Merge branch 'master' into prbrune/mat-matcolor

Conflicts:
src/snes/interface/snesj2.c

Merge branch 'master' into prbrune/removeunwrappedmathfunctions

Merge branch 'maint'

* maint:
MatXAIJSetPreallocation: use array[] notation to help out Fortran

MatXAIJSetPreallocation: use array[] notation to help out Fortran

Merge branch 'master' into knepley/feature-plex-refine-3d

* master: (149 commits)
Bib: Added papers referencing PETSc from ResearchGate
Bib: Fixed urls for some refs Suggested-by: Michele De Ste

Merge branch 'master' into knepley/feature-plex-refine-3d

* master: (149 commits)
Bib: Added papers referencing PETSc from ResearchGate
Bib: Fixed urls for some refs Suggested-by: Michele De Stefano
fixed bug that has appeared recently of false positive errors when there are zero local equations on coarse grids in gamg-agg.
MatSchurComplement: Must initialize KSP package
bib: fix inbook citation
Bib: Updated some refs
SNES: fix copy/paste in man page
fortran: fix KSPCONVERGEDDEFAULT and SNESCONVERGEDSKIP in fortran includes
Mat SBAIJ: avoid invalid memory read in MatSOR_SBAIJ
Revert "MatMPIBAIJSetPreallocationCSR() handled the input matrix entries incorrectly, it treated them as if each row of values"
PCGAMG: fix corruption for multiple solves when MatSetNearNullSpace is used
PCGAMG: remove distracting comment
KSP ex49: restrict near-null space for elasticity example with sym BC
MatMPIBAIJSetPreallocationCSR() handled the input matrix entries incorrectly, it treated them as if each row of values was provided ordered by row within the block rows instead of by block as it was originally designed to be. Also added more discussion to the manual pages on the expected order of the values
Fix accidental creation of the matrices in SNESNCG used for linear analogue LS.
PCGAMG: add man page for PCGAMGType
fortran: fix snesconvergedskip_() kspconvergedskip_() kspconvergeddefault*_()
rm //
Sys: new_ir changed from PetscInt to PetscObjectState - so fix mallocs to use the new type
SNES: Fixed package init in SNESLineSearchCreate()
...

Conflicts:
include/petscdmplex.h
src/dm/impls/plex/examples/tests/ex5.c
src/dm/impls/plex/plex.c
src/dm/interface/dm.c

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Merge branch 'jed/remove-dynamic-loading-option'

Option --with-dynamic-loading has been removed. Similar functionality
is available via the run-time option -dynamic_library_preload.

* jed/remove-d

Merge branch 'jed/remove-dynamic-loading-option'

Option --with-dynamic-loading has been removed. Similar functionality
is available via the run-time option -dynamic_library_preload.

* jed/remove-dynamic-loading-option:
Sys: PetscContainerCreate must call PetscSysInitializePackage
Remove --with-dynamic-loading / PETSC_USE_DYNAMIC_LIBRARIES

Conflicts:
src/dm/impls/mesh/mesh.c
src/dm/interface/dlregisdmdm.c
src/docs/website/documentation/changes/dev.html

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MatHeaderCopy() is very very dangerous; it did not destroy the attached viewer 2 hours debugging

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

Remove --with-dynamic-loading / PETSC_USE_DYNAMIC_LIBRARIES

This option was mostly redundant because normal shared libraries satisfy
all the same needs. This commit adds the run-time option
-dynami

Remove --with-dynamic-loading / PETSC_USE_DYNAMIC_LIBRARIES

This option was mostly redundant because normal shared libraries satisfy
all the same needs. This commit adds the run-time option
-dynamic_library_preload that can be used to load/initialize all the
packages in advance, as used to be done when --with-dynamic-loading.

The PetscDLLibraryRegister_petscxxx functions have been kept, but are
not called unless -dynamic_library_preload is used. The petsc-dev
discussion, "Why --with-dynamic-loading?" did not reach consensus about
whether this was ever useful, so it may also be removable.

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Merged petsc/petsc into rmills/petsc master

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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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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removed path argument to XXXInitializePackage() and XXXRegister()

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

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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Automerge.

Hg-commit: 81500f7e84c8ec0c4dcae9cb31d1cb32892d545d

fixed many more private functions as PETSC_INTERN
renamed a few badly named private functions

Hg-commit: b9e1405ad332ccf13f675f0aa2256f1c838a5595

added PetscObjectComm() and used it to replace (((PetscObject)obj)->comm)

Hg-commit: 3da37c458124ad48ae939f4e9823e4430ee0b8be

removed typeid from PetscHeaderCreate() args since it is not know at create time anyway

Hg-commit: 368e928141e31cf1ff6cf108913006e5886dc6cc

removed PETSC_NULL from C and Fortran (except declaration in C for backward compatibility). Kept PETSC_NULL_xxx for Fortran
Fixed a few bugs where PETSC_NULL had been used incorrectly.

Hg-commit: 05

removed PETSC_NULL from C and Fortran (except declaration in C for backward compatibility). Kept PETSC_NULL_xxx for Fortran
Fixed a few bugs where PETSC_NULL had been used incorrectly.

Hg-commit: 054705a517d7f4388a8a084415d7478cbe95dff4

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commit after merge.

Hg-commit: e15fd985275e9e6c40407ae90b2d69ed97fbf48d

commit after merge

Hg-commit: b5179cc7865f723cd5e23a2244f6bcbc7b905437