Merge branch 'master' into knepley/feature-fem-dgspace

* master: (593 commits)
Bib: Added Top500 and fixed entry
fun3d: update PetscMallocValidate() usage
bib: rename ref with duplicate key

Merge branch 'master' into knepley/feature-fem-dgspace

* master: (593 commits)
Bib: Added Top500 and fixed entry
fun3d: update PetscMallocValidate() usage
bib: rename ref with duplicate key
Webpage: Corrected '-dm_mat_type cusp' to 'dm_mat_type aijcusp'.
Allow calling MatGetBlockSize[s]() before matrix preallocation
SNESLINESEARCHBT: Set the norms when exiting early due to negligible step.
SNESQN: only monitor real part of dot product (fails with C++ complex)
Corrected the #include statement in the man pages for the PetscObjectComposedDataSet/Getwhatever routines.
DMPlex: Added doc for DMPlexGetHybridBounds()
winzip: detect if winzip is used to extract petsc.tar.gz and error out.
configure: remove self.archIndependent as its not being used. [it is used to create externalpackages/package/arch dir which is unused]
configure: fix packages using package-dir/PETSC_ARCH as out-of-source-build location Perhaps this should be changed to package-dir/build?
configure: remove dead code previously used to download BuildSystem
configure: check if compilerDefines [and compilerFixes] exist in framework before using them
configure: save/restore reconfigure.py when --with-clean is used
configure: add --with-clean option to delete buildfiles/externalpackages in PETSC_DIR/PETSC_ARCH and potential externalpackages in --with-external-package-dir/PETSC_ARCH
configure: With --with-externalpackages-dir=dir store/build packages in dir/PETSC_ARCH
Add MatSeqSBAIJSetPreallocationCSR()
configure: switch to using PETSC_DIR/PETSC_ARCH/externalpackages by updating package.py to use externalpackages.py as the externalPackagesDirProvider
configure: move dead code configureExternalPackagesDir() from petscdir.py to externalpackagesdir.py Also set PETSC_DIR/PETSC_ARCH/externalpackages as the externalpackagesdir
...

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Merge branch 'master' into barry/saws

Conflicts:
src/ksp/pc/impls/gamg/gamg.c
src/sys/classes/viewer/impls/ams/ams.c
src/sys/objects/pinit.c

Merge branch 'master' into knepley/feature-dmda-section

* master: (397 commits)
PetscSynchronizedFGets: fix deadlock at EOF
Compiler: Fix warnings from MPI impls which do not initialize outputs

Merge branch 'master' into knepley/feature-dmda-section

* master: (397 commits)
PetscSynchronizedFGets: fix deadlock at EOF
Compiler: Fix warnings from MPI impls which do not initialize outputs
Increase patchlevel to 3.4.3
SNES: Now work vectors come from the DM
SNES ex62: Remove code generation
SNES: Move setup involving snes->vec_sol from SNESSetUp() to SNESolve()
Compiler: Fix warnings from MPI impls which do not initialize outputs
DMPlex ex7: Added missing test output
SNES ex52: Removed old Jacobian stuff, and fixed call to DMPlexProjectFunction() - Fixed calls for new element handling
SNES ex12: Added a performance profiling mode
DMPlex ex8: Fixed leak
PetscSection: Must reset the section when changing the number of fields
DMPlex ex7: Fixed test output - Corrected orientations in interpolation
DMPlex ex1: Fixed test output - Uniform refinement for quads changed
DMPlex: Fix overagressive checks
PC: Removed support graph PC
configure: both downloadonWindows and worksonWindows refer to MS compilers. Also fix isWindows() -> isWindows(CC).
MatXAIJSetPreallocation: use array[] notation to help out Fortran
__float128: when blas/lapack is not found instruct using f2cblaslapack
Configure: Package.downloadonWindows is supposed to mean that Windows compilers work. not Cygwin - Also changed doc for Package.worksonWindows, which does refer to Cygwin
...

