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madams/sr-driver

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madams/sr-driver
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Author Commit Message Date Builds
250+ commits behind master.
Mark Adams
finished up adding serial DMPlex test with a convergance test on a 5-point Laplacian finite volume test problem
Mark Adams
cleaning up
Mark Adams
merge after conflicts
Mark Adams
cleaning up
Matthew Knepley
TS ex32: Added a parallel test
Matthew Knepley
TS ex32: Fixed some problems in MonitorVTK() - Also added a Builder run
Matthew Knepley
DMLabel: Fixed index for ranges with nonzero lower limit
Mark Adams
added convergence test. Fails
Matthew Knepley
TS ex32: Fixed Face Sets after refinement
Mark Adams
added debugging code for Matt
Mark Adams
fixed some bugs. 4x4 grid solve looks OK.
Mark Adams
protected test for null vector for when FD Jacobians produced with SNES without a solve. Added simplified version of ex11 for a Laplacian with DMPlex with FD Jacobian and test with exact solution for convergance testing
Mark Adams
running code with error with refinement.
Mark Adams
temp version
Mark Adams
...
Mark Adams
start of driver for segmetal refimenent.
Mark Adams
Merge branch 'madams/sr-driver' of bitbucket.org:petsc/petsc into madams/sr-driver
Matthew Knepley
TS ex32: Fixed some problems in MonitorVTK() - Also added a Builder run
Matthew Knepley
DMLabel: Fixed index for ranges with nonzero lower limit
Mark Adams
Merge branch 'next' of bitbucket.org:petsc/petsc into madams/sr-driver
Matthew Knepley
Merge branch 'knepley/feature-plex-refine-3d' into next * knepley/feature-plex-refine-3d: DMPlex ex5: Added test output for 2D quad test with fault ending in the domain DMPlex: Major fix for hybrid cell creation - Faults that ended in the domain created inconsistent meshes - I now add a cohesive cell at the edge of a fault which may have some pieces "unsplit" - Unsplit points are connected by hybrid points, but are not replicated - This has only be…
Peter Brune
Merge branch 'prbrune/snes-fasfull' into next
Mark Adams
added convergence test. Fails
Jed Brown
Merge branch 'hzhang/snes-jacobiancoloropt' into next Optimize MatFDColoring for AIJ and BAIJ. MatFdColoringCreate_SeqXAIJ(), MatFdColoringCreate_MPIXAIJ(), MatFdColoringApply_AIJ() and MatFdColoringApply_BAIJ() use struct coloring->matentry to access addresses of Jacobian values directly, thus avoids calling MatSetValues(). The struct also enables (row, col, valaddr) to be stored together for efficient data accessing in FdColoringApply(). The new i…
Matthew Knepley
TS ex32: Fixed Face Sets after refinement
Mark Adams
added debugging code for Matt
Jed Brown
Merge branch 'jed/mat-setvalues-col-bs' into next * jed/mat-setvalues-col-bs: Mat: non-square block support for MatSetValuesBlocked
Peter Brune
Merge branch 'prbrune/mat-matcolor' into next
Matthew Knepley
Merge branch 'knepley/fix-plex-ghost-cells' into madams/sr-driver * knepley/fix-plex-ghost-cells: DMPlex: Fixed DMPlexConstructGhostCells() to filter out non-faces from the label DMPlex: Added DMLabelFilter() Conflicts: include/petscdmplex.h
Matthew Knepley
Merge branch 'knepley/fix-plex-ghost-cells' into next * knepley/fix-plex-ghost-cells: DMPlex: Fixed DMPlexConstructGhostCells() to filter out non-faces from the label DMPlex: Added DMLabelFilter() Conflicts: include/petscdmplex.h
Karl Rupp
Merge branch 'karlrupp/fix-cuda-viennacl-vecaypx' into next
Mark Adams
Merge branch 'next' of bitbucket.org:petsc/petsc into madams/sr-driver
Mark Adams
fixed some bugs. 4x4 grid solve looks OK.
Jed Brown
Merge branch 'barry/fix-mat-checkinode-factorlu' into next Improve performance of inode handling for factored matrices. * barry/fix-mat-checkinode-factorlu: move Mat_CheckInode_FactorLU to symbolic factorization so it doesn't get called in EVERY numeric factorization removed mallocs from inner loop of Mat_CheckInode_FactorLU, also added a bunch of const to array variables in that file
Jed Brown
Merge branch 'master' into next * master: TS ex31: fix Jacobian destruction TSRK: remove TSRKSetTolerance because we now use TSAdapt
Mark Adams
merging after conflict
Mark Adams
protected test for null vector for when FD Jacobians produced with SNES without a solve. Added simplified version of ex11 for a Laplacian with DMPlex with FD Jacobian and test with exact solution for convergance testing
Peter Brune
Merge branch 'prbrune/mat-matcolor' into next Conflicts: src/docs/website/documentation/changes/dev.html
Mark Adams
running code with error with refinement.
