Merge branch 'denera/tao-nls-ntr-ksp-tag-fix' [PR #1174]

* denera/tao-nls-ntr-ksp-tag-fix:
Tao: NLS, NTR and NTL options and doc cleanup

defunct options removed from options database comments

code style fixes

replacing strlcat calls with KSP prefix API

Tao KSP prefixes fixed to account for multiple Tao solvers with their own prefixes

KSP prefix updated for unconstrained Newton solvers

Merge branch 'denera/tao-gauss-newton-wrapper' [PR #1151]

* denera/tao-gauss-newton-wrapper:
Regularized Gauss-Newton algorithm/wrapper
New BRGN algorithm added for regularized Gauss-Newton formulat

Merge branch 'denera/tao-gauss-newton-wrapper' [PR #1151]

* denera/tao-gauss-newton-wrapper:
Regularized Gauss-Newton algorithm/wrapper
New BRGN algorithm added for regularized Gauss-Newton formulation.
This algorithm is a thin wrapper that relies on TaoSetResidualRoutine() and TaoSetResidualJacobianRoutine() interfaces to accept the residual and Jacobian associated with a least-squares problem,
and then construct the internal objective, gradient and Hessian evaluation functions for the regularized problem formulation.
Currently only Tikhonov regularization is available, but other smooth regularizers are planned in the future.
The resulting regularized problem is passed onto an existing bound-constrained algorithm (e.g.: BQNLS or BNTL), controlled by the -tao_brgn_subsolver flag.

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Regularization changed to x-x_old, user hook added into optimization loops, eliminated explicit MatTransposeMatMult option in Hessian computation

Merged petsc/petsc into master

Merge branch 'master' into knepley/fix-superdm-is

* master: (455 commits)
bib: spell out some names for format consistency with related refs
bib: two 2018 pubs now appeared
cleaning up analyze

Merge branch 'master' into knepley/fix-superdm-is

* master: (455 commits)
bib: spell out some names for format consistency with related refs
bib: two 2018 pubs now appeared
cleaning up analyzer warnings
compile fixes (workarround PGI bug?):
undoing the branch's changes to leastsquares outputs
more fixes for complex builds
compile error fix for complex builds
1) Look for 64 bit integer MKL BLAS if 64 bit indices are used with PETSc 2) Fix Pardiso code to only compile pardiso_init64 when needed, otherwise can generate warnings/errors
jenkins: run 'cleantest' before 'allgtest-tap' - an attempt to fix errors of type:
cuda: protect cuda includes
fix cuda warnings.
fix complex compile error
Revert "Improved polymorphism of interfaces for MatSetValuesBlocked()"
Bib: Updated ref
Doc: More function documentation
petscvec: move PetscSFCreateFromZero from vscat to vec sources
Fixed an uninitialized variable and got rid of an unused one.
memleak fixed and output files updated
fixing build errors on some archs
Mat: obey options prefix of Mat in MatNullSpaceTest
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Conflicts:
include/petsc/private/dmpleximpl.h
src/dm/interface/dmi.c

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Merge branch 'master' into knepley/feature-plex-functionals

* master: (984 commits)
netcdf: set zlib as optional dependency corretly [wrt --enable-netcdf-4] - otherwise netcdf configure errors out

Merge branch 'master' into knepley/feature-plex-functionals

* master: (984 commits)
netcdf: set zlib as optional dependency corretly [wrt --enable-netcdf-4] - otherwise netcdf configure errors out
fix gcov obj path
-options_table was changed to options_view in 2014 but documentation was not updated to reflect it
configure: fix F2003 test
Dev manual: remove duplicate entry
Plex test ex5: Removed "future" test, as it resulted in issues in the nightly tests.
Some minor typos in TS
Add ADIOS2.py which I forgot to git add in the past
Plex ex5: Disable test
Doc: Added note for interface change
KSPLSQRMonitorDefault fixed for quad precision
Tao: Added alternative output for chwirut2 test.
TS ex45,ex46: Removed overly refined tests for faster nightly tests.
KSP ex72: Fixed needlessly long-running PCTFS tests.
SNES ex56: Reduced test size to speed up nightly test suite.
KSPSolve_LSQR: don't compute unused norm of rhs
SNES ex13: Reduced problem sizes for nightly tests.
PetscOptionsDeprecated(): fix for NULL prefix
PetscOptionsDeprecated(): add option to print additional info
SNES ex12: Reduced sizes for BDDC tests.
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Merge branch 'master' into knepley/feature-plex-elasticity-test

