fix ex5.c so SNES counts linear solve over all grid sequencing steps to match cummulative counts of linear solver

updated PETSc directory layout to match standard packaging strategies

include/petsc finclude,private,mpiuni
lib/petsc conf
bin/petsc*

added KSPGetTotalIterations() to access count of all iterations since KSP object was created

Suggested-by: Christiaan Klaij <C.Klaij@marin.nl>

Merge branch 'master' of bitbucket.org:petsc/petsc

Merge branch 'knepley/feature-viewer-partial-read'

* knepley/feature-viewer-partial-read:
Viewer: Fixed initialization
TS: Updated example to new interface
Plex: Fix compiler warning
Viewer:

Merge branch 'knepley/feature-viewer-partial-read'

* knepley/feature-viewer-partial-read:
Viewer: Fixed initialization
TS: Updated example to new interface
Plex: Fix compiler warning
Viewer: Now ViewerRead() takes an extra argument to return the number of items read - An error is thrown for insufficient data unless the extra argument is non-NULL
Viewer: Fixes for new Read interface - Fixed example - Fixed Fortran 90 binding - Fixed type
Builder: Allow a local dictionary for run parameters
Viewer: PetscViewerRead() should return the number of items actually read - This also applies to all its implementations

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Viewer: Now ViewerRead() takes an extra argument to return the number of items read
- An error is thrown for insufficient data unless the extra argument is non-NULL

Merge branch 'master' into knepley/feature-viewer-partial-read

* master: (48 commits)
ViennaCL: Fixes memory leak when destructing an aijviennacl matrix.
MatLoad_MPIDense() always allocated arra

Merge branch 'master' into knepley/feature-viewer-partial-read

* master: (48 commits)
ViennaCL: Fixes memory leak when destructing an aijviennacl matrix.
MatLoad_MPIDense() always allocated array space even if it was previously provided
Clarified lumping options for PCFieldSplitSchurPreType SELFP.
fixed up PetscInfo in GAMG
TSErrorWeightedNorm[2|Infinity]: API changes
MatLoad_SeqDense() always allocated new space for the data even if the user already provided it
Fixed DMCompositeGetAccessArray() to support readonly vectors
Fix obviously-wrong aspects of documentation on SNESVINEWTONRSLS and SNESVINEWTONSSLS.
fixed example to compile - demonstrates a bug
var name 'len' was F90 key word
For user provided Jacobian functions they should always assembly into the second matrix, the one from which the preconditioner is built because the first may be used as matrix-free with -snes_mf_operator
Suggest --with-64-bit-indices if users mistakenly use --with-64bit-indices
Fix configure logging of integer size.
missing underscore in #define of vecgetarrayread translation of fortran stub for VECGETARRAYREAD
updated test output files to reflect differences introduced previously in PCView output
-ksp_type preonly does not support -ksp_monitor_short so remove from test line to prevent extranious warning output
missing CHKERRQ; and ugly double declaration of ierr
Plex: Reorganized PlexPoint interface - Added DMPlexGetPointLocalField() and DMPlexGetPointGlobalField() - Now the DMPlexGetLocalOffset*_Private() functions return start and end - Uniformly use private functions
Plex: Put in explicit cast
MatSetValuesMPISBAIJ will now print correct global indices when error generated due to new nonzero location
...

# Please enter a commit message to explain why this merge is necessary,
# especially if it merges an updated upstream into a topic branch.
#
# Lines starting with '#' will be ignored, and an empty message aborts
# the commit.

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Merge branch 'master' into tisaac/dmforest

If we're going to start developing on this again, the recent changes to the
location of configuration files will make it annoying to switch to and from
thi

Merge branch 'master' into tisaac/dmforest

If we're going to start developing on this again, the recent changes to the
location of configuration files will make it annoying to switch to and from
this branch. Matt's and my fixes in DMPlex will also be relevant.

