KSPMonitorLGTrueResidualNormCreate: Remove unused MPI_Comm argument

Merge branch 'master' into shri/ts-is-for-differential-variables

Conflicts:
include/petsc-private/tsimpl.h
src/ts/impls/eimex/eimex.c
src/ts/interface/ts.c

Merge branch 'barry/clean-gamg'

Conflicts:
src/ksp/pc/impls/gamg/gamg.c

Merge branch 'master' into jed/chem
Note merging a branch with good stuff in it for a year and a half is insane!

Conflicts:
src/ts/examples/tutorials/makefile
src/ts/interface/ts.c

removed KSPSPECEST KSP type since that functionality is now handled inside the KSPCHEBYSHEV method

unify naming of KSPChebyshevEstEig... functions and command line options

Merge branch 'master' into barry/clean-gamg

Need updates to KSPCHEBYSHEV since I will be adding to them

Merge branch 'tisaac/ksp-cheby-use-mat-state'

KSPChebyshev: added KSPChebshevGetEstEigKSP()

Without this, the kspest can only be modified from the command line
options.

KSPChebyshev: use matrix id/state to determine when to estimate eigenvalues

Before: if KSPSetOperators() is called, ksp->setupstate is changed to KSP_SETUP_NEWMATRIX
when KSPSetUp() is calle

KSPChebyshev: use matrix id/state to determine when to estimate eigenvalues

Before: if KSPSetOperators() is called, ksp->setupstate is changed to KSP_SETUP_NEWMATRIX
when KSPSetUp() is called, if ksp->setupstate == KSP_SETUP_NEWMATRIX,
call a special routine KSPChebyshevSetNewMatrix()
Now: when eigenvalues are estimated, store state/id of Amat and Pmat
when KSPSolve() is called, if state or id has changed, redo estimates

This removes an ugly special case for Chebyshev in the KSP interface.

Potentially dangerous: a mat implementation could forget to increase the state,
but we already rely on state to determine when to call PCSetUp(), so
not really any more dangerous than already

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Merge branch 'master' into stefano_zampini/pcbddc-adaptive-selection

Merge branch 'master' into knepley/feature-harmonic-advection

* master: (205 commits)
Bib: Added bio refs
Don't print SAWs URL since it disturbs all the test output
missing (double) cast in pr

Merge branch 'master' into knepley/feature-harmonic-advection

* master: (205 commits)
Bib: Added bio refs
Don't print SAWs URL since it disturbs all the test output
missing (double) cast in print statement
don't output to test file all 12 digits of values
fixes and additions to SNESQM manual pages
PetscViewerBinaryGetDescriptor() is now a collective and must be treated as such fixed some calls to PetscViewerBinarySetUseMPIIO() removed some test runs that take too long
removed dead routine
ViennaCL: Added MCS download mirror URL for version 1.6.2
shift order of processing options for TS to be compatiable with SAWs Fix options handling for SAWs to duplicate array that previously was deleted too soon for SAWs processing
remove some dead code for AD and old AMS java and Matlab utilities
add missing PetscFunctionBegin; that messed up displaying of stack
Viewer: Fixed PetscViewerBinarySetUseMPIIO() in some examples
removed unused variables, removed dead code from AMS
git is so freaking annoying I accidently made a bunch of updates in next which I pushed lets see if this diff makes the same changes in my branch Why can't git just forbid me to make changes or next or set up some utility to prevent it!
moved saws directory to proper share directory location updated source to point to it.
rm checkboxes at top of pcoptions.html (ugly and not useful) and centered display of solver
PetscOptionsObject->prefix was freed before using in SAWs post processing hence SAWs was unable to change any type which had a prefix
display URL to point to to access SAWs server
missing break in case for handling string arguments better description for Options database option handling
removed extern PC_CLASSID and KSP_CLASSID that don't belong in petscoptions.h
...

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Merge branch 'barry/saws-options-merge-master'

Merge branch 'master' into stefano_zampini/pcbddc-adaptive-selection

Conflicts:
src/ksp/pc/impls/bddc/bddcprivate.c

Merge branch 'master' into barry/saws-options-merge-master

Totally confusing manual merge, could be wrong

Conflicts:
include/petscoptions.h
src/dm/impls/da/dacreate.c
src/sys/objects/aoptions.c

Merge branch 'master' into barry/saws-options-merge-master

Totally confusing manual merge, could be wrong

Conflicts:
include/petscoptions.h
src/dm/impls/da/dacreate.c
src/sys/objects/aoptions.c
src/sys/threadcomm/interface/threadcomm.c

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Merge branch 'tisaac/simplify-register-all'

Removed the XXXRegisterAll() functions from the public interface. These should now only be handled by the package intialization functions.

Merge branch 'master' into pr252/dmay/PetscViewerBinarySkipHeaderVecViewLoad
Manual merge of makefile

Conflicts:
src/sys/classes/viewer/examples/tutorials/makefile

Merge branch 'master' into stefano_zampini/pcbddc-adaptive-selection

Merge branch 'karpeev/fix-ksp-matgetschurcomplement-pmatreuse' into barry/experiment

Conflicts:
src/ksp/ksp/utils/schurm.c

Merge branch 'barry/update-sowing'

Conflicts:
tutorials/HandsOnExercise.html

update to use Sowing 1.17
fixed many documentation errors as well

Merge branch 'master' of bitbucket.org:petsc/petsc into mark/gamg-crs-ksp2

mv include/finclude to include/petsc-finclude for namespacing in installs

mv include/finclude to include/petsc-finclude for namespacing in installs

Merge branch 'master' into barry/ksp-converged-reason-viewer

Conflicts:
src/sys/objects/options.c