Jed Brown
Merge branch 'master' into next * master: Conflicts: src/ts/examples/tutorials/makefile
Jed Brown
Merge branch 'balay/remove-sdir' into next * balay/remove-sdir: __SDIR__: remove remaining traces and document in changes.html Conflicts: src/docs/website/documentation/changes/dev.html
Jed Brown
Merge branch 'barry/fix-scalartypes' into next * barry/fix-scalartypes: setCompilers() zeros out anything set in LIBS so all tests that affect LIBS must be made after MPI
Matthew Knepley
Merge branch 'knepley/feature-plex-refine-3d' into next * knepley/feature-plex-refine-3d: DMPlex: Fix bug with multiple point labels for cohesive completion DMPlex: Allow an increase in support size for split points in hybrid construction DMPlex: Fixed compiler warning DMPlex ex5: Added a new quad test - Its broken for a good reason, need to deal with fault boundaries DMPlex ex5: Added test output DMPlex ex4 and ex5: Added new hexahedral te…
Jed Brown
Merge branch 'madams/gamg-parmtests' into next PCGAMG default smoother changed from Jacobi to SOR. * madams/gamg-parmtests: changes/dev.html: document PCGAMG change from PCJACOBI to PCSOR gamg tests: made file names more consistant; removed excess parameters to make test sort of orthogal with other test in that there are not parameters or combinations of parameters that are tested in another test; added a hypre test with two degrees of fr…
Jed Brown
Merge branch 'rlacroix/mpibaij-permute' into next * rlacroix/mpibaij-permute: Fix MatPermute for MPIBAIJ matrices. Make the tests for MatPermute more foolproof. Really test MatPermute for MPIAIJ and MPIBAIJ matrices. Conflicts: src/mat/examples/tests/makefile
Jed Brown
Merge branch 'emil/ts-poststage' into next * emil/ts-poststage: Added a post-stage function for time-integrators
Jed Brown
Merge branch 'emil/ts-new-examples' into next Add Hull test suite for ODE integrators, with exact solutions. A subsequent patch series should (a) add nightly tests using new integrators and (b) fix registration so that new examples can be easily registered. * emil/ts-new-examples: (25 commits) TS example: fix whitespace before CHKERRQ TS example: fix mixed declarations and code TS example: nuke trailing whitespace Bugfix in IJacobia…
Jed Brown
Merge branch 'emil/ts-rk-rehab' into next Renovate explicit Runge-Kutta methods to use TSAdapt and support easy registration of additional schemes. * emil/ts-rk-rehab: Updated the documentation for using RK schemes with variable timesteps Changed the default RK type to be RK3BS (Bogacki-Shampine) which has an embedded method minor edits in rk and adding petsc math types in ex31 Added comments documenting the Dormand-Prince and Bo…
Karl Rupp
Merge branch 'karlrupp/fix-viennacl-warnings' into next
Satish Balay
Merge branch 'balay/remove-sdir' into next
Peter Brune
Merge branch 'prbrune/mat-matcolor' into next
Satish Balay
Merge branch 'balay/fix-package-dir-rel-path' into next
Jed Brown
Merge branch 'emil/ts-arkimex-mods' into next * emil/ts-arkimex-mods: TSARKIMEX: add test for -ts_arkimex_initial_guess_extrapolate
Jed Brown
Merge branch 'knepley/feature-dmda-section' into next Also fixes use of DMPlexGetCoordinateSection from 'knepley/feature-plex-refine-3d'. This function was changed to DMGetCoordinateSection in 'knepley/feature-dmda-section' so whichever merges to master *last* will need to apply this fix. It is a build error rather than a silent semantic conflict, however, so it should be discovered before pushing the merge. * knepley/feature-dmda-section: DMDA:…
Jed Brown
Revert "Revert "Merge branch 'knepley/feature-dmda-section' into next"" Yes, this is a revert of a revert, so now 'next' should have everything from 'knepley/feature-dmda-section'. This reverts commit ff1c6abbdbe1b537e349779bbf0cf5ab40389f4c.
Matthew Knepley
Merge branch 'knepley/feature-dmda-section' into next * knepley/feature-dmda-section: DMPlex ex3: Fixed multicomponent functions - These were zero in all but the first component due to an earlier error
Matthew Knepley
Merge branch 'knepley/feature-dmda-section' into next * knepley/feature-dmda-section: DMPlex: Cleaned up uses of DMPlexGet/SetCoordinateSection() DMPlex: Cleaned up uses of DMPlexGet/SetCoordinateSection() Conflicts: src/dm/impls/plex/plex.c src/dm/impls/plex/plexinterpolate.c
Jed Brown
Merge branch 'emil/ts-arkimex-mods' into next Extrapolated initial guess -ts_arkimex_initial_guess_extrapolate. Currently no programmatic interface. Also fixes interpolation sign error in TSARKIMEX. * emil/ts-arkimex-mods: TSARKIMEX: do not use extrapolation after stage rejection TSARKIMEX: track whether cached stages are available TSARKIMEX: add test of interpolation In TSARKIMEX, If b is not specified, it is equal to bt, not last …
Jed Brown
Revert "Merge branch 'knepley/feature-dmda-section' into next" DMPlexGetCoordinateSection was lost in the merge. Several other warnings and errors that I think will need to be fixed in the branch. This reverts commit 26ee7ca0ddf6649eec5ac2d68a44ed8e0fa81806, reversing changes made to 31736f3da177f5ca045cb2a5cc03d74d483f856b.
