Merge branch 'tisaac/plex-fix-copy-coordinates' into tisaac/dm-boundary-in-ds

Fixes some regression tests so that I can verify the changes of this branch

* tisaac/plex-fix-copy-coordinates:
DMPle

Merge branch 'tisaac/plex-fix-copy-coordinates' into tisaac/dm-boundary-in-ds

Fixes some regression tests so that I can verify the changes of this branch

* tisaac/plex-fix-copy-coordinates:
DMPlex: don't copy coordinates to self
add X monitoring of residual norm and true residual norm to example since not currently tested
TSAdaptSetType() had no manual page
remove a couple of seemingly strange unneeded PetscReturnFunction(ierr)
manual page for PetscLogObjectMemory()
missing manual page for TaoConvergedReason
tree: workarround bug 'cannot handle multipe #requirespackage listing'.
add no-change test for KSPCR and KSPLCD
configure: improve -fPIC test for ubuntu 16.10
sys: print scanf/PetscInt with --with-clanguage=C++ --with-64-bit-indices=1 --with-scalar-type=complex --with-mpi=0
Fix PCTFS and add test code for symmetric and non-symmetric version
fix a bug due to Lisandro Dalcin's commit d61f013 TS: Run forward cost integral after event handling if step not rolled back
name space Event* and Class* utility functions with Petsc

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missing manual page for TaoConvergedReason

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

Merged petsc/petsc into master

Merge remote-tracking branch 'origin/knepley/fix-plex-hdf5-label' into tisaac/dmforest

* origin/knepley/fix-plex-hdf5-label: (50 commits)
Plex: Fixed HDF5 output for DMLabel - The ISAllGather() wa

Merge remote-tracking branch 'origin/knepley/fix-plex-hdf5-label' into tisaac/dmforest

* origin/knepley/fix-plex-hdf5-label: (50 commits)
Plex: Fixed HDF5 output for DMLabel - The ISAllGather() was being called with an IS that had COMM_SELF - Also, we needed to protect for empty index arrays
superlu_dist: install target should first make sure prefix/[include,lib] dirs exist - similar to superlu
dm: add DMRemoveLabel() fortran interface
nightlybuilds: allocate more time to run arch-linux-xsdk-dbg build...
Remove superfluous information messages
Cannot have rank 1 print before parallel print since it may end up before or after the print from process 0. There change to have rank 0 print the sequential matrix
Bib: Added ref
Plex: Update ex12_5 with correct level-2 overlap
DMLabel: Add missing cleanup for DMLabelGather()
mpiuni: check for "long_long" before checking for "__int64" [as "typedef __int64" gives error with icc] Note: cannot use 'int64_t' as 'typedef unsigned int64_t foo' gives eror with icc
Add filter for solaris linker scope warning to master since that is used in nightly tests of next
Previous commit did not correctly handle downloading from --with-packages-dir
Use special error code of 10 for output list of needed downloaded package tarballs otherwise the outer configure.py script converts the error code to an error message we do not want.
Have ./configure return a nonzero exit code when --with-packages-dir detects missing packages so that calling scripts know this is occurred simplify some code
Completed support for --with-packages-dir=directory that allows --download-xxx features to be cleanly used behind firewalls etc also updated to docs to indicate this new feature
Adding supporting for --download-xxx to reported needed downloads when off line or behind a firewall and using local copies when available with the --with-packages-dir=directory option
Fix typos in linesearch impls:armijo, morethuente, owarmijo.
PetscDraw: Explicitly save draw in KSP/SNES/TS monitors
PetscViewerDraw: Propagate prefix from viewer to draw contexts
PetscDraw: Explicitly save draw in {Vec|Mat|DMDA}View() routines
...

