Merge remote-tracking branch 'origin/barry/fix/even-huger-flaw-in-ts'

Merge remote-tracking branch 'origin/barry/consistent-formating-ascii-solver-viewers'

Merge remote-tracking branch 'origin/knepley/feature-convergence-estimator'

* origin/knepley/feature-convergence-estimator:
ConvEst: Restore the SNES to the original condition after estimation
C

Merge remote-tracking branch 'origin/knepley/feature-convergence-estimator'

* origin/knepley/feature-convergence-estimator:
ConvEst: Restore the SNES to the original condition after estimation
ConvEst: Discretization can change, so move name extraction into loop
SNES ex13: Fixed test dependencies
SNES ex13: Update to new API
ConvEst: Initialize variables
Fortran: Fixed Fortran bindings - Need custom binding for all View() to handle default viewers
ConvEst: I hate Fortran
ConvEst: Damn damn damn
ConvEst: Added Fortran type
ConvEst: Fixed spelling, fixed type
ConvEst: Fixing LAPACK type
SNES ex13: Now estimate convergence using built-in test
SNES: Allow convergence estimation using -snes_convergence_estimate
PetscConvEst: Added an object which estimates the convergence rate of a discretization
PetscDT: Turn on Fortran binding
SNES ex13: Added test output
SNES ex13: Looking at automatic convergence estimation
PetscDS: Added exact solution functions - We will use these to evaluate convergence using MMS

Conflicts:
include/petsc/private/petscdsimpl.h
src/dm/dt/interface/dtds.c

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Add an interface to return a flag that indicates

whether there is dm in snes.

Make ASCII PC/KSP/SNES/TSView() code and output in a standard style

The code that prints the ASCII view for solvers was occasionally inconsistent:
1) TSView printed the type specific information aft

Make ASCII PC/KSP/SNES/TSView() code and output in a standard style

The code that prints the ASCII view for solvers was occasionally inconsistent:
1) TSView printed the type specific information after the general info while
all other solvers printed it before (right after the name of the type is printed)
2) KSPView consistently printed the name of the subtype on EACH line of the subtypes
output as did a few of the PC and SNES viewers. Since they are all printed indented
directly below the subtype name there is no reason to print this information on each line
3) TSView printed output about number of linear solvers and SNES even for explicit
methods, which is goofy.
4) a few other minor formatting and consistency issues where fix.

Commit-type: style-fix, feature
Time: 16 hours

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Add an interface to return a flag that indicates

whether there is dm in snes.

Merge branch 'master' into knepley/feature-plex-sphere-mesh

* master: (2633 commits)
Bib: Added ref
SNES ex56: Update test output
add a citation to petsc.bib
Plex: Initialize variables
ini

Merge branch 'master' into knepley/feature-plex-sphere-mesh

* master: (2633 commits)
Bib: Added ref
SNES ex56: Update test output
add a citation to petsc.bib
Plex: Initialize variables
initialize ap as complained by the nightly tests
Plex ex3: Update to new point function API
initialize some variables as complained by nightly tests
SNES ex12: Mix misnaming Nf --> Nc
update tests
add tests
add MatView_SeqXAIJ_ASCII_structonly(); enable A->structure_only in MatSetValuesBlocked_SeqBAIJ
typo
fill-in some references
Bib: Fixed ref
Plex: Added PLY to file support
Plex: Adding PLY support
PetscDS: Turn off Fortran bindings for Constants
Plex tests: Updated to new point function API
SNES ex56: Moved tests to new format
DM: Allow field projection functions to take an array of scalars - This will allow us to pass in user data to kernels without void *, more efficiency than aux fields
...