Matthew Knepley
Merge branch 'knepley/feature-dmda-section' into next * knepley/feature-dmda-section: DMPlex ex3: Added 2D Q_1 and 3D P_2 tests - Added -simplex argument - Uses DMDA for quad tests DMDA: Added DMDAProjectFunction() and DMDAComputeL2Diff() DMDA: Fixed 2D geometry - Should reuse DMPlex routines DMDA: Fix bug in 2D closure operation for cells DMDA: Make closure operations also return the size DMDA: Changed DMDACreateSection() to emulate DMPl…
Mark Adams
Merge branch 'next' of bitbucket.org:petsc/petsc into madams/sr-driver
Jed Brown
Merge branch 'madams/gamg-default-type' into next * madams/gamg-default-type: PCGAMG: set default type (AGG); PCSetUp_GAMG crashes if not set
Jed Brown
Merge branch 'master' into next * master: PetscSynchronizedFGets: fix deadlock at EOF Compiler: Fix warnings from MPI impls which do not initialize outputs
Mark Adams
temp version
Matthew Knepley
Merge branch 'knepley/feature-test-parser' into next * knepley/feature-test-parser: Builder: Reorganized test output checking - Output replacement and file checking moved outside of checker - 'parser' test argument now used to set output parser class - Use SolverParser for simple KSP and SNES output parsing - Parser returns lines it did not process, which gets checked in the normal way Builder: Added really simplistic parser for KSP and SNES out…
Mark Adams
Merge branch 'next' of bitbucket.org:petsc/petsc into madams/sr-driver
Peter Brune
Merge branch 'prbrune/removeunwrappedmathfunctions' into next
Matthew Knepley
Merge branch 'knepley/feature-plex-reordering' into next * knepley/feature-plex-reordering: DMPlex: Fixed compiler warning
Matthew Knepley
Merge branch 'knepley/fix-compiler-warnings' into next * knepley/fix-compiler-warnings: SNES: Fix missing include Compiler: Fix warnings
Mark Adams
Merge branch 'next' of bitbucket.org:petsc/petsc into madams/sr-driver
Mark Adams
Merge branch 'master' of bitbucket.org:petsc/petsc into madams/sr-driver
Matthew Knepley
Merge branch 'knepley/feature-plex-refine-3d' into next * knepley/feature-plex-refine-3d: DMPlex ex4: Added hybrid hex tests
Matthew Knepley
Merge branch 'knepley/fix-snes-setup' into next * knepley/fix-snes-setup: SNES: Now work vectors come from the DM
Matthew Knepley
Merge branch 'knepley/fix-plex-examples' into next * knepley/fix-plex-examples: SNES ex62: Remove code generation
Matthew Knepley
Merge branch 'knepley/feature-plex-refine-3d' into next * knepley/feature-plex-refine-3d: DMPlex ex4: Added test with 6 tets DMPlex ex4: Now check initial mesh for consistency DMPlex: Fix bug with DMPlexLabelCohesiveComplete() - Must mark point with correct dimension DMPlex: Removed old DMMesh tests DMPlex: Fix bug in uniform refinement - Prevent negative result in subface helper function DMPlex: Fix bug with hybrid mesh creation - Have to …
Karl Rupp
Merge branch 'karlrupp/fix-cuda-viennacl-vecaypx' into next
Matthew Knepley
Merge branch 'knepley/fix-snes-setup' into next * knepley/fix-snes-setup: SNES: Move setup involving snes->vec_sol from SNESSetUp() to SNESolve()
Matthew Knepley
Merge branch 'knepley/feature-plex-refine-3d' into next * knepley/feature-plex-refine-3d: DMPlex: Fixed fortran binding for DMPlexCreateSubmesh()
Matthew Knepley
Merge branch 'knepley/fix-var-init' into next * knepley/fix-var-init: Compiler: Fix warnings from MPI impls which do not initialize outputs
Stefano Zampini
Merge branch 'stefano_zampini/pcbddc-reusebddc' into next
Jed Brown
Merge branch 'jed/git-download-user-url' into next * jed/git-download-user-url: config download: track whether the user provided a URL
Matthew Knepley
Merge branch 'knepley/fix-plex-examples' into next * knepley/fix-plex-examples: 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 in…
Matthew Knepley
Merge branch 'knepley/feature-plex-refine-3d' into next * knepley/feature-plex-refine-3d: DMPlex ex4: Fixed test output
Matthew Knepley
Merge branch 'knepley/feature-plex-reordering' into next * knepley/feature-plex-reordering: DMPlex ex10: Fixed test output
Matthew Knepley
Merge branch 'knepley/feature-plex-refine-3d' into next * knepley/feature-plex-refine-3d: DMPlex: Fixed leak in submesh creation
Satish Balay
Merge branch 'jed/elemental-int64' into next
Matthew Knepley
Merge branch 'knepley/feature-plex-refine-3d' into next * knepley/feature-plex-refine-3d: DMPlex ex4: Added 3D simplicial hybrid test cases - The testnum = 1 is still non-functional DMPlex: Can now uniformly refine 3D simplicial hybrid meshes - I know its a large number of changes, but I did not see a good way to break it up DMPlex: Added DMPlexCreateHybridMesh() - This was formerly done in a few steps by creating a submesh, making the label, and…
