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fix outdated PetscOptionsList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 branch 'barry/saws'

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

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

fix name for PetscOptionsFList() and get FList() and EList() working properly with SAWs legal values

Merge branch 'barry/fix-PetscObjectPrintClassNamePrefixType'

* barry/fix-PetscObjectPrintClassNamePrefixType:
update tests of src/mat/examples/tests/ex136.c
Use classname in object for object na

Merge branch 'barry/fix-PetscObjectPrintClassNamePrefixType'

* barry/fix-PetscObjectPrintClassNamePrefixType:
update tests of src/mat/examples/tests/ex136.c
Use classname in object for object name when calling PetscObjectPrintClassNamePrefixType() instead of some string with less precise name passed in

Conflicts:
src/snes/interface/snes.c

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Merged petsc/petsc into rmills/petsc master.

Use classname in object for object name when calling PetscObjectPrintClassNamePrefixType() instead of some string with less precise name passed in

Modified interface for TS error norm calculation.

Renamed TSErrorNormWRMS to TSErrorWeightedNorm.
Implemented infinite weighted norm calculation.
Added option -ts_adapt_wnormtype to set the type of

Modified interface for TS error norm calculation.

Renamed TSErrorNormWRMS to TSErrorWeightedNorm.
Implemented infinite weighted norm calculation.
Added option -ts_adapt_wnormtype to set the type of norm computed.

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Merge branch 'jed/tsgetadapt'

* jed/tsgetadapt:
TSGetAdapt: restore name from TSGetTSAdapt

TSGetAdapt: restore name from TSGetTSAdapt

This function was called TSGetAdapt in petsc-3.3 and was changed to
TSGetTSAdapt in:

commit ad6bc4219076b084d4a49a29c04a77944f238f10
Author: Barry Smi

TSGetAdapt: restore name from TSGetTSAdapt

This function was called TSGetAdapt in petsc-3.3 and was changed to
TSGetTSAdapt in:

commit ad6bc4219076b084d4a49a29c04a77944f238f10
Author: Barry Smith <bsmith@mcs.anl.gov>
Date: Sun Dec 9 18:14:24 2012 -0600

My first TS restart just 8 million other changes needed PETSc!
TSGetAdapt() changed to TSGetTSAdapt() because it gets a TSAdapt object, not an Adapt object
added TSAdapt binary view and load

This rationale does not match the more established convention used by
functions such as the following.

MatGetInfo
MatGetColoring
MatGetNullSpace
MatGetLocalToGlobalMapping
MatGetLocalToGlobalMappingBlock (31 characters)
SNESGetConvergedReason

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Merge branch 'barry/rm-xxxregisteralldestroy'

* barry/rm-xxxregisteralldestroy:
TSSSP: Fix to use proper TSSSPInitializePackage() system
flag should have been false
removed unnneeded and unuse

Merge branch 'barry/rm-xxxregisteralldestroy'

* barry/rm-xxxregisteralldestroy:
TSSSP: Fix to use proper TSSSPInitializePackage() system
flag should have been false
removed unnneeded and unused XXXRegisterDestroy() routines
removed PetscFunctionListDestroyAll() and put PetscFunctionListDestroy(&XXXList) into the package finalize

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Merged petsc/petsc into rmills/petsc master

removed unnneeded and unused XXXRegisterDestroy() routines

removed PetscFunctionListDestroyAll() and put PetscFunctionListDestroy(&XXXList) into the package finalize

Merge branch 'jed/functionlist-nocast'

* jed/functionlist-nocast:
docs: simplify explanation of function lists/composition
PetscObjectQueryFunction: use macro to hide PetscVoidFunction* cast
P

Merge branch 'jed/functionlist-nocast'

* jed/functionlist-nocast:
docs: simplify explanation of function lists/composition
PetscObjectQueryFunction: use macro to hide PetscVoidFunction* cast
PetscFunctionListAdd: use macro to hide (PetscVoidFunction) cast
PetscFunctionListFind: use macro to hide (PetscVoidFunction*) cast

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Merge branch 'barry/rm-xxxregisterdynamic'

* barry/rm-xxxregisterdynamic:
Registration: remove stale 'XXRegisterDynamic)' entries in man pages
TS examples: fix use of PetscFunctionList and add t

Merge branch 'barry/rm-xxxregisterdynamic'

* barry/rm-xxxregisterdynamic:
Registration: remove stale 'XXRegisterDynamic)' entries in man pages
TS examples: fix use of PetscFunctionList and add to nightlies
Changes: Note updates to XRegisterDynamic/PetscObjectComposeFunctionDynamic
PetscObjectComposeFunctionDynamic: remove stale docs and usage
developers.tex: remove complications from function composition with dlls
removed string version of function name for XXXRegister(), PetscFunctionListAdd() and PetscObjectComposeFunction()
changes: document PetscFunctionListAdd() API change
developers.tex: update documentation of PetscObjectComposeFunction
removed path and MPI_Comm arguments from PetscFunctionListFind/Add()
removed path argument to XXXInitializePackage() and XXXRegister()
removed XXXRegisterDynamic() but kept the APIs for everything else underneath the same phase I of the update to handling registering function pointers

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PetscFunctionListAdd: use macro to hide (PetscVoidFunction) cast

Same rationale as the last commit:

Casting using PetscVoidFunction instead of (void(*)(void)) is needed
with C++ compilers that will

PetscFunctionListAdd: use macro to hide (PetscVoidFunction) cast

Same rationale as the last commit:

Casting using PetscVoidFunction instead of (void(*)(void)) is needed
with C++ compilers that will not implicitly convert C++ language linkage
to C language linkage. Since PetscFunctionListAdd() is meant to operate
on generic function pointers, we hide this language linkage detail
(which is inconsistently implemented) in a cast.

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PetscFunctionListFind: use macro to hide (PetscVoidFunction*) cast

Casting using PetscVoidFunction* instead of (void(**)(void)) is needed
with C++ compilers that will not implicitly convert C++ lang

PetscFunctionListFind: use macro to hide (PetscVoidFunction*) cast

Casting using PetscVoidFunction* instead of (void(**)(void)) is needed
with C++ compilers that will not implicitly convert C++ language linkage
to C language linkage. Since PetscFunctionListFind() is meant to operate
on generic function pointers, we hide this language linkage detail
(which is inconsistently implemented) in a cast.

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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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removed string version of function name for XXXRegister(), PetscFunctionListAdd() and PetscObjectComposeFunction()

removed path and MPI_Comm arguments from PetscFunctionListFind/Add()

removed path argument to XXXInitializePackage() and XXXRegister()