Merge branch 'master' into knepley/feature-pc-patch

* master: (33 commits)
cleanup very ugly PCGAMG manual page
minor clarifications for VecScatterCreate() manual page
gcov: PETSC_ARCH is requ

Merge branch 'master' into knepley/feature-pc-patch

* master: (33 commits)
cleanup very ugly PCGAMG manual page
minor clarifications for VecScatterCreate() manual page
gcov: PETSC_ARCH is required onlyfor -run_gcov - and not for -merge_gcov [where it doesn't exist]
make clearer in help statements what --with-external-packages-dir is for.
Website: Added news entry for PETSc User Meeting 2018 on main page.
KSPGUESSPOD: exclude negative of zero eigenvalues from the energy computation
KSPGUESSFISCHER: use PetscInfo for KSP class
CUDA: Further test output fixes for mat_tests-ex2
Turn off elemental test for parmetis running since this does not work on batch systems.
3.8 Changes: KSPCHEBYSHEV
CUDA: Fixed most test errors due to MatMultTranspose*
KSPFGMRES: add KSP_NORM_NONE / PC_RIGHT as supported
KSPSetSupportedNorm man page: remove old note about default support for KSP_NORM_NONE
Dev manual: copyedit
DMPlexDistributeLabels: Propagate the output flag
cuda/cusp: update minimum supported versions of cuda to 7.5 and cusp to 0.5.0
cuda: remove configure option -with-cuda-arch. [use CUDAFLAGS instead]
projected gradient code fixed to obey recent convergence test changed
Merge conflicts resolved after rebase
norm update bug fixed in GPGC, test output reverted
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Merge remote-tracking branch 'origin/knepley/fix-snes-ex69' into tisaac/feature-dmfield

* origin/knepley/fix-snes-ex69: (311 commits)
PetscFECreateDefault: fix custom Fortran interface to use MPI_

Merge remote-tracking branch 'origin/knepley/fix-snes-ex69' into tisaac/feature-dmfield

* origin/knepley/fix-snes-ex69: (311 commits)
PetscFECreateDefault: fix custom Fortran interface to use MPI_Comm
SNES ex69: Updated test output
SNES ex69: Removed all mantle stuff and change fields to constants - Also use dsymutil for executables
SNES ex69: Removed special partition
SNES ex69: Fixed null space creation - Null space locks its vectors
PetscFE: PetscFECreateDefault() now takes MPI_Comm instead of DM
cleanup very ugly PCGAMG manual page
minor clarifications for VecScatterCreate() manual page
gcov: PETSC_ARCH is required onlyfor -run_gcov - and not for -merge_gcov [where it doesn't exist]
make clearer in help statements what --with-external-packages-dir is for.
Website: Added news entry for PETSc User Meeting 2018 on main page.
CUDA: Further test output fixes for mat_tests-ex2
Turn off elemental test for parmetis running since this does not work on batch systems.
3.8 Changes: KSPCHEBYSHEV
CUDA: Fixed most test errors due to MatMultTranspose*
website: update urls
website: fix Jason's name to match pic. Also add Todd's pic
Dev manual: copyedit
DMPlexDistributeLabels: Propagate the output flag
cuda/cusp: update minimum supported versions of cuda to 7.5 and cusp to 0.5.0
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Merge branch 'denera/tao-convergence-check-fix' [PR #886]

* denera/tao-convergence-check-fix:
TaoMonitor no longer has double-duty for both monitoring and updating the converged reason.
The converge

Merge branch 'denera/tao-convergence-check-fix' [PR #886]

* denera/tao-convergence-check-fix:
TaoMonitor no longer has double-duty for both monitoring and updating the converged reason.
The convergence function is now called explicitly in the algorithms following the monitor call, mimicking the current implementation of SNES.

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fix propagated throughout, convergence tolerance bug discovered and fixed in toy problem

Merge branch 'denera/fix-tablevels-for-views' [PR #869]

* denera/fix-tablevels-for-views:
Instead of manual push-pop tab operations, views now inherit tablevels automatically.
This makes views consi

Merge branch 'denera/fix-tablevels-for-views' [PR #869]

* denera/fix-tablevels-for-views:
Instead of manual push-pop tab operations, views now inherit tablevels automatically.
This makes views consistent with default convergence monitors.

