Vec example should only include petscvec.h not petsc.h

a variety of corrections suggested by the clang static analyzer

Time: 1 hour

PetscSFDistributeSection(): handle case when nrooots < end of chart

PetscSF: fix PetscSFGetMultiSF() for sparse leaves

PetscSF: make regression test that fails

The multiSF doesn't use the sf->mine array.

Merge branch 'tisaac/dmforest'

* tisaac/dmforest: (36 commits)
DMP4est: fix transfer of labels to parents
DMPlexCreateInterpolatorTree: fix handling of global dofs (can be < 0)
DMPlexComputeIn

Merge branch 'tisaac/dmforest'

* tisaac/dmforest: (36 commits)
DMP4est: fix transfer of labels to parents
DMPlexCreateInterpolatorTree: fix handling of global dofs (can be < 0)
DMPlexComputeInterpolatorTree(): fix workspace size
DM: warn when no injection implemented
DMPlexComputeInterpolatorTree(): use row layout to preallocate
DMP4est: all processes agree on root type
DMPlexComputeInterpolatorTree(): valgrind fixes
DMP4est: reset childID if anctecedent is not parent
DMP4est: send labels from children to parents and bcast
DMForest: added DMForestGetAdaptivityPurpose()
DMP4est: enable caching of results of DMPforestGetTransferSF()
Plex: fix empty partition errors
DMPforestGetTransferSF_Internal(): handle different type roots on different processes
DMP4est: broadcast labels when transfering for agreement
PetscSFBasic: fix usage of MPI_Reduce_local
DMPforestLabelsInitialize(): search through parents when finding a point in the closure
DMP4est: try to connect high strata points when transfering
DMP4est: can't use PetscSFCreateSectionSF. It compresses when we don't want to
DMP4est: expand transfer sfs by the CellSF
DMP4est: add DMForestCreateCellSF_p4est
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Merge branch 'barry/fix-private-functions'

PetscSFBasic: fix usage of MPI_Reduce_local

If we couldn't use one of the predefined ops, then the user must specify
an op that operates on the whole datatype passed to
PetscSFReduceBegin()/PetscSFR

PetscSFBasic: fix usage of MPI_Reduce_local

If we couldn't use one of the predefined ops, then the user must specify
an op that operates on the whole datatype passed to
PetscSFReduceBegin()/PetscSFReduceEnd(). In this setting, a block size
(link->bs) that is not equal to 1 is sometimes calculated, because it
may be determined that the datatype is in fact a contiguously packed set
of e.g., PetscInt. That block size must be ignored in this setting,
because (link->bs * typesize) is not the data stride, typesize is.

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More decreasing visibility of symbols from outside libraries
Also fix a few bugs related to having multiple PETSc libraries

convert private functions to static to decrease the unneccessary function in
the public interface in the libraries

Merge branch 'master' into tisaac/dmforest

* master: (87 commits)
fixed --download-xxx=/directory to not mistake other options such as --download-mpich-pm=hydra etc
Correct spelling for Autotool

Merge branch 'master' into tisaac/dmforest

* master: (87 commits)
fixed --download-xxx=/directory to not mistake other options such as --download-mpich-pm=hydra etc
Correct spelling for Autotools libtoolize in commit a0848688a08a6eb150afdc95a2f6ce49cd4cd079
Fix for commit c8b462efbd8e8a5f06df500cf417f3a48f2b88d9 Put back the gitpreReq() check that was needed for MOAB
website: fix Fluidity link
bib/cite: add UMFPACK
nightlybuilds: update test tu use newer intel compiler [detect and use compiler path]
nightlybuilds: fix vec/ex7,ex7f link issue by using the correct LIBS option
Added support for users to provide their own download package installers --download-xxx=/directory where the directory contains the file xxx.py that is a standard PETSc package definition like in config/BuildSystem/config/packages/xxx.py
nightlybuilds: switch default intel compiler [& MKL] from 13.1.3 to 16.0.0.
mkl_pardiso: fix runex125_mkl_pardiso
mkl_pardiso: fix runex2_mkl_pardiso_cholesky
nightlybuilds: switch OSX to use boost from brew [as --download-boost is broken]
trilinos: gitcommit - always specify branch as origin/branch
Add error check to boost.py when running on Mac OS because the shared libraries created do not work since they do not have the proper rpath set
Update output files for mpi matrices that use to be seq
Move PostProcess() runs until after PETSc configure has saved all data to the filesystem so that make install will work correctly.
Switch to Trilinos release candidate for --download-trilinos Tested, failed with unresolved Kokos methods, Issue report to Trilinos team
Some configure packages UnitTest-CPP requires libtoolize to be called before autoreconf on some systems
--download-ideas now downloads unittest-cpp
simplied ./configure packages that need autoreconf to be run first (like moab and unittest-cpp) added unittest-ccp download changed downloadfilename to downloaddirname since that is what it is
...