Shrirang Abhyankar
Merge branch 'shri/feature-dm-circuit' into next
Shrirang Abhyankar
Merge branch 'shri/feature-dm-circuit' into next
Stefano Zampini
Merge branch 'stefano_zampini/pcbddc-baijfixes' into next
Shrirang Abhyankar
Merge branch 'shri/feature-dm-circuit' into next
Shrirang Abhyankar
Merge branch 'shri/feature-dm-circuit' into next
Jed Brown
Merge branch 'jed/makefile-recurse-dirs' into next * jed/makefile-recurse-dirs: makefile: fix path to interfaces directory
Jed Brown
Merge remote-tracking branch 'bb/next' into next Clean up after ungraceful loss of racy merge. * bb/next: DMCircuit: Forgot to modify extern declaration for DMCreateMatrix_Circuit DMCircuit: DMCreateMatrix() related fix for circuit example DMCircuit: Fixes for fortran stubs
Shrirang Abhyankar
Merge branch 'shri/feature-dm-circuit' into next
Shrirang Abhyankar
Merge branch 'shri/feature-dm-circuit' into next
Shrirang Abhyankar
Merge branch 'next' of bitbucket.org:petsc/petsc into next
Matthew Knepley
Merge branch 'knepley/fix-remove-pc-supportgraph' into next * knepley/fix-remove-pc-supportgraph: PC: Removed support graph PC MatXAIJSetPreallocation: use array[] notation to help out Fortran
Satish Balay
Merge branch 'jed/elemental-int64' into next
Shrirang Abhyankar
Merge branch 'shri/feature-dm-circuit' into next
Shrirang Abhyankar
Merge branch 'shri/feature-dm-circuit' into next Conflicts: src/dm/impls/makefile src/dm/interface/dmregall.c
Satish Balay
Merge branch 'knepley/fix-windows-download' into next
Jed Brown
Merge branch 'jed/elemental-int64' into next * jed/elemental-int64: Elemental: use self.framework.getCompilerFlags()
Satish Balay
Merge branch 'balay/__float128-fix-download-f2cblas-mesg' into next
Matthew Knepley
Merge branch 'knepley/fix-windows-download' into next * knepley/fix-windows-download: Configure: Package.downloadonWindows is supposed to mean that Windows compilers work. not Cygwin - Also changed doc for Package.worksonWindows, which does refer to Cygwin
Jed Brown
Merge branch 'jed/datafiles-inherit' into next * jed/datafiles-inherit: config: only define DATAFILESPATH for non-null value
Jed Brown
Merge branch 'jed/elemental-int64' into next * jed/elemental-int64: Elemental: add support for 64-bit indices Elemental: upgrade to development version that requires C++11 config: add with-cxx-dialect and check for C++11 Elemental: fix setting of CMAKE_CXX_FLAGS config: write CXX_FLAGS for building C++ even when clanguage=C
BarryFSmith
Merge branch 'barry/wirth-fusion-materials' into next
Jed Brown
Merge branch 'jed/options-insert-bcast-bgq' into next * jed/options-insert-bcast-bgq: PetscOptionsInsertFile: combine Bcasts for alias and values
Matthew Knepley
Merge branch 'knepley/feature-plex-refine-3d' into next * knepley/feature-plex-refine-3d: DMPlex ex5: Added checks and fixed output - Fixes for supports DMPlex: Fix for hybrid cell creation - Adding hybrid face in support should not have been in loop DMPlex: Fix distribution of hybrid cell information - Fixed bizarre code intended for cell-vertex meshes DMPlex ex5: Fixed tests for new hybrid cell formation - Added in supports for cohesive edges…
Jed Brown
Merge branch 'jed/fix-restrict-cxx' into next Fix C/C++ choice for PETSC_RESTRICT and PETSC_STATIC_INLINE. * jed/fix-restrict-cxx: config: define lang-specific macros in petscconf.h, choose in petscsys.h
Jed Brown
Revert "Merge branch 'karlrupp/fix-restrict-keyword' into next" This approach added a magic infix "[C/CXX-SPLIT]" operator, but this puts logic in petscconf.h that confounds ad-hoc parsing (e.g., grep). Reverting this makes way for the simpler approach of defining PETSC_RESTRICT in petscconf.h (consistent with treatment of PETSC_FUNCTION_NAME). This reverts commit 8ab1f236c21ec085ac4c952206a73980138fa0cd, reversing changes made to 193eec4c38c0ab5f9a0e1b6844f2…
Jed Brown
Merge branch 'jed/fix-fieldsplit-mg-example' into next * jed/fix-fieldsplit-mg-example: SNES runex19_draw: check output and report errors SNES runex19_draw: use -fieldsplit_x_velocity_pc_mg_galerkin
Jed Brown
Merge branch 'jed/fix-matop-enum' into next * jed/fix-matop-enum: Mat: add MATOP_ values for missing functions
Jed Brown
Merge branch 'jed/dmvecmattypes-stdcoords' into next * jed/dmvecmattypes-stdcoords: DMPlex: use VECSTANDARD for coordinates Conflicts: src/dm/impls/plex/plex.c
Mark Adams
...
