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

Merge branch 'master' into barry/saws

Conflicts:
src/ksp/pc/impls/gamg/gamg.c
src/sys/classes/viewer/impls/ams/ams.c
src/sys/objects/pinit.c

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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PetscStack: use same definitions for PetscStack functions

If the user compiles their code with debugging, perhaps calling
PetscStack functions, it would be useful for the implementations to make
a b

PetscStack: use same definitions for PetscStack functions

If the user compiles their code with debugging, perhaps calling
PetscStack functions, it would be useful for the implementations to make
a best-effort at displaying the stack usefully when they subsequently
LD_PRELOAD an optimized version of the library. These functions are
tiny so code size is not an excuse for keeping the complexity of
different versions.

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PetscStack: declare types regardless of debug vs. optimized

There is no performance advantage to avoiding defining the PetscStack
type and it is simpler to have them defined when switching between d

PetscStack: declare types regardless of debug vs. optimized

There is no performance advantage to avoiding defining the PetscStack
type and it is simpler to have them defined when switching between debug
and optimized versions of PETSc.

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Merge branch 'balay/remove-sdir'

__SDIR__ is gone. This is an ABI change (PetscError) so dependent
packages must be recompiled.

* balay/remove-sdir:
__SDIR__: remove remaining traces and documen

Merge branch 'balay/remove-sdir'

__SDIR__ is gone. This is an ABI change (PetscError) so dependent
packages must be recompiled.

* balay/remove-sdir:
__SDIR__: remove remaining traces and document in changes.html
__SDIR__: remove usage of __SDIR__ from PETSc sources.

This merge fixes one instance of __SDIR__ that was added after
'balay/remove-sdir' branched off.

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__SDIR__: remove usage of __SDIR__ from PETSc sources.

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

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

updated to _ and __ variable name support in SAWs
when displaying options don't display man_# or text_#

Merge branch 'barry/dmvecmattypes' into barry/saws

Needed to work with version of PETSc that did not have constant calls to VecSetFromOptions() etc

Conflicts:
src/ksp/ksp/interface/ams/kspams.c
s

Merge branch 'barry/dmvecmattypes' into barry/saws

Needed to work with version of PETSc that did not have constant calls to VecSetFromOptions() etc

Conflicts:
src/ksp/ksp/interface/ams/kspams.c
src/snes/impls/composite/snescomposite.c
src/snes/impls/gs/snesgs.c
src/snes/impls/nasm/nasm.c
src/snes/impls/ngmres/snesngmres.c

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SAWs now compiles and runs in PETSc with parallel PETSc

added PetscStackCallSAWs() everywhere possible

introduced published variables that are not displayed by default marked by _

fix calls to publish SAWs

locking object cannot involve locking stack or code hangs on the second lock