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

Merge branch 'maint'

Conflicts:
config/PETSc/packages/SuiteSparse.py

build: fix error with mpiuni - when configure is run multiple times - we get error:


use mpi
1
Fatal Error: Can't open module file 'mpi.mod' for reading at (1): No such file or di

build: fix error with mpiuni - when configure is run multiple times - we get error:


use mpi
1
Fatal Error: Can't open module file 'mpi.mod' for reading at (1): No such file or directory

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Merge branch 'master' into shri/ts-is-for-differential-variables

Conflicts:
include/petsc-private/tsimpl.h
src/ts/impls/eimex/eimex.c
src/ts/interface/ts.c

Merge branch 'master' into jed/chem
Note merging a branch with good stuff in it for a year and a half is insane!

Conflicts:
src/ts/examples/tutorials/makefile
src/ts/interface/ts.c

Merge branch 'master' into stefano_zampini/pcbddc-adaptive-selection

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

Merge branch 'master' into barry/saws-options-merge-master

Totally confusing manual merge, could be wrong

Conflicts:
include/petscoptions.h
src/dm/impls/da/dacreate.c
src/sys/objects/aoptions.c

Merge branch 'master' into barry/saws-options-merge-master

Totally confusing manual merge, could be wrong

Conflicts:
include/petscoptions.h
src/dm/impls/da/dacreate.c
src/sys/objects/aoptions.c
src/sys/threadcomm/interface/threadcomm.c

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Merge branch 'master' into pr252/dmay/PetscViewerBinarySkipHeaderVecViewLoad
Manual merge of makefile

Conflicts:
src/sys/classes/viewer/examples/tutorials/makefile

Merge branch 'tisaac/feature-gamg-extensible' into barry/experiment

Conflicts:
src/ksp/pc/impls/gamg/gamg.h

Merge branch 'knepley/feature-dm-sf-local-copy' into knepley/feature-ts-fem+fvm-example

* knepley/feature-dm-sf-local-copy:
DM: Added support for INSERT_VALUES in DMLocalToGlobal() with an SF, whe

Merge branch 'knepley/feature-dm-sf-local-copy' into knepley/feature-ts-fem+fvm-example

* knepley/feature-dm-sf-local-copy:
DM: Added support for INSERT_VALUES in DMLocalToGlobal() with an SF, where it just does a local copy
fortranstubs: do not process files in .git
setup.py: Fix install of package's __init__.py file
f2cblaslapack: use correct location to copy tmpmakefile for subsequent self.installNeeded() to work.
doc: exclude tutorials/HandsOnExercise.html from 'docsetdate'
setup.py: Better handling of $PETSC_CONFIGURE_OPTIONS
setup.py: Simplify code to support just pip install
Don't install $PETSC_ARCH/lib/.DIR
Move install.py and gmakegen.py from lib/petsc-conf/ to config/
updated gamg tests
fixed squaring graph on all levels in GAMG
fixed gamg coarse grid to be general

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

Merged in dalcinl/pip-install (pull request #247)

Update support for pip install

Move install.py and gmakegen.py from lib/petsc-conf/ to config/

Merge branch 'master' of bitbucket.org:petsc/petsc into mark/gamg-crs-ksp2

manual merge of conflict

Three directory namespace changes for better --prefix install support

1) include/finclude becomes include/petsc-finclude
2) include/mpiuni becomes include/petsc-mpiuni
3) conf (both $PETSC_DIR/conf

Three directory namespace changes for better --prefix install support

1) include/finclude becomes include/petsc-finclude
2) include/mpiuni becomes include/petsc-mpiuni
3) conf (both $PETSC_DIR/conf and $PETSC_DIR/$PETSC_ARCH/conf become) lib/petsc-conf

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Merge branch 'master' into mlange/refactor-plex-distribute

Conflicts:
src/dm/impls/plex/examples/tests/output/ex12_1.out
src/dm/impls/plex/examples/tests/output/ex12_2.out

Merge branch 'balay/add-clean'

build: add toplevel makefile targets clean, distclean
clean - delete libraries built by 'make all'
distclean - delete build files created by configure [and make all]

clean in example dirs continues

build: add toplevel makefile targets clean, distclean
clean - delete libraries built by 'make all'
distclean - delete build files created by configure [and make all]

clean in example dirs continues to work as before..