Matthew Knepley
Merge branch 'knepley/feature-plex-reordering' into next * knepley/feature-plex-reordering: DMPlex: Added missing declarations Conflicts: include/petscdmplex.h
Matthew Knepley
Merge branch 'knepley/feature-plex-reordering' into next * knepley/feature-plex-reordering: DMPlex: Fixed misuse of PetscObjectSetName()
Jed Brown
Merge branch 'knepley/feature-plex-reordering' into next Fixes build error and bad MPI type. * knepley/feature-plex-reordering: MatComputeBandwidth: use PetscInt instead of PetscMPIInt Conflicts: include/petscdmplex.h
Matthew Knepley
Merge branch 'knepley/feature-plex-reordering' into next * knepley/feature-plex-reordering: Mat: Fixed declaration
Matthew Knepley
Merge branch 'knepley/feature-plex-reordering' into next * knepley/feature-plex-reordering: Mat: Changed MatCalcBandwidth() to MatComputeBandwidth() - Added Fortran interface
Matthew Knepley
Merge branch 'knepley/feature-plex-reordering' into next * knepley/feature-plex-reordering: DMPlex ex10: This tests reordering of meshes DMPlex: Added DMPlexGetOrdering() and DMPlexPermute() PetscSection: Added PetscSectionPermute() DMLabel: Added DMLabelPermute() DMPlex: Added DMPlexCreateDoublet() DMPlex: Added DMPlexCopyLabels() Mat: Added MatCalcBandwidth() MatOrdering: Moved private header into petsc-private - Fix to pointer checks …
Jed Brown
Merge branch 'madams/gamg-agg-bug' into next * madams/gamg-agg-bug: fixed bug that has appeared recently of false positive errors when there are zero local equations on coarse grids in gamg-agg.
Mark Adams
start of driver for segmetal refimenent.
Jed Brown
Merge branch 'rlacroix/mpibaij-matgetcolumnnorms' into next * rlacroix/mpibaij-matgetcolumnnorms: Extend and enable the test for MatGetColumnNorms. Add MatGetColumnNorms for MPIBAIJ matrices. Spot of trailing whitespace in test.
Hong Zhang
Merge branch 'hzhang/mat-redundant' into next
Matthew Knepley
Merge branch 'knepley/fix-plex-preallocation' into next * knepley/fix-plex-preallocation: PetscSF: Fixed PetscSFCreateEmbeddedSF() - We were using sf->nleaves for the leaf buffer, which is completely wrong. We have to use the largest thing in sf->mine[]
Jed Brown
Merge branch 'master' into next * master: MatSchurComplement: Must initialize KSP package bib: fix inbook citation Bib: Updated some refs SNES: fix copy/paste in man page Conflicts: src/docs/website/documentation/changes/dev.html
Matthew Knepley
Merge branch 'knepley/feature-plex-refine-3d' into next * knepley/feature-plex-refine-3d: DMPlex ex4: Test for hex refinement now working - Fixed deadlock with parallel test DMPlex: Fix support of face edges using orientation info in hex refinement DMPlex: Fix interiors faces in hex refinement DMPlex: Get correct support for split faces by using orientation info in hex refinement DMPlex: Properly orient split faces in hex refinement DMPlex:…
Satish Balay
Merge branch 'master' into next
Jed Brown
Merge branch 'jed/fix-mat-sbaij-sor-prefetch' into next * jed/fix-mat-sbaij-sor-prefetch: Mat SBAIJ: avoid invalid memory read in MatSOR_SBAIJ
Jed Brown
Merge branch 'jed/mat-baij-row-oriented' into next * jed/mat-baij-row-oriented: Mat BAIJ: fix typos (build errors)
Jed Brown
Merge branch 'jed/mat-baij-row-oriented' into next * jed/mat-baij-row-oriented: Mat BAIJ: respect MAT_ROW_ORIENTED in Mat*BAIJSetPreallocationCSR Conflicts: src/docs/website/documentation/changes/dev.html
Jed Brown
Merge branch 'master' into next * master: Revert "MatMPIBAIJSetPreallocationCSR() handled the input matrix entries incorrectly, it treated them as if each row of values" 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 th…
Jed Brown
Merge branch 'jed/doc-restore-zeros-pointer' into next * jed/doc-restore-zeros-pointer: DMPlex: fix my mistake using NULL in place of (int) 0
