Merge branch 'tisaac/fix-dm-tests' into tisaac/feature-plex-tests-new

* tisaac/fix-dm-tests:
dmplex tests ex1: update output for ISLocalToGlobalMapping changes
DMNetwork: Use the default section

Merge branch 'tisaac/fix-dm-tests' into tisaac/feature-plex-tests-new

* tisaac/fix-dm-tests:
dmplex tests ex1: update output for ISLocalToGlobalMapping changes
DMNetwork: Use the default sections with plex when getting offset.
Add another extchem test case
Fix for extchem.c when envelop monitor is on, but graphical monitoring is off
TSAdapt ascii view should show dt_min and dt_max
Forgot to include example file
Change extchem.c to accept mole values for initial conditions instead of mole fractions
Update extchem.c example to 1) use pressure, 2) use options file, 3) read initial conditions from file
DMNetwork: API to return the underlying DMPlex.
deprecate MatGetSubMatXXX Requested-by: Jed Brown <jed@jedbrown.org>
Work around for Apple Xcode bug with rpath
DMPlex_GMSH: triangles are inverted
bib: fix URL for StarForest note
rm MatLUFactorNumeric_SeqBAIJ_11_NaturalOrdering() because it does not improve performance add MatSolve_SeqBAIJ_bs_NaturalOrdering(), bs=12,...,14 add test runex50_2
experiment PetscKernel_A_gets_A_minus_B_times_C_11
add timer to MatLUFactorNumeric_SeqBAIJ_11_NaturalOrdering()
test new A = A*B
implement MatSolve_SeqBAIJ_11_NaturalOrdering
Merge two line TSAdapt monitor to a single line, shorten line, reorder presented values
implement PetscKernel_A_gets_A_times_B_11()

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Mat: forgot the update enum and fortran for MatMatSolveTranspose

Mat: Added schur and schur_status to the private implementation

This permits to simplify a lot the code for handling Schur complements computations
from factorization packages.
Added factorschur.c t

Mat: Added schur and schur_status to the private implementation

This permits to simplify a lot the code for handling Schur complements computations
from factorization packages.
Added factorschur.c to store intermediate routines
Removed MatFactorSetSchurComplementSolver that was horrible

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Mat: added interface function for MatMatSolveTranspose

Mat: added MatFactorSchurStatus to enable the user to progress factorization/inversion of the Schur complement

Merge branch 'hzhang/deprecate-getsubmat'

deprecate MatGetSubMatXXX
Requested-by: Jed Brown <jed@jedbrown.org>

Merge branch 'knepley/fix-plex-example-logging' into knepley/feature-plex-torus

* knepley/fix-plex-example-logging: (151 commits)
Plex ex12: Added logging stages
Plex ex1: Added logging stages

Merge branch 'knepley/fix-plex-example-logging' into knepley/feature-plex-torus

* knepley/fix-plex-example-logging: (151 commits)
Plex ex12: Added logging stages
Plex ex1: Added logging stages
update to latest hypre tag on github
fix 'inf' vs 'Inf' diff wrt vec_vec_utils_tagger_tutorials-ex1_8,9,18,19
MatSetOption(mat,MAT_IGNORE_ZERO_ENTRIES,PETSC_TRUE) no longer applies to zero values set or added to the matrix diagonal, they are now not ignored and are included in the matrix nonzero structure. This is useful for Jacobians passed to TS.
replace use/mention of depreciated -log_summary in many places
add extchem.py which was written years ago but never put in the distribution (hence it is broken).
petsc4py: update to snapshot with MatGetSubMatrices -> MatCreateSubMatrices etc API changes
Minor fixes for tchem examples due to changes in PETSc infrastructure
update webpage about API changes
add help menu for MatCreateSubMatricesMPI()
PetscCMPLX: assume type punning is safe
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
...

