Merge branch 'barry/propagate-pcsetup-failures'

Merge branch 'barry/remove-thread-classes-master'

Infrastructure that allows failures in PCSetUp(), PCApply(), MatMult() etc due to, for example a zero pivot or function evaluation outside its domain, to propagate up and become a KSP_DIVERGED inste

Infrastructure that allows failures in PCSetUp(), PCApply(), MatMult() etc due to, for example a zero pivot or function evaluation outside its domain, to propagate up and become a KSP_DIVERGED instead of generating an error that stops the program. In response to Issue 96. This includes failures in MatCreateSNESMF() applications due to domain errors. The mechanism to propagate some errors is by setting Info or Nan into the output vector and using the norm or inner product reductions in SNES or KSP to propagate the error condition to all processes and then handling them immediately after the norm or inner product.

This allows, for example, ODE integrators to try again with a smaller time-step if the PCSetUp failed instead of requiring a complete restart of the run with other options.

Currently some error conditions, such as function domain error in a line search may not get progated up using the correct SNESConvergedReason

See src/snes/examples/tests/ex69.c for the handling of several conditions

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Merge branch 'master' into knepley/feature-composable-callbacks

* master: (151 commits)
PetscMalloc: Fix handling of zero-sized allocations
add note to DMGetLocal/GlobalVector() about intended s

Merge branch 'master' into knepley/feature-composable-callbacks

* master: (151 commits)
PetscMalloc: Fix handling of zero-sized allocations
add note to DMGetLocal/GlobalVector() about intended short-time usage of the vectors.
sf: use patched openmpi tarball that has a potential fix for sf example hang
SNES problems that set VI bounds must use a VI solver since the other solvers ignore the bounds
pounders viewer did not cast PetscReal to double in printf nor use %D instead of %d
fix ts ex20adj
fix ts theta
fixed another variable declaration in the middle of a code block
example main() had PetscInt return type and argument that should be int
DMDAVTKWriteAll_VTS: Fix handling of higher-dimension coordinates
fixed example that declared variables in the middle of a function
C programs do not return PetscInt nor do they take an argument that is PetscInt, fixed example that did
You cannot declare variables in the middle of functions in PETSc.
add ierr checking to PetscOptionsBegin/End() in example
configure: add error check if user specifies PETSC_ARCH=-dbg [i.e starts with a '-']
scale norm of vector difference by norm of vector to insure it is small enough to consider the two vectors equal
missing PetscViewerDestroy() added
MatNestGetISs: use custom fortranstub to handle PETSC_NULL_OBJECT
update location of open-mx website on FAQ page
If the user sets bounds and calls a solver that does not support them, throw an error.
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Merge remote-tracking branch 'origin/stefano_zampini/mattransposedense-ldafix' into stefano_zampini/pcbddc-adaptive-selection

Merged petsc/petsc into master

MatGetSubMatricesParallel —> MatGetSubMatricesMPI. Implementation rewritten, tests added.

stripped out all PETSc threadcomm code

stripped out all PETSc threadcomm code

Merge branch 'barry/fix-matload-mpidense-denseinfile'

Merge branch 'pr192/Fande-Kong/scalable-matincreaseoverlap/master' of https://bitbucket.org/petsc/petsc

Merged petsc/petsc into master

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

Conflicts:
src/ksp/pc/impls/bddc/bddcprivate.c
src/ksp/pc/impls/bddc/bddcscalingbasic.c
src/mat/impls/aij/mpi/mumps/mumps.c
s

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

Conflicts:
src/ksp/pc/impls/bddc/bddcprivate.c
src/ksp/pc/impls/bddc/bddcscalingbasic.c
src/mat/impls/aij/mpi/mumps/mumps.c
src/mat/impls/is/matis.h

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Merged master into semihozmen/ksp-fcg-eigen-comp-support

Merge branch 'master' into pr192/Fande-Kong/scalable-matincreaseoverlap/master

Needed to merge master to update to new calling sequence PetscCommBuildTwoSided

Merged petsc/petsc into master

Merge branch 'barry/fix-directory-layout'

updated PETSc directory layout to match standard packaging strategies

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

Buffer space used for loading dense matrix from file was too small when first process didn't have largest part of the matrix
also simplified the MatLoad_MPIDense() code slightly

Merge branch 'tisaac/mat-get-submatrix-unordered'

Merge branch 'barry/optimize-matshift'

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
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# especially if it merges an updated upstream into a topic branch.
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# Lines starting with '#' will be ignored, and an empty message aborts
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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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Optimized MatShift() for a completely empty matrix since this is commonly used with SLEPc to produce diagonal matrices

Reported-by: Jose Roman <jroman@dsic.upv.es>

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