Jed Brown
Merge branch 'jed/fix-pcgamg-nearnullspace-corruption' into next * jed/fix-pcgamg-nearnullspace-corruption: PCGAMG: fix corruption for multiple solves when MatSetNearNullSpace is used PCGAMG: remove distracting comment Conflicts: src/ksp/ksp/examples/tutorials/makefile
Jed Brown
Merge branch 'madams/dm-compitebug' into next Fixes PCFieldSplit unable to match index sets when comparing ISGeneral as though it was an ISStride. * madams/dm-compitebug: replaced ISCreateGeneral in CompositeDM with ISCreateStride. MatNest calls ISStrideGetInfo on these vectors, which was causing errors
Jed Brown
Merge branch 'jed/ksp-ex49-constrain-near-null' into next * jed/ksp-ex49-constrain-near-null: KSP ex49: restrict near-null space for elasticity example with sym BC
Peter Brune
Merge branch 'prbrune/snes-removencgmatrix' into next Conflicts: src/snes/impls/ncg/snesncg.c
BarryFSmith
Merge branch 'barry/add-vecgetarray-fortran-derived-type' into next
Matthew Knepley
Merge branch 'knepley/fix-plex-preallocation' into next * knepley/fix-plex-preallocation: DMPlex: Fix completely broken code in PetscSFCreateRemoteOffsets() - Non-broken example was in PetscSFDistributeSection() DMPlex: Fix leaks in preallocation debugging DMPlex: Put in guard for preallocation sections which are smaller than the SF
Peter Brune
Merge branch 'prbrune/snes-qnscaling' into next
Karl Rupp
Merge branch 'paulmullowney/cusp-vector-scatter-with-fix' into next
Satish Balay
Merge branch 'master' into next
Peter Brune
Added better defaults to the individual SNESQN types
Satish Balay
Merge branch 'master' into next
Matthew Knepley
Merge branch 'knepley/fix-plex-ex12' into next * knepley/fix-plex-ex12: DMPlex ex12: Give mesh a name - Fixed test output DMPlex: Fix leaks
Satish Balay
Merge branch 'master' into next
Jed Brown
Merge branch 'jed/ts-ex11-c++' into next * jed/ts-ex11-c++: TS ex11: subtype struct naming convention TS ex11: fix C++ casts for assignment of void* to typed pointer
Jed Brown
Merge branch 'jed/doc-restore-zeros-pointer' into next * jed/doc-restore-zeros-pointer: doc: restore functions in PETSc zero their arguments
Satish Balay
Merge branch 'balay/fix-fenv.h-check-on-cygwin64' into next Conflicts: config/PETSc/Configure.py
Matthew Knepley
Merge branch 'knepley/fix-configure-dll' into next * knepley/fix-configure-dll: Configure: Added a DLL trial to the shared linker tests
Matthew Knepley
Merge branch 'knepley/fix-coordinate-dm' into next * knepley/fix-coordinate-dm: DM: Added DMSetCoordinateDM() PetscObjectStateGet: fix stale comments about *StateQuery
Jed Brown
Merge branch 'jed/config-opencl' into next * jed/config-opencl: config: check for libOpenCL.a (Linux)
Jed Brown
Merge branch 'mlange05/threadcomm-matmult-baij' into next * mlange05/threadcomm-matmult-baij: Threadcomm: Threading MatMult_SeqBAIJ Threadcomm: Adding "first touch" allocation to Mat_SeqBAIJ
Satish Balay
Merge branch 'jed/gnumake' into next
Jed Brown
Merge branch 'rlacroix/mpibaij-matgetcolumnnorms' into next * rlacroix/mpibaij-matgetcolumnnorms: Add MatGetColumnNorms for MPIBAIJ matrices. MatGetColumnNorms_MPIAIJ: Use PetscObjectComm to access the communicator.
Jed Brown
Merge branch 'master' into next * master: Mat: fix Fortran interface for MatGetColumnNorms
Jed Brown
Merge branch 'prbrune/snes-qnscaling' into next * prbrune/snes-qnscaling: SNESQN: only monitor real part of dot product (fails with C++ complex)
Jed Brown
SNESQN: only monitor real part of dot product (fails with C++ complex)
Jed Brown
Merge branch 'barry/dmvecmattypes' into next * barry/dmvecmattypes: DMPlex ExodusII: fix dm->vectype pointer syntax
Jed Brown
Merge branch 'placasse/matsor-log-flops' into next * placasse/matsor-log-flops: Bad LogFlops in MatSOR_SeqSBAIJ.
