Merge branch 'master' into barry/dmvecmattypes
possible some messed up manual merges!

Conflicts:
src/dm/impls/mesh/examples/tutorials/ex4f90.F
src/dm/impls/mesh/mesh.c
src/dm/impls/mesh/meshcreat

Merge branch 'master' into barry/dmvecmattypes
possible some messed up manual merges!

Conflicts:
src/dm/impls/mesh/examples/tutorials/ex4f90.F
src/dm/impls/mesh/mesh.c
src/dm/impls/mesh/meshcreate.c
src/dm/impls/mesh/section.c
src/snes/examples/tutorials/ex10.c
src/snes/examples/tutorials/ex12.c
src/snes/examples/tutorials/ex52.c
src/snes/examples/tutorials/ex62.c
src/snes/utils/mesh/dmmeshsnes.c

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Merge branch 'knepley/remove-sieve'

Conflicts:
src/dm/impls/mesh/examples/tests/output/ex10_0.out
src/dm/impls/mesh/examples/tests/output/ex10_1.out
src/dm/impls/mesh/examples/tests/output/ex11f9

Merge branch 'knepley/remove-sieve'

Conflicts:
src/dm/impls/mesh/examples/tests/output/ex10_0.out
src/dm/impls/mesh/examples/tests/output/ex10_1.out
src/dm/impls/mesh/examples/tests/output/ex11f90_0.out
src/dm/impls/mesh/examples/tests/output/ex11f90_1.out
src/dm/impls/mesh/examples/tests/output/ex3_0.out
src/dm/impls/mesh/examples/tests/output/ex3_1.out
src/dm/impls/mesh/examples/tests/output/ex3_2.out
src/dm/impls/mesh/examples/tests/output/ex3_3.out
src/dm/impls/mesh/examples/tests/output/ex8_0.out
src/dm/impls/mesh/examples/tests/output/ex9f90_0.out
src/dm/impls/mesh/examples/tests/output/ex9f90_1.out
src/dm/impls/mesh/mesh.c
src/dm/interface/dlregisdmdm.c
src/vec/vec/interface/vecregall.c

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

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

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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Merge branch 'jed/fix-ts-jacobian-linear' into maint

* jed/fix-ts-jacobian-linear:
TS: fix MSVC compiler error: non-POD member of anonymous struct
TS tests/ex3: SNESFD and TSComputeIJacobianCons

Merge branch 'jed/fix-ts-jacobian-linear' into maint

* jed/fix-ts-jacobian-linear:
TS: fix MSVC compiler error: non-POD member of anonymous struct
TS tests/ex3: SNESFD and TSComputeIJacobianConstant are incompatible
TS: fix shortcut scaling; document TSComputeIJacobianConstant limitations
TS tests/ex3: fix example and inclusion in nightlies
TS tests/ex5*: re-activate test and fix monitor interval
TS: add TSRHSJacobianSetReuse, fixes TSComputeRHSJacobianConstant

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Merged petsc/petsc into rmills/petsc master.

Merge branch 'jed/fix-ts-jacobian-linear'

* jed/fix-ts-jacobian-linear:
TS: fix MSVC compiler error: non-POD member of anonymous struct
TS tests/ex3: SNESFD and TSComputeIJacobianConstant are in

Merge branch 'jed/fix-ts-jacobian-linear'

* jed/fix-ts-jacobian-linear:
TS: fix MSVC compiler error: non-POD member of anonymous struct
TS tests/ex3: SNESFD and TSComputeIJacobianConstant are incompatible
TS: fix shortcut scaling; document TSComputeIJacobianConstant limitations
TS tests/ex3: fix example and inclusion in nightlies
TS tests/ex5*: re-activate test and fix monitor interval
TS: add TSRHSJacobianSetReuse, fixes TSComputeRHSJacobianConstant

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TS: fix shortcut scaling; document TSComputeIJacobianConstant limitations

The shortcut re-shifting on re-evaluation of the IJacobian can only be
used when the implicit system is just the "mass matri

TS: fix shortcut scaling; document TSComputeIJacobianConstant limitations

The shortcut re-shifting on re-evaluation of the IJacobian can only be
used when the implicit system is just the "mass matrix". This
re-scaling also needs to be recorded for the next iteration. Since this
logic cannot work in general, it is now moved to
TSComputeIJacobianConstant. This funtion seems to be of limited use
beyond "explicit" finite element computations (especially those that use
a consistent mass matrix) and similar.

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TS: add TSRHSJacobianSetReuse, fixes TSComputeRHSJacobianConstant

When using a constant RHS and no IJacobian, the RHS Jacobian is shifted
to make it function as an IJacobian (shift*I - Arhs), which

TS: add TSRHSJacobianSetReuse, fixes TSComputeRHSJacobianConstant

When using a constant RHS and no IJacobian, the RHS Jacobian is shifted
to make it function as an IJacobian (shift*I - Arhs), which is the matrix
used by SNES. We don't want to duplicate the full matrix because that
uses a lot of memory, so we play this game of recording the shift and
scale, then unshifting in TSComputeRHSJacobian. Add tests that fail
prior to this bug fix.

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DMMesh: Removed all trace and salted the earth, Carthago delenda est!

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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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
x

Hg-commit: 5ca7425bdc061d16496b42615f4a99db34a78eec

Uncrustified src/ts/*

Hg-commit: 688366eb7a8ecbc6948bb32d69e2de3093f22e25

commit aftr merge

Hg-commit: 854807b200896ff0e3d6fb344a549ed1a2b93850

Replaced '#ifdef' and '#ifndef' with '#if defined()' and '#if !defined()'.

Hg-commit: b3ebae8b626a88c2ac067fd7c3f04f229b43f305

silly code formatting problems; some people still need to read the style guide

Hg-commit: 7a98cb06baf90914d565ea8801b6900bdc5a04c1