* master: (1553 commits)
-options_table was changed to options_view in 2014 but documentation was not updated to reflect it
config

Merge branch 'master' into knepley/feature-plex-elasticity-test

* master: (1553 commits)
-options_table was changed to options_view in 2014 but documentation was not updated to reflect it
configure: fix F2003 test
Plex test ex5: Removed "future" test, as it resulted in issues in the nightly tests.
Some minor typos in TS
Add ADIOS2.py which I forgot to git add in the past
Plex ex5: Disable test
Doc: Added note for interface change
KSPLSQRMonitorDefault fixed for quad precision
Tao: Added alternative output for chwirut2 test.
TS ex45,ex46: Removed overly refined tests for faster nightly tests.
KSP ex72: Fixed needlessly long-running PCTFS tests.
SNES ex56: Reduced test size to speed up nightly test suite.
KSPSolve_LSQR: don't compute unused norm of rhs
SNES ex13: Reduced problem sizes for nightly tests.
PetscOptionsDeprecated(): fix for NULL prefix
PetscOptionsDeprecated(): add option to print additional info
SNES ex12: Reduced sizes for BDDC tests.
PetscFileRetrieve(): Suppress output to STDERR when downloading a file.
MatMatMult: Fixed unused variable pN.
DMDestroy: Guard call to dm->ops->destroy * Similar guards are in place in many other methods (IS,Vec,Mat) and permit the DM to be destroyed even if DMSetType() was never called.
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Merge branch 'master' into knepley/feature-plex-parallel-submesh

* master: (2931 commits)
remove N in docs for SNESQN
replaced test tolerance with PETSC_SQRT_MACHINE_EPSILON
fortran: PetscComp

Merge branch 'master' into knepley/feature-plex-parallel-submesh

* master: (2931 commits)
remove N in docs for SNESQN
replaced test tolerance with PETSC_SQRT_MACHINE_EPSILON
fortran: PetscComplex type is missing from fortran
initialize variables so that static analyzer doesn't mistakenly think they are used uninitialized.
Move access of prefix until it is actually used
Remove DMDASplitComm2d(), used in one example that was not tested
Functions that do not return PetscErrorCode should not use PetscFunctionBegin/End paradgm
remove unneeded reassignment of same value
Missing CHKERRQ(); Mostly in Tao code
Remove clang static analyser warning about passing NULL variable to strncat()
missing newline in -ts_monitor_extreme
minor fixes for integer counters
Configure: Deal with '__func__' in C89 builds with newer Clang and GCC.
Jenkinsfile: Increased timeout for tests to 5 minutes.
3.9 changes: further clarify removal of -pc_factor_mat_solver_package
Options deprecations: add "PETSc" to inline warning
removing unused variable
MatShift support added to MATSUBMAT. Mimics MATSHELL functionality. Needed for matrix-free Hessians in TAO Newton-Line-Search methods.
Add -ts_monitor_extreme
Dev manual: add note on deprecating options database keys
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Conflicts:
src/dm/impls/plex/examples/tests/ex4.c

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Merge branch 'master' into knepley/fix-plex-submesh-projection

* master: (425 commits)
remove N in docs for SNESQN
replaced test tolerance with PETSC_SQRT_MACHINE_EPSILON
fortran: PetscComplex

Merge branch 'master' into knepley/fix-plex-submesh-projection

* master: (425 commits)
remove N in docs for SNESQN
replaced test tolerance with PETSC_SQRT_MACHINE_EPSILON
fortran: PetscComplex type is missing from fortran
initialize variables so that static analyzer doesn't mistakenly think they are used uninitialized.
Move access of prefix until it is actually used
Remove DMDASplitComm2d(), used in one example that was not tested
Functions that do not return PetscErrorCode should not use PetscFunctionBegin/End paradgm
remove unneeded reassignment of same value
Missing CHKERRQ(); Mostly in Tao code
Remove clang static analyser warning about passing NULL variable to strncat()
missing newline in -ts_monitor_extreme
minor fixes for integer counters
Configure: Deal with '__func__' in C89 builds with newer Clang and GCC.
Jenkinsfile: Increased timeout for tests to 5 minutes.
3.9 changes: further clarify removal of -pc_factor_mat_solver_package
Options deprecations: add "PETSc" to inline warning
removing unused variable
MatShift support added to MATSUBMAT. Mimics MATSHELL functionality. Needed for matrix-free Hessians in TAO Newton-Line-Search methods.
Add -ts_monitor_extreme
Dev manual: add note on deprecating options database keys
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Conflicts:
src/dm/impls/plex/examples/tests/ex4.c