# 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

* master: (136 commits)
Make error message specific to exactly what matrix is supported
Prevent fblaslapack or f2cblaslapack from being compiled with t

Merge branch 'master' into tisaac/dmforest

* master: (136 commits)
Make error message specific to exactly what matrix is supported
Prevent fblaslapack or f2cblaslapack from being compiled with the -no-prec-dev Intel compiler option since it can produce incorrect results
Fix for PCReset_HYPRE to make it reentrant.
replace default superlu_dist '-mat_superlu_dist_colperm METIS_AT_PLUS_A' with MMD_ATA to avoid different random numbers for nightly tests
fixes for merge from maint patch
Added PCReset_HYPRE() so it may be used with SNESVI solvers
remove Microsoft compiler message for paste macros used for handling Blas/Lapack macro name mangling for example
Increase the number of PetscViewerPushFormat() possible to 25 and use a macro PETSCVIEWERFORMATPUSHESMAX for the value
Configure: Remove redundant logging
Bib: Added ref
nightlybuids: fix permissions of script
MatRegisterDestroy() does not exist but it is listed in manual pages
externalpackages-git: save local changes if any - in git stash - before 'git checkout -f' Useful incase --with-package-commit=HEAD option was msissing [perhaps due to a typo]
nightlybuilds: add xsdk builds
Add architectures for testing xsdk package downloads (Trilinos, Hypre, SuperLU)
create another version of TurnForward() for adaptive time stepping specifically
Configure: Give proper default if HOME is missing from the environment
fix abbreviation
allow zeropivot for MatSOR_SeqAIJ_Inode, node size=1
add test case using adpative time stepping for checkpointing type 'NONE'
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A fix for fieldsplit pcs when using snes virs.

When reset pc fieldsplit saves a copy of the original IS. SNES VIRS then calls a new function, PCFieldSplitRestrictIS, and supplies
the inactive set t

A fix for fieldsplit pcs when using snes virs.

When reset pc fieldsplit saves a copy of the original IS. SNES VIRS then calls a new function, PCFieldSplitRestrictIS, and supplies
the inactive set to create new ISs for the fieldsplit. This is then reindexed and passed down to any nested fieldsplits.

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Merge branch 'hzhang/update-networkex'

Merge branch 'master' into tisaac/dmforest

* master: (143 commits)
Revert "revolve: c++ compile fix" - as revolve now does not require 'bool' anymore
revolve: c++ compile fix
revolve: enable t

Merge branch 'master' into tisaac/dmforest

* master: (143 commits)
Revert "revolve: c++ compile fix" - as revolve now does not require 'bool' anymore
revolve: c++ compile fix
revolve: enable tests and add to nightlybuilds
fix download url for revolve
remove outdated unused script
removed outdated use of the term petsc-dev for the development version of PETSc
streams: precompute NPMAX - and use this value. And now user can use it optionally as:
mpich: default to using ver 3.2 on OSX/ElCapitan as 3.1.3 does not build on Barry's laptop
Revert "mpich: update version to mpich-3.2"
superlu/dist: disable build on freebsd - as this test is with bsdmake [and superlu requires gnumake]
superlu/dist: enable in complex nightly builds
fortran: fix typo with MATSEQAIJRESTOREARRAYF90
Documentation for Dense and SeqAIJ Get/RestoreArrayf90 had incorrect dimensions
Docs for MatGetRowIJF90() cut and paste and never fixed
Bib: NPC refs
superlu: no longer requires xerbla slamch dlamch ? $ nm -Ao libsuperlu_dist_4.3.a |egrep \(xerbla\|slamch\|dlamch\)
superlu_dist: update to version 4.3
Bib: More of our refs
added whitespaces to align numbers in verbatim environment
Added verbatim environment to special tokens
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Fix remaining valgrind complains: Calloc data to make sure it is initialized to zero