Jed Brown
Merge branch 'master' into next * master: Fix for accidentally duplicated refcount decrement in dm->x
Jed Brown
Merge branch 'madams/mat-residual' into next * madams/mat-residual: refactored residuals by adding a 'residual' method to Mat
BarryFSmith
the master next branch model is NOT perfect. And shit is hanging around far to long in pull requests and next before going into master! Or damn damn damn for short
BarryFSmith
Merge branch 'barry/dmvecmattypes' into next Conflicts: src/dm/interface/dlregisdmdm.c
BarryFSmith
Merge branch 'barry/dmvecmattypes' into next Conflicts: src/dm/impls/da/fdda.c 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/dm/impls/plex/plex.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
Jed Brown
Merge branch 'jed/object-id' into next * jed/object-id: Sys: mark PetscObjectState modification as logically collective Sys: convert object ID to 64-bit and add PetscObjectGetId() Sys: typedef PetscObjectState and change all accessors
Peter Brune
Merge branch 'prbrune/snes-qnscaling' into next
Peter Brune
Added a Broyden run example
Jed Brown
Merge branch 'jed/gnumake' into next * jed/gnumake: gmake: clean MPIUNI_MOD
Jed Brown
Merge branch 'jed/gnumake' into next * jed/gnumake: config: rename PETSC_BUILD_USING_GNUMAKE to MAKE_IS_GNUMAKE gmake: Fortran module dependencies gmake: use MODDIR for F90 module dest (PETSC_ARCH/include) gmake: clean use petsc*.mod [as *.mod might delete mpi.mod aswell]
BarryFSmith
Merge branch 'barry/remove-timelogging' into next
BarryFSmith
Merge branch 'barry/fix-petscobjectsetstate' into next Conflicts: src/docs/website/documentation/changes/dev.html
Jed Brown
Merge branch 'barry/fix-dgmres.c' into next * barry/fix-dgmres.c: KSPDGMRES: fix conditional variable declarations
Jed Brown
Merge branch 'jed/gnumake' into next * jed/gnumake: gmake: put object files in obj/ instead of obj-gmake/
Matthew Knepley
Merge branch 'knepley/fix-fem-0d' into next * knepley/fix-fem-0d: PetscDualSpace: Updated to new PetscQuadrature names
Matthew Knepley
Merge branch 'knepley/fix-fem-0d' into next * knepley/fix-fem-0d: PetscDualSpace: Add 0d corner case PetscQuadrature: Add a 0d corner case
Satish Balay
Merge branch 'knepley/feature-plex-generic-distribute' into next
Satish Balay
Merge branch 'jed/gnumake' into next
Satish Balay
Merge branch 'jed/gnumake' into next
Hong Zhang
Merge branch 'hzhang/mat-cleanup' into next
Hong Zhang
Merge branch 'hzhang/mat-redundant' into next
Satish Balay
Merge branch 'balay/update-sowing' into next
Jed Brown
Merge branch 'jed/gnumake' into next GNU Make (v2.81 or later) is now the default build, --download-make is supported. * jed/gnumake: 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 …
Jed Brown
Merge branch 'knepley/feature-plex-generic-distribute' into next * knepley/feature-plex-generic-distribute: DMPlex: add missing declarations DMPlexDistribute{Field,Data} Conflicts: include/petscdmplex.h
Jed Brown
Merge branch 'jed/avoid-getpwuid' into next * jed/avoid-getpwuid: Sys ex13: avoid non-portable realpath(1) in verification test
Peter Brune
Merge branch 'prbrune/snes-fixviexampleoutput' into next
Jed Brown
Merge branch 'jed/remove-dynamic-loading-option' into next * jed/remove-dynamic-loading-option: Sys: PetscContainerCreate must call PetscSysInitializePackage
BarryFSmith
Merge branch 'knepley/remove-sieve' into next I guessed about the ViennaCL stuff Conflicts: include/petscsnes.h src/dm/impls/mesh/examples/tests/output/ex10_0.out src/dm/impls/mesh/examples/tests/output/ex10_1.out src/dm/impls/mesh/examples/tests/output/ex11f90_0.out src/dm/impls/mesh/examples/tests/output/ex11f90_1.out src/dm/impls/mesh/examples/tests/output/ex3_0.out src/dm/impls/mesh/examples/tests/output/ex3_1.out src/dm/impls/me…
Matthew Knepley
Merge branch 'knepley/feature-plex-refine-3d' into next * knepley/feature-plex-refine-3d: DMPlex: Fixed small bug - Was not initializing cone size
Matthew Knepley
Merge branch 'knepley/feature-plex-generic-distribute' into next * knepley/feature-plex-generic-distribute: DMPlex: Added DMPlexDistributeData() to distribute arbitrary data types DMPlex: Change DMPlexDistribute() to give back the PetscSF - This can be used to distribute sections and fields Doc: Reverted f0bf76b17391 - We can use this http://tex.stackexchange.com/questions/36660/only-authors-initials-in-bibtex-natbib-using-named-style to fix our papers …
Matthew Knepley
Merge branch 'knepley/feature-plex-refine-3d' into next * knepley/feature-plex-refine-3d: DMPlex ex4: All tests now passing - Added output for quads and parallel tet DMPlex ex4: Fixed parallel hang DMPlex: Fixed orientation for interpolated face - Damn, this whole code has to be gone over again and orientations worked out correctly DMPlex: For tet refinement added GetTriSubface_Static() - Need to use everywhere DMPlex ex4: Added debugging D…
Peter Brune
Bugfix in Broyden.
Matthew Knepley
Merge branch 'knepley/feature-fem-dgspace' into next * knepley/feature-fem-dgspace: PetscFE: Fixed quadrature names for OpenCL
Peter Brune
generalized the Powell condition to the jacobian scaling case.