Conflicts:
src/dm/impls/da/dalocal.c

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Merge branch 'barry/dmvecmattypes' into shri/feature-dm-circuit

Conflicts:
src/dm/impls/makefile
src/dm/interface/dmregall.c

Merge branch 'master' into knepley/feature-plex-refine-3d

* master: (149 commits)
Bib: Added papers referencing PETSc from ResearchGate
Bib: Fixed urls for some refs Suggested-by: Michele De Ste

Merge branch 'master' into knepley/feature-plex-refine-3d

* master: (149 commits)
Bib: Added papers referencing PETSc from ResearchGate
Bib: Fixed urls for some refs Suggested-by: Michele De Stefano
fixed bug that has appeared recently of false positive errors when there are zero local equations on coarse grids in gamg-agg.
MatSchurComplement: Must initialize KSP package
bib: fix inbook citation
Bib: Updated some refs
SNES: fix copy/paste in man page
fortran: fix KSPCONVERGEDDEFAULT and SNESCONVERGEDSKIP in fortran includes
Mat SBAIJ: avoid invalid memory read in MatSOR_SBAIJ
Revert "MatMPIBAIJSetPreallocationCSR() handled the input matrix entries incorrectly, it treated them as if each row of values"
PCGAMG: fix corruption for multiple solves when MatSetNearNullSpace is used
PCGAMG: remove distracting comment
KSP ex49: restrict near-null space for elasticity example with sym BC
MatMPIBAIJSetPreallocationCSR() handled the input matrix entries incorrectly, it treated them as if each row of values was provided ordered by row within the block rows instead of by block as it was originally designed to be. Also added more discussion to the manual pages on the expected order of the values
Fix accidental creation of the matrices in SNESNCG used for linear analogue LS.
PCGAMG: add man page for PCGAMGType
fortran: fix snesconvergedskip_() kspconvergedskip_() kspconvergeddefault*_()
rm //
Sys: new_ir changed from PetscInt to PetscObjectState - so fix mallocs to use the new type
SNES: Fixed package init in SNESLineSearchCreate()
...

Conflicts:
include/petscdmplex.h
src/dm/impls/plex/examples/tests/ex5.c
src/dm/impls/plex/plex.c
src/dm/interface/dm.c

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Merge branch 'hzhang/snes-jacobiancoloropt' of bitbucket.org:petsc/petsc into hzhang/snes-jacobiancoloropt

Merge branch 'hzhang/snes-jacobiancoloropt' of bitbucket.org:petsc/petsc into hzhang/snes-jacobiancoloropt

Merge branch 'master' into barry/dmvecmattypes
possible some messed up manual merges!

Conflicts:
src/dm/impls/mesh/examples/tutorials/ex4f90.F
src/dm/impls/mesh/mesh.c
src/dm/impls/mesh/meshcreat

Merge branch 'master' into barry/dmvecmattypes
possible some messed up manual merges!

Conflicts:
src/dm/impls/mesh/examples/tutorials/ex4f90.F
src/dm/impls/mesh/mesh.c
src/dm/impls/mesh/meshcreate.c
src/dm/impls/mesh/section.c
src/snes/examples/tutorials/ex10.c
src/snes/examples/tutorials/ex12.c
src/snes/examples/tutorials/ex52.c
src/snes/examples/tutorials/ex62.c
src/snes/utils/mesh/dmmeshsnes.c

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Merge branch 'jed/gnumake'

GNU Make (v3.81 or later) is now the default build, --download-make is supported.

* jed/gnumake: (44 commits)
gmake: put object files in obj/ instead of obj-gmake/
gm

Merge branch 'jed/gnumake'

GNU Make (v3.81 or later) is now the default build, --download-make is supported.

