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
...

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 'master' into knepley/feature-dm-bc-components

* master: (320 commits)
fix compile warning: /sandbox/petsc/petsc.clone/src/snes/examples/tests/ex2.c:250:8: warning: ‘pointsAllProcs’ m

Merge branch 'master' into knepley/feature-dm-bc-components

* master: (320 commits)
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
output has changed with e6d0a238963c2a97dd04845ea512b529992c7cdb so update the output file
...

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Merge remote-tracking branch 'origin/barry/update-petscfileretrieve'

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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add -snes_monitor_scaling

Commit-type: feature
Funded-by: IMEX
Project: chemistry
Time: .25 hours

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' into knepley/fix-plex-examples-cleanup

* master: (24 commits)
Bib: Added ref
shorten a url
remove the outdated paragraph on Eclipse instructions
Docs: manual - copyedit

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

* master: (24 commits)
Bib: Added ref
shorten a url
remove the outdated paragraph on Eclipse instructions
Docs: manual - copyedit for @caidao22 's update
I missed a n -> ierr changed needed in one of the error macros
Fix Fortran SETERRQ() to new calling sequence when compiled with no error checking
minor modifications for the added text
add Eclipse instructions to manual
PCHYPRE: add block nodal interpolations from command line customization
Plex: Now DMPlexGetRedundantDM() has more sensible behavior on 1 proc
SNES tutorial ex5s: fix typo ("parallism")
DMDA: fix typo in error messages ("parallism")
Plex: Drawing Vecs now works for multiple fields and components
SNES ex69: Started mantle test
SNES ex69: Fixed test
SNES ex69: Started a composite viscostiy test
SNES ex69: Updated BC specification
SNES ex69: Must use -pc_use_amat with FieldSplit
Plex+Draw: Improve viewer - Nice title - Allow override of min/max scale - Allow P0 and P1 (just quick and dirty)
Plex+VTK: Set boundary values with the time specified by the OutputSequence number
...

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Merge branch 'knepley/feature-snes-stokes-test'

* knepley/feature-snes-stokes-test:
Plex: Drawing Vecs now works for multiple fields and components
SNES ex69: Started mantle test
SNES ex69: Fi

Merge branch 'knepley/feature-snes-stokes-test'

* knepley/feature-snes-stokes-test:
Plex: Drawing Vecs now works for multiple fields and components
SNES ex69: Started mantle test
SNES ex69: Fixed test
SNES ex69: Started a composite viscostiy test
SNES ex69: Updated BC specification
SNES ex69: Must use -pc_use_amat with FieldSplit
Plex+Draw: Improve viewer - Nice title - Allow override of min/max scale - Allow P0 and P1 (just quick and dirty)
Plex+VTK: Set boundary values with the time specified by the OutputSequence number
Plex: Now only local vectors are used with the Draw viewer - Set boundary values with the time specified by the OutputSequence number
Plex: Fixed raw array access in DMPlexVecGetClosure()
Doc+SNES: I think the option should also be with the monitor function
TS ex47: Advection with Plex - I want to see if I can use MG

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Merge branch 'knepley/feature-plex-ex-advection' into knepley/feature-snes-stokes-test

* knepley/feature-plex-ex-advection:
Plex+Draw: Improve viewer - Nice title - Allow override of min/max sca

Merge branch 'knepley/feature-plex-ex-advection' into knepley/feature-snes-stokes-test

* knepley/feature-plex-ex-advection:
Plex+Draw: Improve viewer - Nice title - Allow override of min/max scale - Allow P0 and P1 (just quick and dirty)
Plex+VTK: Set boundary values with the time specified by the OutputSequence number
Plex: Now only local vectors are used with the Draw viewer - Set boundary values with the time specified by the OutputSequence number
Plex: Fixed raw array access in DMPlexVecGetClosure()
Doc+SNES: I think the option should also be with the monitor function
TS ex47: Advection with Plex - I want to see if I can use MG

Conflicts:
src/dm/impls/plex/plex.c

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Merge branch 'barry/remove-funct'

Doc+SNES: I think the option should also be with the monitor function

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

This is needed to deal with some changes in MatNullSpace from commit 9d2471e

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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Merged in pefarrell/snes-divergence-tolerance (pull request #586)

Add SNESSetDivergenceTolerance / -snes_divergence_tolerance.

Add SNESSetDivergenceTolerance / -snes_divergence_tolerance.

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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Merge branch 'master' into barry/fix-successful-numerical-factorization-after-failure/master

The maint patch for the given problem cannot merge cleanly into next due to changes
in the same code in m

Merge branch 'master' into barry/fix-successful-numerical-factorization-after-failure/master

The maint patch for the given problem cannot merge cleanly into next due to changes
in the same code in master (the introduction of MatFactorGetError()) therefor need
to merge in master and use the new construct before merging to next

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Merge branch 'master' into psanan/pc-telescope-nearnullspace

Merge branch 'master' into mark/snes-ex56

* master: (93 commits)
Web: Added a tutorial
typo
rename X -> U
sowing: update to version that creates manpage URLs for 'enum' types/values
Increa

Merge branch 'master' into mark/snes-ex56

* master: (93 commits)
Web: Added a tutorial
typo
rename X -> U
sowing: update to version that creates manpage URLs for 'enum' types/values
Increase patchlevel to 3.7.3
move runex3_3 to NOTSINGLE [ partial backport 9ed0bd76d5c329eb91401ebabfbd851446214e20 ]
DMPlex: local coordinate vector should be a sequential vector
DM: Name coordinate vectors in subdomain and restrict hooks
tests: disable a couple of TS examples from single precision tests
reduce TS ex12_2 output
fix PetscFormatRealArray() to cast PetscReal in print statement to double so works for __float128 precision
Vec: enable Fortran interfaces for VecGetLocalVectorRead and VecRestoreLocalVectorRead
Bib: Added refs
PCShell: man page fixes
update handling of latex in example code to use https
fix typo in isltog comment
test: Avoid conversion of object <-> function pointer type [-Wpedantic]
fortran: enable interface for VecGetLocalVector(), VecRestoreLocalVector()
update citation for cmz2016
PCBDDC: silent compilation warnings from nightlybuilds
...

# 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 'barry/add-snes-divtol'

add a divergence checker for SNES

Reported-by: Andrew Ho <andrewh0@uw.edu>

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