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Merge branch 'master' into knepley/feature-pc-patch

* master: (226 commits)
fix bib
type in bibtex entry
copy edits to bibtex items
Hypre matrix: small fix
Hypre matrix: fixed compiler war

Merge branch 'master' into knepley/feature-pc-patch

* master: (226 commits)
fix bib
type in bibtex entry
copy edits to bibtex items
Hypre matrix: small fix
Hypre matrix: fixed compiler warnings
Plex: Fixed missing PetscRealPart() in partition balance.
Added MatZeroEntries_HYPRE
Removed outdated mention of cusp and thrust from installations instructions; remove cusp from example configurations
Remove another location where fshift was used with -1 to indicate handling of error condition which was never handled
Generate an immediate error, if requested, if CG detects indefinite PC or Mat
Remove hack of using special fshift value of -1 to indicate error handling, was broken for MatSOR_SeqAIJ and did nothing constructive in the other cases
Options: Fix sys_tests-ex6 to not print options
PetscOptionsDestroy: Add missing free() call
Configure: Pragmatic now requires Cxx11
Error check that the communicator in the IS matches that in the matrix otherwise ISAllGather() produces incorrect results.
Options: Code reorganization and faster option lookup
fix compile warning
Doc: Fixed manpage for PCFieldSplitSetSchurPre()
mpiuni: build somempifort.o after mpiuni.mod
Remove use of common block from MPIUNI code
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Conflicts:
include/petscdm.h
include/petscpc.h
include/petscpctypes.h
src/dm/impls/plex/plexcreate.c
src/dm/impls/plex/plexdistribute.c
src/ksp/pc/impls/makefile
src/ksp/pc/interface/pcregis.c

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Merge branch 'master' into arcowie-rem/feature-error-logging

* master: (353 commits)
Configure: Pragmatic now requires Cxx11
fix compile warning
mpiuni: build somempifort.o after mpiuni.mod

Merge branch 'master' into arcowie-rem/feature-error-logging

* master: (353 commits)
Configure: Pragmatic now requires Cxx11
fix compile warning
mpiuni: build somempifort.o after mpiuni.mod
Remove use of common block from MPIUNI code
use was in wrong location
Fortran line extends past 72 char
Moved the rest of the PETSc common block variables over to petscsys module
tests: fix breakage due to cd93b0e13c6da70ee1e038f55989cf888bc1d1c5
Need to use petscsys to get PETSC_COMM_SELF defined in example
Mat ex23 and ex40: fix errors reported from nightly tests
Put declaration on too lines because otherwise it generates an error for truncated line
Move PETSC_COMM_WORLD and PETSC_COMM_SELF from common blocks to petscsys module
tests: fix requires - and create out files for seqaijmkl tests
KSP ex72: nested dissection is likely to be different between machines
cmake: downgrade to version 3.9 - as newer versions require cxx11 compiler [which is not universal]. However stick with version 3.11 on opensolaris
Mat ex23: fix memory leaks
Bib: Some new refs
KSP examples: add missing casts to double in printf
updated GAMG KSP tests
PetscRound() should be PetscRoundReal() in __fp16
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Conflicts:
include/petsclog.h
src/sys/logging/plog.c
src/sys/logging/utils/eventlog.c

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Merge remote-tracking branch 'origin/denera/lmvm-mat-and-pc'

LMVM matrices can now define J0 with another LMVM matrix, and DiagBrdn scaling implemented for relevant TAO algorithms

LMVM matrix changes propaged to TAO algorithms and test outputs updated

Name refactoring for LMVM matrices

derived LMVM types added and moved into the KSP package

Merge branch 'master' into knepley/feature-snes-ex13-spectral

* master: (2350 commits)
migrate warning fix from next-tmp
Revert "Remove dead code."
clarifying comment in the code
Remove dead