Conflicts:
config/builder.py
include/petscdmplex.h
src/dm/impls/plex/examples/tests/ex1.c
src/dm/impls/plex/plexcreate.c
src/dm/impls/plex/plexgmsh.c
src/snes/examples/tutorials/ex63.c

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ConvEst: Fixed spelling, fixed type

SNES: Allow convergence estimation using -snes_convergence_estimate

Update manual page listed with -help to most appropriate

Commit-type: documentation
Reported-by: Lisandro Dalcin <dalcinl@gmail.com>

Fix bug where user provided only RHSJacobian and uses -snes_mf_operator

trouble because IJacobian now thinks there are separate IJacobian and
RHS matrices. Make TS aware that Jacobian is managed by

Fix bug where user provided only RHSJacobian and uses -snes_mf_operator

trouble because IJacobian now thinks there are separate IJacobian and
RHS matrices. Make TS aware that Jacobian is managed by SNES so that TS should
not adjust the matrix for the timestep

Commit-type: bug-fix
Funded-by: IMEX
Time: 2 hour
Reported-by: Ed Bueler <elbueler@alaska.edu>

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

* master: (1379 commits)
Minor fixes for tchem examples due to changes in PETSc infrastructure
update webpage about API changes

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

* master: (1379 commits)
Minor fixes for tchem examples due to changes in PETSc infrastructure
update webpage about API changes
add help menu for MatCreateSubMatricesMPI()
rename struct Mat_SubMat -> Mat_SubSppt
add a little information to the manual about using tchem
rename MatCreateSubMatrixComposite -> MatCreateSubMatrixVirtual; Mat_SubMatrix -> Mat_SubVirtual
need to protect the \ passed on the makefile on my Mac
Bib: Updated ref
update src/mat/examples/tests/output/ex23_#.out
rename MatGetSubMat -> MatCreateSubMat
Mark MatCreateMPIAIJWithSplitArrays() and MatMPIAIJSetPreallocationCSR() with MAT_NO_OFF_PROC_ENTRIES
superlu: libray is installed in PREFIX/lib64 - fix this to use PREFIX/lib
backport fixes cc105cc3 2b35c90a - required for 3bf428d - that was backported from master - 80c96bb
'echo -n' fails on opensolaris/osx - so avoid using it.
fix diffs in nightlybuilds due to options in ~/.petscrc
add Kelley03 to src/docs/tex/petsc.bib
build: determine moudles, mpi.h used during buildtime and print in 'info'
fix analyzer warnings
fix build failure on opensolaris - where -lm from flibs is removed due to -lm in cxxlibs. But then - only flib gets used for some configure tests [blaslapack, parms]
config: prefer __restrict over C99 restrict keyword
...

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Merge branch 'master' into knepley/fix-plex-examples-cleanup

* master: (53 commits)
Docs: update manual author list with P. Sanan
Docs: manual - Eclipse Users edit
Docs: manual - rearrange Oth

Merge branch 'master' into knepley/fix-plex-examples-cleanup

* master: (53 commits)
Docs: update manual author list with P. Sanan
Docs: manual - Eclipse Users edit
Docs: manual - rearrange Other PETSc features sections so that XXX Users section are grouped together at the end
Docs: manual - remove newline in Numbers section title
Docs: manual - update Visual Studio section name
Docs: manual - Qt creator section copyedit (content still would benefit from an update from M. Mirzadeh)
Docs: manual - remove stub headings in TS using fully implicit methods section
Docs: manual - update PetscLogEvent signature and example (copied from man page)
Docs: manual - update Makefile chapter
Docs: remove PetscLogEventMPEActivate and PetscLogEventMPEDeactivate references from man pages and FAQ
Docs: manual - remove reference to specific MPE event deactivation
Docs: manual - XCode section copyedit
Docs: manual - SAWs section name fix
Docs: manual - format debugger names
Docs: manual - add short mentions of TikZ and Movie capabilities
Docs: manual - Graphics section copyedit
Docs: manual - add subsection on viewing from options
Docs: manual - Viewers section copyedit
Docs: manual SAWs section - format and copyedit
Docs: Manual - update and consolidate library overview graphics
...

