DMNetwork: Setting/accessing variables for components.

DMNetwork till now only allowed setting/accessing the variables at a vertex or edge. For vertices/edges that have multiple components (which pr

DMNetwork: Setting/accessing variables for components.

DMNetwork till now only allowed setting/accessing the variables at a vertex or edge. For vertices/edges that have multiple components (which presumably could represent different physics) the user would need to some book-keeping to keep track of variable offsets associated with a component. This feature avoids the need of this book-keeping by allowing setting variables for components and managing the variable offsets for them.

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Merge branch 'hzhang/fix-dmnetwork-memory' into 'master'

Hzhang/fix dmnetwork memory

See merge request petsc/petsc!2301

bugfix for DMNetworkGetSubnetworkCoupleInfo(); add more error checking

add DMNetworkGetSizes()
Contributed-by: Betrie, Getnet <gbetrie@anl.gov>

Merge branch 'hzhang/dmnetwork-vltogordering' [PR #1882]

* hzhang/dmnetwork-vltogordering:
add Set/GetVertexLocalToGlobalOrdering(), used by constrained optimization application
bugfix for IPMUpdate

Merge branch 'hzhang/dmnetwork-vltogordering' [PR #1882]

* hzhang/dmnetwork-vltogordering:
add Set/GetVertexLocalToGlobalOrdering(), used by constrained optimization application
bugfix for IPMUpdateAi() in Tao. Create Ai using local column size
bugfix for DMInitialize_Network(). contibuted by Shri

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add Set/GetVertexLocalToGlobalOrdering(), used by constrained optimization application

Merge branch 'maint'

Remove use of _ and __ in front of PETSc include guards. Reason: C99 Reserved Identifiers

Commit-type: portability-fix

Merged in hzhang/dmnetwork-add_matpreallocation_err-cleanup (pull request #1649)

Hzhang/dmnetwork add matpreallocation err cleanup

Approved-by: Matthew Knepley <knepley@gmail.com>
Approved-by: Shri

Merged in hzhang/dmnetwork-add_matpreallocation_err-cleanup (pull request #1649)

Hzhang/dmnetwork add matpreallocation err cleanup

Approved-by: Matthew Knepley <knepley@gmail.com>
Approved-by: Shrirang Abhyankar <shri@pnnl.gov>
Approved-by: BarryFSmith <bsmith@mcs.anl.gov>

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Add error checking MatSetOption(*J,MAT_NEW_NONZERO_ALLOCATION_ERR,PETSC_TRUE) in DMCreateMatrix_Network()
Add '-dm_view' runtime option to view dmnetwork edgelist
Cleanup

Merge branch 'hzhang/pdmnetwork-setup' [PR #1561]

* hzhang/pdmnetwork-setup:
Add parallel creation of DMNetwork

add parallel creation of DMNetwork in DMNetworkLayoutSetUp()
change API for DMNetworkSetSizes()
add DMNetworkGetSubnetworkCoupleInfo()
implement DMView_Network()
update DMNetworkGetGlobalXXXIndex()
u

add parallel creation of DMNetwork in DMNetworkLayoutSetUp()
change API for DMNetworkSetSizes()
add DMNetworkGetSubnetworkCoupleInfo()
implement DMView_Network()
update DMNetworkGetGlobalXXXIndex()
update/rewrite pipes1.c

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Merged in hzhang/dmnetworkmonitor-xminmax (pull request #1491)

Hzhang/dmnetworkmonitor xminmax

Approved-by: BarryFSmith <bsmith@mcs.anl.gov>

dmnetwork: add xmin, xmax to DMNetworkMonitorAdd()

add PETSC_VIEWER_DRAW_LG_XRANGE and update VecView_Seq_Draw_LG()

Requested-by: "Betrie, Getnet" <gbetrie@anl.gov>
Suggested-by: "Smith, Barry F."

dmnetwork: add xmin, xmax to DMNetworkMonitorAdd()

add PETSC_VIEWER_DRAW_LG_XRANGE and update VecView_Seq_Draw_LG()

Requested-by: "Betrie, Getnet" <gbetrie@anl.gov>
Suggested-by: "Smith, Barry F." <bsmith@mcs.anl.gov>

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Merge branch 'master' into knepley/feature-plex-elasticity-test

* master: (1553 commits)
-options_table was changed to options_view in 2014 but documentation was not updated to reflect it
config

Merge branch 'master' into knepley/feature-plex-elasticity-test

* master: (1553 commits)
-options_table was changed to options_view in 2014 but documentation was not updated to reflect it
configure: fix F2003 test
Plex test ex5: Removed "future" test, as it resulted in issues in the nightly tests.
Some minor typos in TS
Add ADIOS2.py which I forgot to git add in the past
Plex ex5: Disable test
Doc: Added note for interface change
KSPLSQRMonitorDefault fixed for quad precision
Tao: Added alternative output for chwirut2 test.
TS ex45,ex46: Removed overly refined tests for faster nightly tests.
KSP ex72: Fixed needlessly long-running PCTFS tests.
SNES ex56: Reduced test size to speed up nightly test suite.
KSPSolve_LSQR: don't compute unused norm of rhs
SNES ex13: Reduced problem sizes for nightly tests.
PetscOptionsDeprecated(): fix for NULL prefix
PetscOptionsDeprecated(): add option to print additional info
SNES ex12: Reduced sizes for BDDC tests.
PetscFileRetrieve(): Suppress output to STDERR when downloading a file.
MatMatMult: Fixed unused variable pN.
DMDestroy: Guard call to dm->ops->destroy * Similar guards are in place in many other methods (IS,Vec,Mat) and permit the DM to be destroyed even if DMSetType() was never called.
...