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Wrapping up for a pull request

Merge branch 'master' into stefano_zampini/feature-gmsh-periodic

* master: (1016 commits)
metis: setself.downloaddirnames for change in 6d90219d8fa4f8b2fd242cc6ff9008358d87c26f
fix compile warni

Merge branch 'master' into stefano_zampini/feature-gmsh-periodic

* master: (1016 commits)
metis: setself.downloaddirnames for change in 6d90219d8fa4f8b2fd242cc6ff9008358d87c26f
fix compile warning: /sandbox/petsc/petsc.clone/src/snes/examples/tests/ex2.c:250:8: warning: ‘pointsAllProcs’ may be used uninitialized in this function [-Wmaybe-uninitialized] ierr = DMInterpolationSetUp(interpolator, dm, pointsAllProcs);CHKERRQ(ierr);
migrate 'build requires: !mpiuni' to new format
migrate 'build requires: !complex' to new format
workarround 'division by zero' compiler warning on windows C:\cygwin64\home\petsc\PETSC~3.CLO\src\ts\examples\TUTORI~1\ex11.c(416): warning #39: division by zero if (uL->h < 0 || uR->h < 0) {for (i=0; i<1+dim; i++) flux[i] = 0./0.; return;} /* SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Reconstructed thickness is negative"); */
dos2unix to prevent warnings on opensolaris "/export/home/petsc/petsc.clone/src/ksp/ksp/examples/tests/ex53.c", line 6: warning: invalid white space character in directive
fix output file - corresponding to code changes in efd4aadf157bf1ba2d80c2be092fcf4247860003
disable test on windows
update log from opensolaris so that the diff is clean on linux aswell
update grep in sync with change in efd4aadf157bf1ba2d80c2be092fcf4247860003
Fixed code that did not correctly set current color for block insertion
Update output files that did not get fixed after previous merges
Change MPIUni to not immediately abort on operations it cannot perform, instead return error code
Add filter for example that can produce 1 different iteration count
Example add system calloc, bad formating of %d in print, commented out code
Always use (void) for functions that take no arguments, never ()
always need to caste PetscReal variables to (double) in print statements
updates to manual page for clarity
update help menu for MatRARt() -- MatRARt_mpiaij_mpiaij is supported now, but not efficient.
fix nightlybuild error with c1cbb1def3f8ddca04c3998b9c06618fd1ffef35 on arch-linux-IPL64 src/ksp/pc/examples/tests ex5_1
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Conflicts:
include/petscdm.h
src/dm/impls/plex/plexcreate.c
src/dm/impls/plex/plexgmsh.c
src/dm/impls/plex/plexhdf5.c

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Merge branch 'scott/test-datafiles-fix' of https://bitbucket.org/petsc/petsc into scott/test-datafiles-fix

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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Merge branch 'master' into stefano_zampini/feature-fetidp-ex69

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

Merged in dalcinl/fix-math (pull request #675)

Fix math calls to use the macros in petscmath.h

Approved-by: BarryFSmith <bsmith@mcs.anl.gov>

Fix math calls to use the macros in petscmath.h

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

Merge branch 'master' into knepley/feature-plex-handle-func-failure

* master: (378 commits)
SNES ex5: Fix coordinate determination for empty subdomains
fixed petsc.bib entry
p4est: fix syntax

Merge branch 'master' into knepley/feature-plex-handle-func-failure

* master: (378 commits)
SNES ex5: Fix coordinate determination for empty subdomains
fixed petsc.bib entry
p4est: fix syntax error with error message
SNES ex5: Correct Jacobian handling on patches
SNES ex5: Stupid complex fixes
DMP4est: fix transfer of labels to parents
petsc4py: update to latest snapshot. Fixes da example breakage in petsc4py test suite
Plex: Correct setting of options on refined or coarsened meshes
Plex: Add info for grid hashing
Plex: Add logging in interpolator creation
Plex: Correct use of tabs in ASCII viewer
DM: Shorten long event name
Plex ex12: Create boundary label automatically at all levels of mesh hierarchy
Plex ex12: Change PetscViewerSetFormat --> PetscViewerPushFormat - Fix order of SetMode and SetFilename
Plex ex12: Change all functions to static
Since DMDA with periodic boundary conditions does support P0 interpolation remove checks that error out under those conditions
ascem-io.py and amanzi.py need to handle self.hdf5.include being None correctly
fix MPI Uni to recycle communicators so it won't run out like with the petsc4py tests also fix check for location of python shared library on mac to check all cases each time
Switch back to Sherry's version since she accepted by pull request
PetscDraw: Update help messages for -draw_save* options
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Conflicts:
src/dm/impls/plex/plexfem.c

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Merged petsc/petsc into master

Merge branch 'barry/fix-private-functions'

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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labeled a variety of additional internal functions as static
to prevent them from being publically available in the library

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

Merge branch 'tisaac/dmforest' of bitbucket.org:petsc/petsc into tisaac/dmforest

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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