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Merge branch 'knepley/fix-plex-pmat'

* knepley/fix-plex-pmat:
SNES: Fix for mat, pmat when mat is defined
SNES: Now need DS header so I can correctly make two DM matrices
SNES ex69: Updated te

Merge branch 'knepley/fix-plex-pmat'

* knepley/fix-plex-pmat:
SNES: Fix for mat, pmat when mat is defined
SNES: Now need DS header so I can correctly make two DM matrices
SNES ex69: Updated tests for better Schur preconditioning
SNES ex69: Added the mass matrix as a Schur preconditioner
SNES+DS: If we are forming both a mat and pmat, we have to create both with the DM
Plex: If using a mat and pmat, the DMSNES check should use the mat
Plex: If using both a mat and pmat, we need to zero the mat when assembling

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SNES: Fix for mat, pmat when mat is defined

SNES: Now need DS header so I can correctly make two DM matrices

SNES+DS: If we are forming both a mat and pmat, we have to create both with the DM

Merge branch 'barry/remove-funct'

Merge branch 'barry/half-precision'

Remove the use and definition of __FUNCT__ throughout the code

Since all modern C/C++ compilers provide this functionality we no longer need to provide it manually in PETSc
Time: 1.5 hours
Thanks-t

Remove the use and definition of __FUNCT__ throughout the code

Since all modern C/C++ compilers provide this functionality we no longer need to provide it manually in PETSc
Time: 1.5 hours
Thanks-to: Andreas Mang <andreas@ices.utexas.edu>

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Support for half-precision using __fp16.

Requires repository trunk of gcc and ARM systems
Configure with --with-precision=__fp16 --download-f2cblaslapack --with-fc=0 --with-cxx=0
Many standard PETSc

Support for half-precision using __fp16.

Requires repository trunk of gcc and ARM systems
Configure with --with-precision=__fp16 --download-f2cblaslapack --with-fc=0 --with-cxx=0
Many standard PETSc tests fail due to lack of precision

Funded-by: ECP
Project: fp16
Time: 24 hours

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Merge branch 'master' into stefano_zampini/feature-pcbddc-saddlepoint

This is needed to deal with some changes in MatNullSpace from commit 9d2471e

Merge branch 'master' into tisaac/dmplex-feature-real-to-ref

I need updated PetscFE interfaces in what I'm going to do

* master: (603 commits)
parmetis: fix typo in testsuite
Added PETSC_HAVE_A

Merge branch 'master' into tisaac/dmplex-feature-real-to-ref

I need updated PetscFE interfaces in what I'm going to do

* master: (603 commits)
parmetis: fix typo in testsuite
Added PETSC_HAVE_ATTRIBUTEALIGNED flag to makefile
PCSetUp_SVD() used incorrect matrix for matrix size in parallel, also need to skip LAPACK call if matrix size is zero
strumpack: update to latest version 1.0.4
Remove valgrind warning about MPI_Allreduce() with uninitialized data
sed for test output that has atol convergence with quad precision
updated ex1_nest tests
fixed incorrect key value
fix: bad merge a69d34a
test: move runex78 to TESTEXAMPLES_C_NOTSINGLE
build: fix warnings
sys: update test to produce same result - irrespective of debug/opt build - and presence of ~/.petscrc
sys: src/sys/examples/tests/ex30.c -> src/sys/examples/tests/ex32.c to avoid conflict in master
Sed output, since quad precision reduces below atol on these tests
remove automatically generated matrix names from test output files since can be different
Fixes for MatMPIXXXSetPreallocation(), they were not reentrant, since they kept the information used for matrix-vector products
GAMG: fix PCView_GAMG() format - and update output/ex56_0.out
superlu_dist: 64-bit-indices fix https://github.com/xiaoyeli/superlu_dist/issues/4
Add SNESSetDivergenceTolerance / -snes_divergence_tolerance.
fixed unit read in Plex
...

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Merged in pefarrell/snes-divergence-tolerance (pull request #586)

Add SNESSetDivergenceTolerance / -snes_divergence_tolerance.

Add SNESSetDivergenceTolerance / -snes_divergence_tolerance.