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Merge branch 'sarich/feature-tao-pounders-add-correlations'

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

Conflicts:
src/ksp/pc/impls/bddc/bddc.c
src/ksp/pc/impls/bddc/bddcgraph.c
src/ksp/pc/impls/bddc/bddcprivate.c
src/ksp/pc/imp

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

Conflicts:
src/ksp/pc/impls/bddc/bddc.c
src/ksp/pc/impls/bddc/bddcgraph.c
src/ksp/pc/impls/bddc/bddcprivate.c
src/ksp/pc/impls/bddc/bddcscalingbasic.c
src/ksp/pc/impls/bddc/bddcschurs.c
src/mat/impls/is/matis.c

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Merge branch 'master' into barry/add-pcfieldsplit-logevent

add correlations to subproblem

Merge branch 'master' into barry/add-pcreset-hypre-for-master

Needed to move PCDestroy_HYPRE() added to master to PCReset_HYPRE() since that was introduced
as a bug fix for maint

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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Merge branch 'master' into hongzh/checkpointing

Manual merges for a couple of PetscOptions changes in master

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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Merge branch 'master' into pr391/zianekhodja/lilia/tsirm/master

add correlations to subproblem

Merge branch 'sarich/fix-tao-documentation-type'

fix typo in TaoGetFunctionLowerBound documentation

Merge branch 'master' into knepley/feature-plex-add-time

* master: (57 commits)
add fortran stub for TSMonitorLGSetTransform() and fix TSMonitorLG for multiple fields but no names provided for fie

Merge branch 'master' into knepley/feature-plex-add-time

* master: (57 commits)
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
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
mark variable as unused so compiler doesn't warn about unused value
configure: use 'git cat-file -e' to check for existance of a commit in localrepo. ['git rev-parse' does not give error for a hash thats not in repo]
petsc4py: revert to manually syncing petsc4py with petsc master changes
configure: revert gitcommit default value to Null. If a pacakge using giturl does not change this value - raise an error
fix: revert change in a44bcdf that breaks with pgf90
update test output for fixed to hypre interface that now actually pass the interp vectors to BoomerAMG
fixes for merge from Jed's branch that should have been merged into master months ago!
Add to changes dev.html file the change to the PetscOptions routines
...

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

Merge remote-tracking branch 'petsc/master' into moved-partitioning-to-pcgasmsetup

Merge branch 'tisaac/dm-label-promote' into tisaac/dmforest

* tisaac/dm-label-promote: (319 commits)
snes tutorial ex69: give mesh a name for regression purposes
DM: make DMLabel labels a part o

Merge branch 'tisaac/dm-label-promote' into tisaac/dmforest

* tisaac/dm-label-promote: (319 commits)
snes tutorial ex69: give mesh a name for regression purposes
DM: make DMLabel labels a part of all DMs
builder: update regression tests
builder: update some missing package requirements
DM: set coordinate vector name
ts tutorials ex11_sa: make it compile
mark variable as unused so compiler doesn't warn about unused value
configure: use 'git cat-file -e' to check for existance of a commit in localrepo. ['git rev-parse' does not give error for a hash thats not in repo]
petsc4py: revert to manually syncing petsc4py with petsc master changes
configure: revert gitcommit default value to Null. If a pacakge using giturl does not change this value - raise an error
fix: revert change in a44bcdf that breaks with pgf90
update test output for fixed to hypre interface that now actually pass the interp vectors to BoomerAMG
Error message should say use negative threshold value to prevent filtering out zeros
Calls to HYPRE_BoomerAMGSetInterpVectors() did not actually copy the vector data pointer from the PETSc vector to the hypre vector thus resulting in the hypre interp vectors being identically zero and hence not affecting the quality of the AMG hierarchy produced/
DMPlex: Silence overzealous compiler warnings
add row/col orientation to MatConvert_Elemental_Dense
fix formatting error in previous commit [broke nightlybuilds]
fix formating of TSTHETA manual page and add missing command line option
run hwloc with MPIEXEC and binding so it runs on the correct machine
fix: memory leaks [in valgrind test]
...

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Merge branch 'barry/petscoptions-object'

Merge branch 'barry/petscoptions-object' into stefano_zampini/feature-pardiso-schur

Merge branch 'master' into barry/petscoptions-object

Merge remote-tracking branch 'petsc/master' into moved-partitioning-to-pcgasmsetup