Merge branch 'master' into knepley/feature-snes-ex13-spectral

* master: (2350 commits)
migrate warning fix from next-tmp
Revert "Remove dead code."
clarifying comment in the code
Remove dead code.
Add JuMP citation
Copyedits and updates to developers manual
Add more protection to intrinsics
MPI: protect arguments in MPI macros
Add the missing conditionals for 64-bit build
Plex+VTK: Fix field type determination
Fix bug in name cleanup
Bib: Added ref
Plex+VTK: Fix field type determination
Plex: Updated test output - I am now hating this shit
forgot to save file after moving prototypes to petscsys.h
update Apple example project settings per Xcode
Two functions should actually be public, used, for example from Apple MacOS and iOS programs
includes should always be included relative to include directory
Apple removed old locations of docsets
SNES ex12: Updated test output
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Conflicts:
src/snes/examples/tutorials/ex13.c

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Merge branch 'master' into knepley/feature-pc-patch

* master: (33 commits)
cleanup very ugly PCGAMG manual page
minor clarifications for VecScatterCreate() manual page
gcov: PETSC_ARCH is requ

Merge branch 'master' into knepley/feature-pc-patch

* master: (33 commits)
cleanup very ugly PCGAMG manual page
minor clarifications for VecScatterCreate() manual page
gcov: PETSC_ARCH is required onlyfor -run_gcov - and not for -merge_gcov [where it doesn't exist]
make clearer in help statements what --with-external-packages-dir is for.
Website: Added news entry for PETSc User Meeting 2018 on main page.
KSPGUESSPOD: exclude negative of zero eigenvalues from the energy computation
KSPGUESSFISCHER: use PetscInfo for KSP class
CUDA: Further test output fixes for mat_tests-ex2
Turn off elemental test for parmetis running since this does not work on batch systems.
3.8 Changes: KSPCHEBYSHEV
CUDA: Fixed most test errors due to MatMultTranspose*
KSPFGMRES: add KSP_NORM_NONE / PC_RIGHT as supported
KSPSetSupportedNorm man page: remove old note about default support for KSP_NORM_NONE
Dev manual: copyedit
DMPlexDistributeLabels: Propagate the output flag
cuda/cusp: update minimum supported versions of cuda to 7.5 and cusp to 0.5.0
cuda: remove configure option -with-cuda-arch. [use CUDAFLAGS instead]
projected gradient code fixed to obey recent convergence test changed
Merge conflicts resolved after rebase
norm update bug fixed in GPGC, test output reverted
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Merge remote-tracking branch 'origin/knepley/fix-snes-ex69' into tisaac/feature-dmfield

* origin/knepley/fix-snes-ex69: (311 commits)
PetscFECreateDefault: fix custom Fortran interface to use MPI_

Merge remote-tracking branch 'origin/knepley/fix-snes-ex69' into tisaac/feature-dmfield

* origin/knepley/fix-snes-ex69: (311 commits)
PetscFECreateDefault: fix custom Fortran interface to use MPI_Comm
SNES ex69: Updated test output
SNES ex69: Removed all mantle stuff and change fields to constants - Also use dsymutil for executables
SNES ex69: Removed special partition
SNES ex69: Fixed null space creation - Null space locks its vectors
PetscFE: PetscFECreateDefault() now takes MPI_Comm instead of DM
cleanup very ugly PCGAMG manual page
minor clarifications for VecScatterCreate() manual page
gcov: PETSC_ARCH is required onlyfor -run_gcov - and not for -merge_gcov [where it doesn't exist]
make clearer in help statements what --with-external-packages-dir is for.
Website: Added news entry for PETSc User Meeting 2018 on main page.
CUDA: Further test output fixes for mat_tests-ex2
Turn off elemental test for parmetis running since this does not work on batch systems.
3.8 Changes: KSPCHEBYSHEV
CUDA: Fixed most test errors due to MatMultTranspose*
website: update urls
website: fix Jason's name to match pic. Also add Todd's pic
Dev manual: copyedit
DMPlexDistributeLabels: Propagate the output flag
cuda/cusp: update minimum supported versions of cuda to 7.5 and cusp to 0.5.0
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Merge branch 'denera/tao-convergence-check-fix' [PR #886]

* denera/tao-convergence-check-fix:
TaoMonitor no longer has double-duty for both monitoring and updating the converged reason.
The converge

Merge branch 'denera/tao-convergence-check-fix' [PR #886]

* denera/tao-convergence-check-fix:
TaoMonitor no longer has double-duty for both monitoring and updating the converged reason.
The convergence function is now called explicitly in the algorithms following the monitor call, mimicking the current implementation of SNES.

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