Merge branch 'pr388/mapdes/fix-petscsf-create-section-sf/master'

Merge branch 'master' into tisaac/dmforest

* master: (177 commits)
DT ex3: The test should check the number of digits requested
DT ex3: One test fails in single precision
Plex: Do not automati

Merge branch 'master' into tisaac/dmforest

* master: (177 commits)
DT ex3: The test should check the number of digits requested
DT ex3: One test fails in single precision
Plex: Do not automatically create a default section if no fields are defined
Plex: DMPlexCopyCoordinates() needs to create the coordinate section if it is missing
superlu: no longer requires xerbla slamch dlamch ?
superlu: update to v5.1
skip MatSolve() if matrix factorization fails
replacing SETERRQ with error output info and continue execution
SNES ex12: Added parallel tests - These test parallel, unstructured interpolation/restriction using FAS
Plex+SNES: Now in DMPlexComputeJacobian_Internal(), we also form the Jacobian preconditioner matrix
FE: Now we can form either the Jacobian or the Jacobian preconditioned matrix using a flag
DS: Now have point wise function slots for the Jacobian preconditioned matrix - This will allow us to form the "right" operator for preconditioning, like M in the (2,2) block for Stokes
Plex: When swapping Plexes, also swap point SF
Plex: Fix parallel error in Injector
Mat+Plex: Added MatPreallocator which can be called with MatSetValues() and preallocates another Mat - This could have been another "mode" of Mat, but I thought this was cleaner - Use MatPreallocator to preallocator Plex interpolators
DT ex3: Change tolerance and eliminate tests which need MPFR from regular runs
superlu: fix complex build
superlu: update to using 5.0 tarball with the fix for -Werror=format-security
superlu: update to use tarball with -Werror=format-security fix
DM: Clone the coordinate DM instead of reusing in Clone()
...

Conflicts:
config/builder.py
src/dm/impls/plex/plexcreate.c

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PetscSF: compile even if MPI_Reduce_local() is not available

Fix bad function rename and missed rename related to DMProject routines

Merge remote-tracking branch 'origin/knepley/feature-plex-add-time' into tisaac/dmforest

Both branches changeds DM projection behavior, so I wanted to sort it
out before merging

* origin/knepley/fe

Merge remote-tracking branch 'origin/knepley/feature-plex-add-time' into tisaac/dmforest

Both branches changeds DM projection behavior, so I wanted to sort it
out before merging

* origin/knepley/feature-plex-add-time: (59 commits)
SNES ex69: Updated to new function API, fixed test output
SNES ex75: Fixed for new function API
add fortran stub for TSMonitorLGSetTransform() and fix TSMonitorLG for multiple fields but no names provided for fields
add -binary_write_double so __float128 precision can save as double to binary files
TSClone() did not clone Fortran function pointers hence some TS methods would fail if functions provided in Fortan
petsc4py: update to snapshot with 'barry/petscoptions-object' changes
fix bad merge that introduced 2 copies of the MPI_Comm_free()
update example to use MAT_INPLACE_MATRIX, not REUSE
incorrect addition of float to PetscInt
update for new PetscOptions API
TS ex18: Fixed function API and test output
Function now takes PetscOptions as first argument, this was missed during the first round of updates
bugfix for MatSetOption_Elemental()
fix test example no change output that was missing a line
fixes for new PetscOptions.. API that are needed based on problems with nightly build
Plex ex3: Use new function API
SNES ex62: Use new function API
SNES ex12: Use new function API
Plex: Fixed unused options in examples
Plex+DMDA: Add time to signatures
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