* jed/gnumake: (44 commits)
gmake: put object files in obj/ instead of obj-gmake/
gmake: make is no longer at config.programs - so remove old usage of self.make
gmake: pass gmake to mpich/openmpi configure [fixes --download-mpich]
gmake: fix --download-triangle [do not overwrite self.make set by package.py]
make: reduce default verbosity of gnumake build
make: use SL_LINKER_SUFFIX (Mac uses .dylib)
make: change formula to compute make_np [from number of cores] Also remove special code for Barry [probably needed by an a laptop older than his current]
gmake: workarround if FC_MODULE_OUTPUT_FLAG is not found
gnumake: make it the default build mode
make: fix usage from programs.make to self.make [via packages.py]
make: clean up integration of programs.make into make.py
download-make: migrate prior 'make' detection code from programs.py to packages/make.py
download-make: add initial support. [yet to migrate stuff from programs.py]
win32fe: updated binaries now handle 'lib @cmdfile' and 'cvf/ifort -module:PATH'
gmake: read ./conf/petscvariables when not in environment
gmake: support for AR using win32fe response files
__SDIR__: use empty string instead of NULL
config: dependency flags are only needed by compiler, so skip linker test
config: add dependency flags for most compilers
__SDIR__: set to NULL, ignoring __INSDIR__ which is now unnecessary
...

Conflicts:
config/BuildSystem/config/programs.py

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gmake: make is no longer at config.programs - so remove old usage of self.make

Merge bug fix/patch releases up to 3.2-p7 into maint-3.2

* commit 'a9157d915ed96804280c3dc077186a2a633fd603': (157 commits)
Fix PyPI download URL to help pip figure out the release version
#1109

Merge bug fix/patch releases up to 3.2-p7 into maint-3.2

* commit 'a9157d915ed96804280c3dc077186a2a633fd603': (157 commits)
Fix PyPI download URL to help pip figure out the release version
#110990 fix timestamp order for .so vs .a during 'make install'
Update FFTW download
Increase patchlevel to 3.2-p7
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Merge branch 'master' into jed/ts-eimex

Sync to include Git conversion, PETSC_EXTERN, and minor API changes.

Conflicts:
src/ts/interface/tsregall.c

commit after merge
x

Hg-commit: 5ca7425bdc061d16496b42615f4a99db34a78eec

install: print appropriate message when DESTDIR is used.

Hg-commit: 71549909a34e40d69cf05d5290209fd8309ed064

#149503 'make install' should fix pkgconfig/PETSc.pc aswell.
Also redo the order of operations so that fixConf() is done in destDir
so that buildfiles [in current PETSC_DIR] are not modified by this

#149503 'make install' should fix pkgconfig/PETSc.pc aswell.
Also redo the order of operations so that fixConf() is done in destDir
so that buildfiles [in current PETSC_DIR] are not modified by this
install process.

Hg-commit: 5bb8d2354932e4ddff3d4fde7b317607bc677a9e

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merge PetscSF implementation

Hg-commit: 98dccc99445b69cb7a66312149eb16fec359e294

removed trailing spaces from all files

Hg-commit: 1cfa55059afe46c5145e0e830cd797b97216abfb

Merge

Hg-commit: 5fd7344ebb01d47fc51348189c58908ebeb94702

Pulled in changes from petsc-dev. make tests passing. Everything looks good.

Hg-commit: 94eb5d50210da3db6d654576e30f2a31ec2adf25

#117044 remove duplicate PETSC_DIR detection code [for installer]

Hg-commit: 6d532f3c4d646c6e59f625782c0ba8352fa4d5ad

Commit after merge

Hg-commit: 8c5e601e00cdfb6d35c8d12ba9952a5d3a8ea1b8

fix typo

Hg-commit: a165f864f0f42cdef623ceedcc576def3b517d3d

#111534 check if prefix is set in 'make install'. Also reorg destdir check.

Hg-commit: 9f1b353b69be5c24c934d9be75f7e702f48970ab

#110990 fix timestamp order for .so vs .a during 'make install'

Hg-commit: 7f0211769daf56d8e25395178cbd003ad9847740

merge from 32

Hg-commit: 9b67cec165772d54219a7f98edc32421d226fa62