Merged master into barry/update-xxxviewfromoptions

Merge branch 'master' into barry/xcode

Merge branch 'barry/saws-push-header-body' into barry/saws-options

Merge branch 'jed/malloc-array'

Type arguments dropped from PetscMalloc[2-7], PetscNew, and PetscNewLog,
added PetscMalloc1 for allocating typed arrays, add PetscCalloc[1-7] for
allocating cleared (

Merge branch 'jed/malloc-array'

Type arguments dropped from PetscMalloc[2-7], PetscNew, and PetscNewLog,
added PetscMalloc1 for allocating typed arrays, add PetscCalloc[1-7] for
allocating cleared (zeroed) memory.

* jed/malloc-array:
Sys: Add pointer casts from (void **) in calls to PetscMalloc1()
Sys: drop explicit type arguments from PetscNew() and PetscNewLog()
Sys: add PetscCalloc[1-7]
Sys: add PetscMalloc1 macro, array allocation without redundant types
PetscMalloc[2-7]: remove type arguments, infer from pointer type
SNESComputeJacobianDefaultColor: fix uninitialized variable

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Sys: drop explicit type arguments from PetscNew() and PetscNewLog()

git grep -l 'PetscNew\(Log\)\?(' -- $1 | xargs perl -pi -e '
s@PetscNew\([^,;()]+ *, *@PetscNew(@;
s@PetscNewLog\(([^,;()]+) *,[^,

Sys: drop explicit type arguments from PetscNew() and PetscNewLog()

git grep -l 'PetscNew\(Log\)\?(' -- $1 | xargs perl -pi -e '
s@PetscNew\([^,;()]+ *, *@PetscNew(@;
s@PetscNewLog\(([^,;()]+) *,[^,;()]+, *@PetscNewLog($1,@'

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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 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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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

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

Merged petsc/petsc into rmills/petsc master.

added const to char arguement

Merged petsc/petsc into rmills/petsc master

Merge branch 'barry/rm-xxxregisterdynamic' into jed/ts-eimex

PetscObjectComposeFunctionDynamic() and TSRegisterDynamic() were
replaced by PetscObjectComposeFunction() and TSRegister(), both of which

Merge branch 'barry/rm-xxxregisterdynamic' into jed/ts-eimex

PetscObjectComposeFunctionDynamic() and TSRegisterDynamic() were
replaced by PetscObjectComposeFunction() and TSRegister(), both of which
drop the string name argument.

* barry/rm-xxxregisterdynamic: (82 commits)
...

Conflicts:
src/ts/interface/tsregall.c

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Merge branch 'barry/ams' into master

* commit 'eb4227cfdd169cc03749ba3ef12d3932f2f322bf': (24 commits)
forgotten files
basic snooping on PetscStack is now working
split AMSJavascript.py into A

Merge branch 'barry/ams' into master

* commit 'eb4227cfdd169cc03749ba3ef12d3932f2f322bf': (24 commits)
forgotten files
basic snooping on PetscStack is now working
split AMSJavascript.py into AMS.py for AMS javascript and AMSSnoopObjects.py for example showing published objects
fix bug in previous commit
added error returns for JSON-RPC AMS calls
don't let web accessor change length of array setting to publisher
Pass arrays of values back from webserver to AMS publisher
fix for last commit, missing errorcode and wrong variable name
KSPLogResidualHistory and SNESLogConvergenceHistory need to lock for AMS and have error checking when called
shutdown webserver if you started it on PetscFinalize(), what about when crash, should still shut it down
Added support for starting server automatically by application code messed around finding a bug in AMS
got value back from webclient to application
goddman script Jed sent me doesn;t work, it loses changes
split webserver into standalone problem that is not part of running PETSc application had to do this since impossible for AMS publisher and accessor to be in same application better to just totally redo AMS! But that is to large a project
moved webserver code to its own directory and file
added callback for changable fields in pyjs representation of AMS memories
add AMS viewer for PC, server can only run without any memory debugging
changed AMS publishing to use the Viewer model added simple AMS viewer for mat,ksp,snes,ts added --ksp/snes/ts_view_pre for starting the viewer before the solve (ugly but useful for AMS) added PetscStackCalls around AMS function calls when appropriate (note do not want these in webserver because do not webserver stopping just because AMS server is down
more work on moving AMS model to viewer
Fix for SNESSetConvergenceHistory() when input a is null
...

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Merge branch 'master' into jed/ts-eimex

Sync to include Git conversion, PETSC_EXTERN, and minor API changes.

Conflicts:
src/ts/interface/tsregall.c

moved webserver code to its own directory and file

add AMS viewer for PC, server can only run without any memory debugging

changed AMS publishing to use the Viewer model
added simple AMS viewer for mat,ksp,snes,ts
added --ksp/snes/ts_view_pre for starting the viewer before the solve (ugly but useful for AMS)
added PetscS

changed AMS publishing to use the Viewer model
added simple AMS viewer for mat,ksp,snes,ts
added --ksp/snes/ts_view_pre for starting the viewer before the solve (ugly but useful for AMS)
added PetscStackCalls around AMS function calls when appropriate (note do not want these in webserver because do not webserver stopping just because AMS server is down

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more work on moving AMS model to viewer

cleanup of AMS viewer, handle JSON-RPC multiple Comms

Hg-commit: 1c6c1b742ae96264dbd8aad2eb769b7fe76641f3

work on AMS interface, consistent naming, ams.h not included in petscviewer.h, no ifdefs

Hg-commit: 642571a1dc7109fdb7e5b0abb23bf260d10eb970

more work on AMS JSON-RPC Web interface

Hg-commit: 610511a68dcbe0d01c88ee4f8cc7926484939c33

developers nots for AMS JSON-RPC

Hg-commit: 1942f412783e54dc5cc9034876b2ad7aa84c6c8a