Merge branch 'master' into arcowie-rem/feature-error-logging* master: (345 commits) Update dev notes for the coming release Increase patchlevel to 3.9.4 doc fixes Added some AIJSELL tests t
Merge branch 'master' into arcowie-rem/feature-error-logging* master: (345 commits) Update dev notes for the coming release Increase patchlevel to 3.9.4 doc fixes Added some AIJSELL tests that mirror the SELL tests. Bib: More refs Removed use of hardwired -1 to represent PETSC_NULL_XXX object, since the null value is now 0. fix memleaks flagged by valgrind ex62: disable long running test and workaround differences in iteration counts on various builds. Add FAQ we can point to when users get error messages such as: "PETSc was configured with one OpenMPI mpi.h version but now appears to be compiling using a different OpenMPI mpi.h version" swith test from mpich to openmpi as mpich ch3:sock is unuserable per PetscShmCommGet() DM: Forgot to move include statement fix nightlybuild issues - disable hypre [for openmp] and fix uninitialized variables tests: enable openmp and hwloc with one of the mumps tests Default BoomerAMG smoothers Configure: Revert changes from debb90c, so that we are back to the original Libmesh Configure: Reverted change for Libmesh from 83cd5d7 Split vecimpl.h into vecimpl.h and vecscatterimpl.h SNES ex62: Turned off some tests for other precisions and shortened output of sensitive tests Use mmap to allocate the shared pthread barrier if available Add configure test for functional mmap ...Conflicts: include/petscconvest.h src/snes/examples/tutorials/ex13.c src/snes/interface/snes.c src/snes/utils/convest.c
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Section: During SetUp(), change dog ordering based on the pointMajor flag
Section: Added PetscSectionSetFromOptions()
Section: Add a point major flag to allow different dog orderings- Does not do anything right now
PetscSection: Cleanup point iteration in SetUp()
PetscSection: PetscSectionGetField() should not increase the reference count
IS: Move IS utilities out of SNES
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 ...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
ISLocalToGlobalMapping: add ISLocalToGlobalMapping{Get|Restore}NodeInfo to avoid code duplication
Merge branch 'master' into knepley/feature-pc-patch* master: (107 commits) cast in GAMG_HASH so that it works for PetscInt32 near PETSC_INT_MAX without overflow to negative numbers Add link for
Merge branch 'master' into knepley/feature-pc-patch* master: (107 commits) 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 Copy & paste the change on PetscSparseDensePlusDot Fix a wrong macro PetscInfo: Add missing errorchecking Log: various fixes and cleanups ...Conflicts: src/dm/impls/plex/plex.c
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
Update hash table implementation* Upgrade khash.h to version 0.2.8* Add common API for hash table iterators* Add generic hash map and set APIs* Add hash map and set for integer and pair of integ
Update hash table implementation* Upgrade khash.h to version 0.2.8* Add common API for hash table iterators* Add generic hash map and set APIs* Add hash map and set for integer and pair of integers
Merge branch 'maint'
Fix documentation
missing CHKERRQ()Commit-type: bug-fixReported-by: clang static analyzer
Merge branch 'knepley/fix-section-clone'* knepley/fix-section-clone: Plex ex3: Test does not work with single precision Section: Must also copy field symmetries when cloning Section: Allow NU
Merge branch 'knepley/fix-section-clone'* knepley/fix-section-clone: Plex ex3: Test does not work with single precision Section: Must also copy field symmetries when cloning Section: Allow NULL argument to PetscSectionSetSym() Plex ex3: Added tests for Q3 Plex: Added picture for 3D hex interpolation Section: Copy symmetries when cloning
Man pages: add newlines after "Notes:"This allows for proper formatting from sowing.On OS X (using gsed, not the default BSD sed), from the PETSc root directory: find src include -type f \(
Man pages: add newlines after "Notes:"This allows for proper formatting from sowing.On OS X (using gsed, not the default BSD sed), from the PETSc root directory: find src include -type f \( -name "*.c" -or -name "*.h" -or -name "*.cxx" \) | xargs gsed -i 's/Notes\s*:\s*\(\w.*\)/Notes:\n \1/'This adds a newline and 4 spaces whenever "Notes:" is followed by any "word" character, in any .c, .h, or .cxx file in src/ or include/
Section: Must also copy field symmetries when cloning
Section: Allow NULL argument to PetscSectionSetSym()
Section: Copy symmetries when cloning
Merge remote-tracking branch 'origin/tisaac/feature-dmfield'* origin/tisaac/feature-dmfield: (56 commits) Plex: Updated test output for DMLabel change DMLabel: make empty ISs strides DMSwarm:
Merge remote-tracking branch 'origin/tisaac/feature-dmfield'* origin/tisaac/feature-dmfield: (56 commits) Plex: Updated test output for DMLabel change DMLabel: make empty ISs strides DMSwarm: silence static analyzer warning 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 DMField: default initialization of variable PetscFE: fix integration for openCL PetscFEGeomComplete(): correct normal vector in 2D. DMField: c++/complex fixes DMField: empty processor protections DMField regression test fixes DMLabel: try to keep stride IS as stride IS as much as possible DMPlexRefine(): create depth before hybrid-bounded label DMField: documentation of interface DMField: implement shell DMPlex: rename newly created label ...Conflicts: src/dm/dt/interface/dtfe.c src/snes/examples/tutorials/ex69.c src/snes/utils/dmplexsnes.c
Section: Small fix
Merge branch 'master' into knepley/feature-pc-patch* master: (440 commits) revert sources to dev - reset PETSC_VERSION_RELEASE - reset changes/dev.html release: set v3.9 strings fix grep us
Merge branch 'master' into knepley/feature-pc-patch* master: (440 commits) revert sources to dev - reset PETSC_VERSION_RELEASE - reset changes/dev.html release: set v3.9 strings fix grep usage on solaris [use egrep] opensolaris: fix errors Update timer reporting and minor reporting fix Remove redundant if statement. Found by @jedbrown Fixed problem with order of developer photos on website. superlu_dist: use correct flag in example [PETSC_HAVE_SUPERLU -> PETSC_HAVE_SUPERLU_DIST] Bib: PERMON ref fix for osx doc: more author fixes doc: more author fixes Italicized "orderings" in MPI process placement discussion. Added Richard to the user manual author list. Added Richard to the list of active developers on the website. add string check for MS-MPI and IMPI timeout errors opensolaris does not have multiple grep utils - but default one does not support -F. So use fgrep instead Standardizing timeout checks Report wall clock time of total tests Use time instead of date %s ...Conflicts: include/petscpc.h src/ksp/ksp/interface/itfunc.c
Section: Allow global offsets for fields to be non-contiguous- This allows the global operator to segregate fields, rather than having all fields on a point contiguous as was our default
MPI I/O: Support for view/load ISGENERAL
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