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
...

Conflicts:
include/petsclog.h
src/sys/logging/plog.c
src/sys/logging/utils/eventlog.c

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Merge branch 'master' into knepley/fix-plex-project-tests

* master: (477 commits)
Added correct report number for PETSc Developers Guide
Update PETSc Developers Guide title and final pages to ne

Merge branch 'master' into knepley/fix-plex-project-tests

* master: (477 commits)
Added correct report number for PETSc Developers Guide
Update PETSc Developers Guide title and final pages to new ANL style
Hash: Quick documentation fix
PetscBinaryViewerRead -> PetscViewerBinaryRead
cast in GAMG_HASH so that it works for PetscInt32 near PETSC_INT_MAX without overflow to negative numbers
Add link for DrMemory which may serve as an alternative to valgrind on Windows
Finish Gail's copyedits for developers manual.
openmpi: fix namespace conflict [with static build on ppc64le]
two pages of Gail's edits to developers guide
Another chapter of Gail's copyedits for the developers guide
Gail's copyedits on two more chapters of the developers guide
Fix more %d to %D in GAMG code. Fix code style in GAMG code
DMPlexVTK: vertices is int! need to use %d instead of %D
TS ex18: update outputs (reported by nightly tests)
Use %D in error messages for GAMG hash; fix style issues with GAMG hash
config: Update petsc4py git commit
Fix bad plain extern declaration.
Add Gail's copyedits for the initial portion of the developers guide
Add missing common block to subroutine
fix mpiuni tests with xl compilers
...

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

* master: (562 commits)
fix clang-analyzer warning
Developers manual never use system randomizers in PETSc and example source code.
missing

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

* master: (562 commits)
fix clang-analyzer warning
Developers manual never use system randomizers in PETSc and example source code.
missing CHKERRQ()
DT: Reverting the tgamma change broke MPFR - I guess we need a nightly build with it in
Add a test for ex21
Fix error in ex21
Add missing fortran interface that handles null objects
DMComposite: add missing guards
MatPreallocate: fix overpreallocation of local rows
style fixes
MatView_MPI_DA: do not print twice the class prefix
MatSetOperation: stash the original MatView_XXX in the viewnative function pointer
DMCreateInterpolation_DA gracefully error instead of catching FPE signals
MatIncreaseOverlap: preserve communicator of index sets
MatMPIAIJ: fix indentation and missing CHKERRQ
ISBuildTwoSided: remove tabs and fix style
Fix documentation
PetscViewerDraw: fix unininitialized warning from valgrind
MatConvert_SeqAIJ_SeqBAIJ: remove error for non square matrices and add MAT_REUSE_MATRIX case
Mat: MAT_INPLACE_MATRIX can be used for transposition with rectangular matrices
...

Conflicts:
src/dm/dt/interface/dtfe.c
src/dm/impls/plex/plex.c
src/dm/impls/plex/plexfem.c
src/snes/examples/tutorials/ex13.c
src/snes/examples/tutorials/ex62.c
src/snes/examples/tutorials/makefile
src/snes/examples/tutorials/output/ex62_18.out
src/snes/examples/tutorials/output/ex62_19.out
src/snes/examples/tutorials/output/ex62_20.out
src/snes/examples/tutorials/output/ex62_20_parmetis.out
src/snes/examples/tutorials/output/ex62_21.out
src/snes/examples/tutorials/output/ex62_22.out
src/snes/examples/tutorials/output/ex62_23.out
src/snes/examples/tutorials/output/ex62_24.out
src/snes/examples/tutorials/output/ex62_25.out
src/snes/examples/tutorials/output/ex62_26.out
src/snes/examples/tutorials/output/ex62_27.out
src/snes/examples/tutorials/output/ex62_28.out
src/snes/examples/tutorials/output/ex62_29.out
src/snes/examples/tutorials/output/ex62_2d_p3_1.out
src/snes/examples/tutorials/output/ex62_30.out
src/snes/examples/tutorials/output/ex62_31.out
src/snes/examples/tutorials/output/ex62_32.out
src/snes/examples/tutorials/output/ex62_33.out
src/snes/examples/tutorials/output/ex62_34.out
src/snes/examples/tutorials/output/ex62_35.out
src/snes/examples/tutorials/output/ex62_36.out
src/snes/examples/tutorials/output/ex62_pc_simple.out
src/snes/examples/tutorials/output/ex62_pc_simplec.out
src/snes/examples/tutorials/output/ex62_quad_q2p1_full.out
src/snes/examples/tutorials/output/ex62_quad_q2q1_full.out
src/snes/utils/dmplexsnes.c

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Merge branch 'maint'

Merge remote-tracking branch 'origin/balay/win-shlib-check/maint' into maint

windows: disable sharedlibries when fortran compiler is enabled.

And if the user explicitly enables sharedlibraries [with fortran compiler] print an appropriate error message

Reported-by: Helgad As

windows: disable sharedlibries when fortran compiler is enabled.

