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 remote-tracking branch 'origin/knepley/feature-fe-dual-apply' into tisaac/feature-fe-dual-apply

* origin/knepley/feature-fe-dual-apply: (75 commits)
Plex: Screwed up last fix
Plex: Fix ove

Merge remote-tracking branch 'origin/knepley/feature-fe-dual-apply' into tisaac/feature-fe-dual-apply

* origin/knepley/feature-fe-dual-apply: (75 commits)
Plex: Screwed up last fix
Plex: Fix overeager protection of function
PetscFE: Fixed declaration
Travis-CI: Attempt to solve issues with gfortran
Travis-CI: Use newer macOS image
clarify damping and other issues related to SNESLINESEARCHBASIC
change example in new harness to use simple partitioner so gets consistent output on all systems
remove unused function from test file
cleanup formatting in example, plus myrank not rank
all requires need to go on the same line in test definition otherwise they are skipped
missing - makes the manual page formatting wrong
The developer manual clearly states that MPI_Comm_size() returns size it doesn't return numProcs or other nonsense. Pretty soon you'll start using mype instead of rank?
fix typo and cut and paste error in docs
bugfix for !HYPRE
fix warning for ';;'
may switch to scalable only when B->cmap->N > 100000
MatLRC: store in the context the parallel matrices rather than the sequential ones
Bib: Add ref
set default algorithm based on B->cmap->N for MatMatMult_MPIAIJ_MPIAIJ()
Error in VecScatterView_MPI() had the meaning of from and to backwards
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Merge branch 'knepley/feature-plex-tests-new' into knepley/feature-fe-dual-apply

* knepley/feature-plex-tests-new: (73 commits)
Plex: Fix overeager protection of function
Travis-CI: Attempt to s

Merge branch 'knepley/feature-plex-tests-new' into knepley/feature-fe-dual-apply

* knepley/feature-plex-tests-new: (73 commits)
Plex: Fix overeager protection of function
Travis-CI: Attempt to solve issues with gfortran
Travis-CI: Use newer macOS image
clarify damping and other issues related to SNESLINESEARCHBASIC
change example in new harness to use simple partitioner so gets consistent output on all systems
remove unused function from test file
cleanup formatting in example, plus myrank not rank
all requires need to go on the same line in test definition otherwise they are skipped
missing - makes the manual page formatting wrong
The developer manual clearly states that MPI_Comm_size() returns size it doesn't return numProcs or other nonsense. Pretty soon you'll start using mype instead of rank?
fix typo and cut and paste error in docs
bugfix for !HYPRE
fix warning for ';;'
may switch to scalable only when B->cmap->N > 100000
MatLRC: store in the context the parallel matrices rather than the sequential ones
Bib: Add ref
set default algorithm based on B->cmap->N for MatMatMult_MPIAIJ_MPIAIJ()
Error in VecScatterView_MPI() had the meaning of from and to backwards
fix build warning as reported by the nightly tests
Update alquimia.py to use Glenn's branch that updates alquimia for pflotran xsdk
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Merge branch 'master' into knepley/feature-plex-tests-new

* master: (94 commits)
Plex: Fix overeager protection of function
Travis-CI: Attempt to solve issues with gfortran
Travis-CI: Use newe

Merge branch 'master' into knepley/feature-plex-tests-new

* master: (94 commits)
Plex: Fix overeager protection of function
Travis-CI: Attempt to solve issues with gfortran
Travis-CI: Use newer macOS image
clarify damping and other issues related to SNESLINESEARCHBASIC
change example in new harness to use simple partitioner so gets consistent output on all systems
remove unused function from test file
cleanup formatting in example, plus myrank not rank
missing - makes the manual page formatting wrong
The developer manual clearly states that MPI_Comm_size() returns size it doesn't return numProcs or other nonsense. Pretty soon you'll start using mype instead of rank?
fix typo and cut and paste error in docs
bugfix for !HYPRE
fix warning for ';;'
may switch to scalable only when B->cmap->N > 100000
MatLRC: store in the context the parallel matrices rather than the sequential ones
Bib: Add ref
set default algorithm based on B->cmap->N for MatMatMult_MPIAIJ_MPIAIJ()
Error in VecScatterView_MPI() had the meaning of from and to backwards
fix build warning as reported by the nightly tests
Update alquimia.py to use Glenn's branch that updates alquimia for pflotran xsdk
fix divide by zero exposed by 8534686b5096cd4c91a8f3895408b386c0628431 - and produced by petsc4py testsuite
...