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Merge branch 'master' into knepley/feature-plex-parallel-submesh

* master: (2931 commits)
remove N in docs for SNESQN
replaced test tolerance with PETSC_SQRT_MACHINE_EPSILON
fortran: PetscComp

Merge branch 'master' into knepley/feature-plex-parallel-submesh

* master: (2931 commits)
remove N in docs for SNESQN
replaced test tolerance with PETSC_SQRT_MACHINE_EPSILON
fortran: PetscComplex type is missing from fortran
initialize variables so that static analyzer doesn't mistakenly think they are used uninitialized.
Move access of prefix until it is actually used
Remove DMDASplitComm2d(), used in one example that was not tested
Functions that do not return PetscErrorCode should not use PetscFunctionBegin/End paradgm
remove unneeded reassignment of same value
Missing CHKERRQ(); Mostly in Tao code
Remove clang static analyser warning about passing NULL variable to strncat()
missing newline in -ts_monitor_extreme
minor fixes for integer counters
Configure: Deal with '__func__' in C89 builds with newer Clang and GCC.
Jenkinsfile: Increased timeout for tests to 5 minutes.
3.9 changes: further clarify removal of -pc_factor_mat_solver_package
Options deprecations: add "PETSc" to inline warning
removing unused variable
MatShift support added to MATSUBMAT. Mimics MATSHELL functionality. Needed for matrix-free Hessians in TAO Newton-Line-Search methods.
Add -ts_monitor_extreme
Dev manual: add note on deprecating options database keys
...

Conflicts:
src/dm/impls/plex/examples/tests/ex4.c

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Merge branch 'master' into knepley/feature-snes-ex13-spectral

* master: (2350 commits)
migrate warning fix from next-tmp
Revert "Remove dead code."
clarifying comment in the code
Remove dead

Merge branch 'master' into knepley/feature-snes-ex13-spectral

* master: (2350 commits)
migrate warning fix from next-tmp
Revert "Remove dead code."
clarifying comment in the code
Remove dead code.
Add JuMP citation
Copyedits and updates to developers manual
Add more protection to intrinsics
MPI: protect arguments in MPI macros
Add the missing conditionals for 64-bit build
Plex+VTK: Fix field type determination
Fix bug in name cleanup
Bib: Added ref
Plex+VTK: Fix field type determination
Plex: Updated test output - I am now hating this shit
forgot to save file after moving prototypes to petscsys.h
update Apple example project settings per Xcode
Two functions should actually be public, used, for example from Apple MacOS and iOS programs
includes should always be included relative to include directory
Apple removed old locations of docsets
SNES ex12: Updated test output
...

Conflicts:
src/snes/examples/tutorials/ex13.c

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Merge branch 'master' into knepley/feature-pc-patch

* master: (440 commits)
revert sources to dev - reset PETSC_VERSION_RELEASE - reset changes/dev.html
release: set v3.9 strings
fix grep us

Merge branch 'master' into knepley/feature-pc-patch

* master: (440 commits)
revert sources to dev - reset PETSC_VERSION_RELEASE - reset changes/dev.html
release: set v3.9 strings
fix grep usage on solaris [use egrep]
opensolaris: fix errors
Update timer reporting and minor reporting fix
Remove redundant if statement. Found by @jedbrown
Fixed problem with order of developer photos on website.
superlu_dist: use correct flag in example [PETSC_HAVE_SUPERLU -> PETSC_HAVE_SUPERLU_DIST]
Bib: PERMON ref
fix for osx
doc: more author fixes
doc: more author fixes
Italicized "orderings" in MPI process placement discussion.
Added Richard to the user manual author list.
Added Richard to the list of active developers on the website.
add string check for MS-MPI and IMPI timeout errors
opensolaris does not have multiple grep utils - but default one does not support -F. So use fgrep instead
Standardizing timeout checks
Report wall clock time of total tests
Use time instead of date %s
...

Conflicts:
include/petscpc.h
src/ksp/ksp/interface/itfunc.c

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Merge remote-tracking branch 'origin/shri/dmnetwork-subnetworks-rebased'

Git rid of int argument for edgelist with DMNetwork, replace with PetscInt

The DMNetwork examples now don't work with 64 bit indices probably due to some place in
DMPlex that uses int instead of Pet

Git rid of int argument for edgelist with DMNetwork, replace with PetscInt

The DMNetwork examples now don't work with 64 bit indices probably due to some place in
DMPlex that uses int instead of PetscInt. But this means that DMPlex needs to be fixed to
not have this one crazy location with int instead of PetscInt.

Commit-type: style-fix, feature

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rm old DMNetworkLayoutSetUp()

change API of DMNetworkSetEdgeList() to DMNetworkSetEdgeList(DM dm,int *edgelist[],int *edgelistCouple[])

replace DMNetworkSetSizes() with DMNetworkSetSizesCoupled()

implement DMNetworkSetSizesCoupled()

add coupling vertices

DMNetwork: Added DMNetworkGetComponent to get the component data directly.

The component data used to be accessed by obtaining the component data array first
through DMNetworkGetComponentDataArray a

DMNetwork: Added DMNetworkGetComponent to get the component data directly.

The component data used to be accessed by obtaining the component data array first
through DMNetworkGetComponentDataArray and then by getting the offset for a given point
via DMNetworkGetComponentKeyOffset. Added a new function DMNetworkGetComponent through which
the component data can be accessed directly without having to expose the component data array
or the offset.

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