And if the user explicitly enables sharedlibraries [with fortran compiler] print an appropriate error message

Reported-by: Helgad Asdis <asdisprjonar@gmail.com>

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Merge branch 'knepley/feature-error-logging' of bitbucket.org:petsc/petsc into knepley/feature-error-logging

Merge branch 'master' into knepley/feature-error-logging

* master: (324 commits)
DT: Reverting the tgamma change broke MPFR - I guess we need a nightly build with it in
Revert "tgamma: icc on wi

Merge branch 'master' into knepley/feature-error-logging

* master: (324 commits)
DT: Reverting the tgamma change broke MPFR - I guess we need a nightly build with it in
Revert "tgamma: icc on windows requires mathimf.h for tgamma."
setup routine no longer calls PetscCalloc5 if the arrays have already been allocated in a previous setup call
clarify SNESGetFunction()
Move MOAB docs to submansec so as not to clutter DM mansec
doc: remove matlab from doc generation dependency - i.e remove 'alldoc3' and use 'html' to generate corresponding '*.m.html' files.
Remove matlab pounders related cruft that is not required. Document the matlab code better and include an appropriate message in the help text.
Fixed typo.
Remove the inclusion of matlab in testing.
Finalizing comments and the work for the test problems.
Finished the testing and generation of plots. Some simple bug fixes addressed.
Set -Wl,-rpath for Mac OS Matlab mkl directory; don't pass -nojvm to matlab since it causes crashes on Barry's machine and is not needed
Added list of known problems with the code.
Added a comment on ignoring the return from Tao.
Finish with initial implementation of matlab interface to test TAO pounders.
Working through the matlab interface for pounders testing.
Fix typo in manual Reported-by: Jaroslaw Piwonski (CAU) <jpi@informatik.uni-kiel.de>
Fixed mkl_sparse_sypr() calls that were using an unsupported value in the matrix descriptor.
test harness: simplify code that checks for sequential-only tests
Fix the doc for call-backs drdyf drdpf
...

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Merge branch 'maint'

Merge remote-tracking branch 'origin/balay/fix-use-dsymutil-check/maint' into maint

dsymutil: check for it only on OSX. And fix check for shared_darwin target (use check for OSX - not dsymutil check)

Reported-by: Pedro Marcelino <pedronovaesmelo@gmail.com>
Thanks-to: Jed Brown <jed

dsymutil: check for it only on OSX. And fix check for shared_darwin target (use check for OSX - not dsymutil check)

Reported-by: Pedro Marcelino <pedronovaesmelo@gmail.com>
Thanks-to: Jed Brown <jed@jedbrown.org>

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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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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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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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merged new quadrature behavior

Merge branch 'balay/win32-dll'

win32: more build fixes for creating dlls

Merge branch 'master' into knepley/feature-parallel-mesh-load

* master: (180 commits)
Bib: Added ref
-random_view caused error because PetscRandomView() was not provided in PetscRandomCreate()

Merge branch 'master' into knepley/feature-parallel-mesh-load

* master: (180 commits)
Bib: Added ref
-random_view caused error because PetscRandomView() was not provided in PetscRandomCreate()
Update the xSDKTrilinos test message to use interactive session and ctest
gcc6: fix comple warnings with -Wmisleading-indentation
fix compile warning
bugfix for MatTransposeMatMultSymbolic_MPIAIJ_MPIAIJ_nonscalable()
minor formatting cleanup of gamg.c
add ml example to tutorials page for xsdk
bugfix of MatDuplicate for mpiaij matrix product Reported-by: Miorelli, Federico <Federico.Miorelli@cgg.com>
The deprecated -log_summary_exclude was still being used when it should have been -log_exclude
cpardiso: requires mkl_blacs so check for that. Also common code to detect MKL for both pardiso and cpardiso
cpardiso: fix segv and memory leaks
resume MatGetSubMatrix_SeqSBAIJ() because it cannot share routine with BAIJ due to cast
fix bad relative links
replace MatSeqBAIJSetPreallocation_SeqBAIJ with MatSeqBAIJSetPreallocation to skip this call when input mat is sbaij type
fix a variety of set but not used variables in examples detected by clang static analyzer
removed declared but not used variable
ANL Report formatting requires listing authors by affiliation
DMP4est: uncrustify
DMP4est: remove memset()
...

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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

configure: default to static libraries if sharedlib test fails. However error out if user specifies --with-shared-libraries=1

Merge branch 'master' into barry/add-pcfieldsplit-logevent

Merge branch 'master' into barry/add-pcreset-hypre-for-master

Needed to move PCDestroy_HYPRE() added to master to PCReset_HYPRE() since that was introduced
as a bug fix for maint

Merge branch 'master' into barry-allow-vecset-nan-3.6

Merge branch 'master' into pr263/PierreBdR/ts-domain-error-in-stage/master

Merge branch 'master' into tisaac/dmforest

Get 3.6.2 patches

* master: (1360 commits)
remove nasty memory leak with CUDA code when using block Jacobi with multiple blocks per process
print abs

Merge branch 'master' into tisaac/dmforest

Get 3.6.2 patches

* master: (1360 commits)
remove nasty memory leak with CUDA code when using block Jacobi with multiple blocks per process
print abs in Fortran test example in order to have same result with real and complex builds
changed outdate mpirun and -np to mpiexec and -n
force sqrt to be taken in the precision of PetscReal in fortran examples
continuation line too soon for some compilers
stop configure if user selected C++ clanguage, single precision, complex combination since we do not support it
fixes for Fortran examples to compile cleanly in single precision that do not involve complex numbers
fixes to Fortran examples to compile cleanly in single precision complex
fix previous mistake
must cast 1. to PetscScalar before dividing by a PetscScalar (C++ complex class is terrible)
must cast 0.0 to PetscScalar before comparison with a PetscScalar
changed order of suggested locations of downloadable PETSc to Barry's preference
Increase patchlevel to 3.6.2
remove debug print statement from two commits before
remove debug print statements I accidently left in the last commit
PetscDraw: Fix dummy definition of PetscDrawCollective{Begin|End}()
remove cleanupMumps flag from MatDestroy_Mumps() it should always free the memory it allocated Bug detected while adding features to libMesh
improved viewing of fractional counts in xml nested log viewing fixed bug in output of doubles to xml nested log files
chombo: build only libs - not examples
fix typo. 'gcc-4.8 --with-cxx-dialect=C++11' gives a warning with this line - even though its in a #ifdef thats never enabled.
...

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