Conflicts:
src/dm/impls/plex/examples/tests/ex13.c
src/dm/impls/plex/plexgmsh.c
src/snes/examples/tests/ex2.c
src/snes/examples/tests/output/ex2_3.out
src/snes/examples/tests/output/ex2_4.out
src/snes/examples/tests/output/ex2_5.out

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PetscFE+FV: Now discretization can be vector spaces
- Space and DualSpace have a number of components
- Now the dimension of a space incorporates the components, so all size determinations changed
-

PetscFE+FV: Now discretization can be vector spaces
- Space and DualSpace have a number of components
- Now the dimension of a space incorporates the components, so all size determinations changed
- The default is to form direct sums of scalar spaces, e.g. for constants (1, 0) and (0, 1) so every
basis vector is a vector with only one component nonzero
- DualSpaceApply() is now handled by the implementation
- FE now uses numDof directly from the DualSpace
- Changed SpaceDG --> SpacePoint
- Updated ex3 tests (DA and p4est is still broken)

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Merge branch 'master' into scott/test-harness-forloopfix

Merge branch 'knepley/fix-plex-interp-parallel'

* knepley/fix-plex-interp-parallel:
SNES+Plex: Fixed bug with point location indexing - I switch to REMOVE, which changes the length of foundCells[]

Merge branch 'knepley/fix-plex-interp-parallel'

* knepley/fix-plex-interp-parallel:
SNES+Plex: Fixed bug with point location indexing - I switch to REMOVE, which changes the length of foundCells[]
SNES ex2: More tests for interpolation - Fixed test partitioning

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SNES+Plex: Fixed bug with point location indexing
- I switch to REMOVE, which changes the length of foundCells[]

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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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

Merge branch 'barry/remove-funct'

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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Merge branch 'knepley/fix-plex-interp-quad'

* knepley/fix-plex-interp-quad:
Plex: Quad interpolation should default to linear

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

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

Plex: Quad interpolation should default to linear

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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Merge branch 'knepley/feature-plex-bdfunc'

* knepley/feature-plex-bdfunc: (56 commits)
updated snes/ex56
updated snes/ex56
Plex: Goddamn it! Shadowing a variable name
PetscDS: Must be setup

Merge branch 'knepley/feature-plex-bdfunc'

* knepley/feature-plex-bdfunc: (56 commits)
updated snes/ex56
updated snes/ex56
Plex: Goddamn it! Shadowing a variable name
PetscDS: Must be setup in order to access field sizes and components
fix bad merge 44ac993612e1ca111ab14eba1c22039e0ba32a12 wrt src/snes/examples/tutorials/ex56.c [by attempting to redo the merge with kdiff3 - and then comparing the final result with the result in the above merge]
fixed snes/ex56 for PetscDSAddBoundary change
dmplexsnes: Remove more unused variables
Remove unused variables
SNES ex77: Must also set face quadrature
SNES ex12: No longer need boundary discretization orders
SNES ex62: Numerical flutter
SNES ex12: Numerical flutter
Plex: In projection, get Nc from DS instead of calculating it again
PetscFE: Added missing destroy
SNEX ex77: Update boundary args and FE creation
Plex: Update boundary integrals to new API
SNES ex12: Tests of bc from fields
SNES ex12: Added the ability to use finite element fields as boundary conditions
Plex: Need invJ for field projection
Plex: Fix bug with field projection - We must tabulate the FE on the dual basis quadrature points
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dmplexsnes: Remove more unused variables

Remove unused variables

Plex: Update boundary integrals to new API

Merge branch 'pr566/knepley/plex_bd_aux_field/master' into knepley/feature-plex-bdfunc

* pr566/knepley/plex_bd_aux_field/master: (22 commits)
PetscDS: reset max nr values for PetscOptionsIntArray(

Merge branch 'pr566/knepley/plex_bd_aux_field/master' into knepley/feature-plex-bdfunc

* pr566/knepley/plex_bd_aux_field/master: (22 commits)
PetscDS: reset max nr values for PetscOptionsIntArray()
SNES+Plex: dm was destroyed too early
Plex: use tabulation based on quadrature points of dual space, not the default tabulation in DMProjectFieldLocal()
SNES ex77: remove zero pointwise functions
PetscFE: only transform pointwise function if it is present
PetscDS: get rid of boundary discretizations
SNES ex77: update test
SNES ex77: simplify residuals/jacobians and delete unnecessary variables and functions
SNES+Plex: use all cell values to interpolate to face
PetscFE: add face quadrature and tabulation
PetscDS: cache number of components and dimensions of discretization space in PetscDS object
SNES ex77: simplify pointwise residual and jacobian for deformation
SNES ex77: move specifications of boundary conditions to command line options
SNES ex77: use auxiliary field for wall pressure
SNES+Plex: allow auxiliary fields in boundary residual/jacobian calculations
PetscDS: get rid of initialization with PetscContainer
SNES+Plex: move boundary jacobian calculation into seperate function
SNES ex77: remove BdResidual for pressure field
SNES+Plex: remove unnecessary (and wrong) loop in boundary residual/jacobian calculations
SNES+Plex: change DMGetField to PetscDSGetBdDiscretization in residual and jacobian calculation
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Conflicts:
include/petsc/private/petscfeimpl.h
src/dm/dt/interface/dtfe.c
src/dm/impls/plex/plexfem.c
src/snes/examples/tutorials/ex56.c
src/snes/examples/tutorials/ex77.c
src/snes/examples/tutorials/output/ex77_0.out
src/snes/utils/dmplexsnes.c

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Plex+SNES: Fix BC type handling

SNES+Plex: dm was destroyed too early