* master: (1557 commits)
MatLoad_MPIDense() always allocated array space even if it was previously provided
Clarified lumping options for PCFieldSplitSchurPreType SELFP.
fixed up PetscInfo in GAMG
TSErrorWeightedNorm[2|Infinity]: API changes
MatLoad_SeqDense() always allocated new space for the data even if the user already provided it
Fixed DMCompositeGetAccessArray() to support readonly vectors
Fix obviously-wrong aspects of documentation on SNESVINEWTONRSLS and SNESVINEWTONSSLS.
fixed example to compile - demonstrates a bug
var name 'len' was F90 key word
For user provided Jacobian functions they should always assembly into the second matrix, the one from which the preconditioner is built because the first may be used as matrix-free with -snes_mf_operator
Suggest --with-64-bit-indices if users mistakenly use --with-64bit-indices
Fix configure logging of integer size.
missing underscore in #define of vecgetarrayread translation of fortran stub for VECGETARRAYREAD
updated test output files to reflect differences introduced previously in PCView output
-ksp_type preonly does not support -ksp_monitor_short so remove from test line to prevent extranious warning output
missing CHKERRQ; and ugly double declaration of ierr
Plex ex3: For want of a semicolon, the kingdom was lost
MatSetValuesMPISBAIJ will now print correct global indices when error generated due to new nonzero location
completed basic use of MatSetValuesBlocked_SeqBAIJ_Inlined() by MatSetValuesBlocked_MPIBAIJ() to allow proper global indices being printed when error generated by new nonzero locations.
Added inline version of MatSetValuesBlocked_SeqBAIJ() to be used by MatSetValuesBlocked_MPIBAIJ() to print error message for nonzero block with global indices
...

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Merge branch 'master' of https://bitbucket.org/petsc/petsc

Merge branch 'barry/feature-bargraph'

Viewer: PetscViewerRead() should return the number of items actually read
- This also applies to all its implementations

Merge branch 'knepley/feature-harmonic-advection'

* knepley/feature-harmonic-advection: (86 commits)
SNES: Some docs for NASM
TS: Added view for MIMEX
Plex: Silence compiler warnings
Builder

Merge branch 'knepley/feature-harmonic-advection'

* knepley/feature-harmonic-advection: (86 commits)
SNES: Some docs for NASM
TS: Added view for MIMEX
Plex: Silence compiler warnings
Builder: Check for missing numProcs was wrong
PetscFE: Turn off Fortran binding for PetscFECompositeGetMapping()
Plex: Fix big bug in DMPlexGetGlobalFieldOffset_Internal() - If offset is negative (dof is on another proc), then we must have end < start
Builder: Allow override of numProcs
Plex: Fix Fortran wrappers for DMLabelView() and DMPlexDistribute()
Plex+Label: Added Fortran wrapper for DMPlexCreateLabel()
Plex: Dammit, how did this not get checked in?
Plex: Refiner check for hybrid cells must use hybrid faces as well - Ghost cells in FV method are hybrid
TS: MIMEX now uses work vectors for correct grid
Plex: Adding support for FV in automatic interpolator construction - Notice that the injector cannot do the right thing until we scrap VecScatter
Plex+FEM: Using PetscFVGetDualSpace()
SNES+Doc: Added Options Database keys
PetscFV: Added PetscFVRefine() - This allows interpolation to finer grids needed for FAS
PetscFV: Added a dual space for calculating projections
DM: Better error checking in DMCoarsen()
DMDT+PetscFE: Added PetscQuadratureExpandComposite() - Replaces PetscFECompositeExpandQuadrature() - Added PetscFECompositeGetMapping()
Plex: Fixed complex type error
...

Conflicts:
src/dm/impls/plex/ftn-custom/makefile
src/ts/interface/ts.c

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added PetscDrawBar object for drawing bar graphs

SNES+Doc: Added Options Database keys

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

SNES: Added SNESMonitorDefaultField()
- The option is -snes_monitor_field
- It falls back to the default monitor is no field structure is present in a Section

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

Merge branch 'master' into barry/clean-gamg

Need updates to KSPCHEBYSHEV since I will be adding to them

Merge branch 'master' of bitbucket.org:petsc/petsc

Merged in mapdes/petsc/snes-use-injection (pull request #271)

SNES: try using injection matrix to restrict solution

SNES: try using injection matrix to restrict solution

Rather than unconditionally using the restriction matrix plus
rscale (which may be NULL if the user has provided the injection
matrix) to restri

SNES: try using injection matrix to restrict solution

Rather than unconditionally using the restriction matrix plus
rscale (which may be NULL if the user has provided the injection
matrix) to restrict solutions, use the injection matrix if it is
available.

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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