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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A variety of improvements/fixes for saving and accessing trajectories.

Fixed bugs in PetscReadBinaryTrajectory.m
Added PetscBinaryIOTrajectory.py to read in trajectories in Python
Fixed bug in all t

A variety of improvements/fixes for saving and accessing trajectories.

Fixed bugs in PetscReadBinaryTrajectory.m
Added PetscBinaryIOTrajectory.py to read in trajectories in Python
Fixed bug in all the trajectory file saving routines that used PETSC_COMM_WORLD instead of the MPI_Comm associated with the TS object.

Funded-by: IMEX
Project: adjoints
Time: 2 hours
Reported-by: Shashikant M. Aithal <aithal@cels.anl.gov>

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fix -Wstrict-prototypes warnings

Reported-by: Till Martens <till.martens@dlr.de>

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 'pr605/mapdes/runtime-noviewfromoptions/master'

Allow runtime control of viewer creation in PetscOptionsGetViewer

27b0f28 (Added configure option --with-viewfromoptions=0) allows
building PETSc such that PetscOptionsGetViewer never returns a view

Allow runtime control of viewer creation in PetscOptionsGetViewer

27b0f28 (Added configure option --with-viewfromoptions=0) allows
building PETSc such that PetscOptionsGetViewer never returns a viewer.
Sometimes it is useful to control this at runtime. For example, we
would like to still use -log_view and the like, but want to turn off the
expensive XXXViewFromOptions and similar calls inside small subsolves.
Allow this by exposing control at runtime. Typical use case:

PetscOptionsPushGetViewerOff(PETSC_TRUE);
for (i = 0; i < npatch; i++)
KSPSolve(patch[i], ...);
PetscOptionsPopGetViewerOff();

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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 'stefano_zampini/feature-convert-matnest-matis' into stefano_zampini/feature-pcbddc-saddlepoint

I have to merge it here, since there's an API addition for MatIS in stefano_zampini/featu

Merge branch 'stefano_zampini/feature-convert-matnest-matis' into stefano_zampini/feature-pcbddc-saddlepoint

I have to merge it here, since there's an API addition for MatIS in stefano_zampini/feature-pcbddc-saddlepoint
that prevents me to smoothly merge stefano_zampini/feature-convert-matnest-matis into next.

This will also facilitate merging stefano_zampini/feature-pcbddc-saddlepoint into master

Conflicts:
src/docs/website/documentation/changes/dev.html

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Removed crumbs from previous support of Netcdf. Support was removed in 2010

Time: .2 hours

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

Merge branch 'tisaac/sf-fix-multi-sf-leaves' into tisaac/dmp4est-feature-injection

* tisaac/sf-fix-multi-sf-leaves: (174 commits)
PetscSF: fix PetscSFGetMultiSF() for sparse leaves
PetscSF: make

Merge branch 'tisaac/sf-fix-multi-sf-leaves' into tisaac/dmp4est-feature-injection

* tisaac/sf-fix-multi-sf-leaves: (174 commits)
PetscSF: fix PetscSFGetMultiSF() for sparse leaves
PetscSF: make regression test that fails
few more clang static analyzer fixes
many issues detected by clang static analyzer
Update hypre to its release version
Updates for xSDKTrilinos builds
Added --download-xsdktrilinos
Communicator passed to VecCreateSeq should be PETSC_COMM_SELF
PCMG man page: fix typo in options name
Bib: Added refs
DMLabel: Removed unused variable
Metis tries to use backtrace which requires -lexecinfo on some systems such as freebsd Remove -lexecinfo from freebsd configure files since it is only needed by metis
add alternative output that occurs on some systems due to use of random number generator in partitioner
Plex: When creating cohesive submeshes, fix memory leak
Plex ex11: Updated output for new distribution algorithm
Plex: When explicitly distributing the depth label, we must recreate empty strata
Plex: When partitioning, the cell numbering should include hybrid points
Plex: Allow cell and vertex numberings to include hybrid points
need to show diffs of ex22 if it fails
Support two different output for test example, since due to roundoff this example can produce slightly different convergence history
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Merge branch 'master' of https://bitbucket.org/petsc/petsc

Merge branch 'barry/monitor-fromoptions'

Introduce PetscViewerAndFormatCreate() to partner with PetscViewerAndFormatDestroy()

Time: . 1 hours
Thanks-to: Lawrence Mitchell <lawrence.mitchell@imperial.ac.uk>

Fix serious bug introduced with introduction of XXXMonitorSetFromOptions() that resulting in
excessive pushes to viewer formats and caused different viewers to overwrite each others formats

Time: .7

Fix serious bug introduced with introduction of XXXMonitorSetFromOptions() that resulting in
excessive pushes to viewer formats and caused different viewers to overwrite each others formats

Time: .7 hours
Reported-by: Lawrence Mitchell <lawrence.mitchell@imperial.ac.uk>

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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

Merge branch 'master' into barry/downloads

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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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 hongzh/add-checkpointing-support-for-adaptive-ts

Merge branch 'barry/fix-log-summary-format'

Deprecate PetscViewerSetFormat() since it better to use PetscViewerPush/PopFormat() and using
PetscViewerSetFormat() can lead to confusing situations for users when later viewers do not recognize the

Deprecate PetscViewerSetFormat() since it better to use PetscViewerPush/PopFormat() and using
PetscViewerSetFormat() can lead to confusing situations for users when later viewers do not recognize the set
format and thus do not produce any information.

Reported-by: Jed Brown <jed@jedbrown.org>

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