Conflicts:
src/dm/impls/plex/examples/tests/ex1.c
src/dm/impls/plex/examples/tests/ex12.c

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Merge branch 'knepley/fix-plex-example-logging' into knepley/feature-plex-tests-new

* knepley/fix-plex-example-logging: (151 commits)
Plex ex12: Added logging stages
Plex ex1: Added logging stag

Merge branch 'knepley/fix-plex-example-logging' into knepley/feature-plex-tests-new

* knepley/fix-plex-example-logging: (151 commits)
Plex ex12: Added logging stages
Plex ex1: Added logging stages
update to latest hypre tag on github
fix 'inf' vs 'Inf' diff wrt vec_vec_utils_tagger_tutorials-ex1_8,9,18,19
MatSetOption(mat,MAT_IGNORE_ZERO_ENTRIES,PETSC_TRUE) no longer applies to zero values set or added to the matrix diagonal, they are now not ignored and are included in the matrix nonzero structure. This is useful for Jacobians passed to TS.
replace use/mention of depreciated -log_summary in many places
add extchem.py which was written years ago but never put in the distribution (hence it is broken).
petsc4py: update to snapshot with MatGetSubMatrices -> MatCreateSubMatrices etc API changes
Minor fixes for tchem examples due to changes in PETSc infrastructure
update webpage about API changes
add help menu for MatCreateSubMatricesMPI()
PetscCMPLX: assume type punning is safe
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
...

Conflicts:
src/dm/impls/plex/examples/tests/ex12.c

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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 'master' of bitbucket.org:petsc/petsc

Merge remote-tracking branch 'origin/hzhang/rename_matgetsubmats'

rename MatCreateSubMatrixComposite -> MatCreateSubMatrixVirtual; Mat_SubMatrix -> Mat_SubVirtual

rename MatGetSubMat -> MatCreateSubMat

Merge branch 'hzhang/fix-getsubmats-reuse'

add MatDestroySubMatrices(); bugfix

add MATDUMMY for saving matrix reuse data

Merge branch 'master' into knepley/fix-plex-examples-cleanup

* master: (156 commits)
Doc: Added headers for documentation sections
Bib: Small corrections
doc: update example makefiles with del

Merge branch 'master' into knepley/fix-plex-examples-cleanup

* master: (156 commits)
Doc: Added headers for documentation sections
Bib: Small corrections
doc: update example makefiles with deleted sourcefile info
doc: fix manual build errors
doc: fix SOURCEH for some fortran includes that got moved
doc: fix broken manualpages - bug introduced by 1b266c9
MatMissingDiagonal() is actually not a collective operation
PetscFECreateDefault(): allow 0th order quadrature
fix gmakegentest.py to ignore *.xx files that are not source code but are in the files
increase table input size to (A->cmap->n + a->B->cmap->N) for MatTransposeMatMultSymbolic_MPIAIJ_MPIAIJ()
gtest: add TEST and RM clean output for Satish
gtest: set PATH for windows DLL tests, and enable -Dpetsc_EXPORTS only during (dll) build - and not for examples
gtest: use target-specific var to deduplicate FC rules for modules
gtest: for 'allgtest' and 'allgtest-tap' - use V=0 instead of 'grep -v CC' etc..
gtest: quiet absoft compiler commands [so they can be filtered].
remove incorrect requires from more test files, remove output from -fp_trap example in test because it cannot be machine independent
gtest: windows fixes. add filter to remove filename from compiler stdout. And fix filters to use petscdiff
Removed generated requires in the wrong place from test examples.
Fix test output for additional information printed about computed eigenvalues
gtest: fix ex5f.F to use 'format' so that the output from ifort matches the one from gfortran
...

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Merge branch 'barry/convert-clique-to-elemental'

Merge branch 'barry/add-MatSeqSBAIJGetArray'

Add MatSeqSBAIJGetArray() and MatSeqSBAIJRestoreArray()

Interestingly the private functions for SABIJ where already in the source code
Time: .15 hours
Reported-by: Eric Chamberland <Eric.Chamberland

Add MatSeqSBAIJGetArray() and MatSeqSBAIJRestoreArray()

Interestingly the private functions for SABIJ where already in the source code
Time: .15 hours
Reported-by: Eric Chamberland <Eric.Chamberland@giref.ulaval.ca>

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Start to update Clique to SparseElemental interface.

Merge branch 'barry/fix-matreuse'

Add more error checks for use of MatReuse; change MatTranspose() to use MatReuse as used by other functions

Time: 2.5 hours
Reported-by: Stefano Zampini <stefano.zampini@gmail.com>, Eric Chamberlan

Add more error checks for use of MatReuse; change MatTranspose() to use MatReuse as used by other functions

Time: 2.5 hours
Reported-by: Stefano Zampini <stefano.zampini@gmail.com>, Eric Chamberland <Eric.Chamberland@giref.ulaval.ca>

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Merge branch 'pefarrell/mat-galerkin'