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Merge branch 'maint'

* maint:
make: PETSC_ARCH/conf/files depends on PETSC_ARCH/include/petscconf.h
more details in KSPSetComputeOperators() manual page
slightly more documentation in manual p

Merge branch 'maint'

* maint:
make: PETSC_ARCH/conf/files depends on PETSC_ARCH/include/petscconf.h
more details in KSPSetComputeOperators() manual page
slightly more documentation in manual pages on KSPSetComputeOperators/RHS/InitialGuess() Removed out dated mention of MatStructure in KSPSetComputeOperators()

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make: PETSC_ARCH/conf/files depends on PETSC_ARCH/include/petscconf.h

When a PETSC_ARCH is reconfigured with an additional external package,
petscconf.h is updated and we expect conf/files to be reg

make: PETSC_ARCH/conf/files depends on PETSC_ARCH/include/petscconf.h

When a PETSC_ARCH is reconfigured with an additional external package,
petscconf.h is updated and we expect conf/files to be regenerated, but
there was no explicit dependency causing that to happen. I think this
is the cause of the non-reproducible build failures that have been
reported. This commit adds the explicit dependency.

Reported-by: Kai Song <ksong@lbl.gov>
Reported-by: Åsmund Ervik <asmund.ervik@ntnu.no>

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Merge branch 'master' into prbrune/snes-fascontinuation

* master: (855 commits)
fix for moab example had wrong blocksize of mapping
docs:remove src/docs/doxygen/manual [per Barry's instructions]

Merge branch 'master' into prbrune/snes-fascontinuation

* master: (855 commits)
fix for moab example had wrong blocksize of mapping
docs:remove src/docs/doxygen/manual [per Barry's instructions]
gfortran: remove 132 char limit from f90 free-form
SNES: Set up matrix-free *after* copying the user Jacobian to snes->pc
DMPlex-Gmsh: Use trueNumCells when building the coordinate section
Sys: Got guard logic reversed
Sys: The #define guard for PetscMalloc*() must match the one for PetscFree*()
PetscFV: I hate fucking complex
removed ltog scatter from DMDA since functionality can be obtained with gtol scatter and less memory
fix test of DMLocalToGlobalBegin/End and add actual test cases
improve object memory logging for DA, ISLocalToGlobal and ISBLOCK
lower high water mark of constructing parallel scatter by allocating only as much room in svalues as needed
owner in VecScatter construction is the rank, therefor can use PetscMPIInt to hold it do not PetscInt
another reuse of allocated array in 2d/3d DMDA create
improved high water mark of DMDASetups by implementing and using PETSC_USE_POINTER for ISCreateBlock()
PetscFV: Another complex fix
DMPlex+TS: Fixing types
ISIdentity() was wrong for block IS! Indices are NOT scaled by bs
PetscFV: Straighten out complex types
TS ex11: Fix casts and remove unused variable
...

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Merge branch 'master' into barry/saws-options

Merge branch 'master' into stefano_zampini/pcbddc-multilevel-improvement

Conflicts:
src/docs/website/documentation/changes/dev.html
src/ksp/ksp/examples/tutorials/ex59.c
src/ksp/pc/impls/bddc/bdd

Merge branch 'master' into stefano_zampini/pcbddc-multilevel-improvement

Conflicts:
src/docs/website/documentation/changes/dev.html
src/ksp/ksp/examples/tutorials/ex59.c
src/ksp/pc/impls/bddc/bddcprivate.c

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Merge remote-tracking branch 'origin/master' into feature-dmmoab