Peter Brune
Added the line-search based previous step in bad broyden
Peter Brune
Generalized the Shanno scaling condition to all the variants
Matthew Knepley
Merge branch 'knepley/fix-dmda-clone-subdm' into next * knepley/fix-dmda-clone-subdm: DMDA: Fix DMDACreateSection() - Fix setting the default section - Fix setting pointSF DMDA: Fix DMCreateSubDM_DA() - Cannot call DMClone() since we want to change the number of fields - DMDA needs to be fixed to separate dof and topology DMDA: Must call DMSetUp() inside DMClone() DM: In DMClone(), setup should be flagged after implementation setup Conflicts…
Peter Brune
Fix "Bad" Broyden; all of them work now!
Peter Brune
More cleanup of the new Broyden implementation
Matthew Knepley
Merge branch 'knepley/fix-plex-cgns' into next * knepley/fix-plex-cgns: DMPlex: Fix bad conversion in CGNS code
Peter Brune
Better refs for QN methods
Peter Brune
Make the Broyden update work correctly.
Jed Brown
Merge branch 'jed/attribute-deprecated-compat' into next * jed/attribute-deprecated-compat: config: avoid string argument to __attribute((deprecated))
Jed Brown
Merge branch 'jed/converged-default-and-skip' into next This started with SNESDefaultConverged -> SNESConvergedDefault in v3.4, but the other parts have been added piecemeal. Deprecation support in C interface. * jed/converged-default-and-skip: SNES and KSP: add deprecation for *DefaultConverged and *SkipConverged KSP: rename KSPDefaultConverged* to KSPConvergedDefault* KSP: rename KSPSkipConverged -> KSPConvergedSkip SNES: document SNESSkipC…
Matthew Knepley
Merge branch 'knepley/feature-fem-dgspace' into next * knepley/feature-fem-dgspace: PetscSpace: Added a DG space - Defined on a set of quadrature points - Need tests PetscQuadrature: Revamped - Removed basis tabulation - Shortened names - Added PetscQuadratureView() fixed bunch of bibtex items that should ahve used abbreviations only
Matthew Knepley
Merge branch 'knepley/feature-closure-cache' into next * knepley/feature-closure-cache: DMPlex: Added declaration of DMPlexCreateClosureIndex()
Matthew Knepley
Merge branch 'knepley/feature-dt-fem' into next * knepley/feature-dt-fem: SNES ex12: Fix buggy checkin
Hong Zhang
Merge branch 'hzhang/fix-tests' into next
Matthew Knepley
Merge branch 'knepley/fix-label-partition' into next * knepley/fix-label-partition: DMPlex: Replaced algorithm for label distribution with one that does not suck - Need more tests
Matthew Knepley
Merge branch 'knepley/fix-test-output-parsing' into next * knepley/fix-test-output-parsing: Builder: strip test output before comparing
Matthew Knepley
Merge branch 'knepley/feature-dt-fem' into next * knepley/feature-dt-fem: PetscDualSpace: Pointer check barfs for function pointer
Matthew Knepley
Merge branch 'knepley/feature-closure-cache' into next * knepley/feature-closure-cache: SNES ex62: Use closure index DMPlex: Use closure index if available for DMPlexVecGetClosure() DMPlex: Added DMPlexCreateClosureIndex() - Uses a PetscSection+IS and stashes in the original Section PetscSection: Added an index for optimization of closure queries - Added PetscSectionGet/SetClosureIndex() - The index is keyed to the DM which built it (use Petsc…
Hong Zhang
Merge branch 'hzhang/mat-cleanup' into next
Matthew Knepley
Merge branch 'knepley/fix-cublas-init' into next * knepley/fix-cublas-init: Sys: Allow CUBLAS init to be turned off - This causes SEGV on my Air all the time DMPlex: Removed dead declaration (thanks Lisandro) added citation for superlu99 Conflicts: src/sys/objects/pinit.c
Matthew Knepley
Merge branch 'knepley/feature-dt-fem' into next * knepley/feature-dt-fem: Sys: Add ability to turn off CUBLAS initialization - This continually SEGVs on my Air SNES ex62: Updated test output - Matrix now prints attached nullspace indicator - 3D tests are wierdly different, they need to be verified by hand SNES ex12: Updated test output - Mostly for completed labels SNES ex12/62: Changed to new DMPlexProjectFunction() interface - Took DM…
Matthew Knepley
Merge branch 'knepley/fix-plex-closure' into next * knepley/fix-plex-closure: DMPlex: Fixed missing RestoreTransitiveClosure()
Matthew Knepley
Merge branch 'knepley/fix-plex-closure' into next * knepley/fix-plex-closure: DMPlex: Fixed optimized portion of VecGetClosure() for NULL input array
Jed Brown
Merge branch 'madams/sor-opt' into next Reduce SSOR with nonzero initial guess from 2 work units to 1.5 by caching application of lower-triangular part in the forward sweep, for use in backward sweep. * madams/sor-opt: KSP ex54: explicitly call KSPSetUp so that it is distinct in the profile MatSOR_SeqAIJ_Inode: optimize to cache lower-triangular part MatSOR_SeqAIJ: optimize to cache the application of the lower-triangular part
Matthew Knepley
Merge branch 'knepley/fix-plex-closure' into next * knepley/fix-plex-closure: DMPlex: Allow NULL array as input to DMPlexVecGetClosure()
Matthew Knepley
Merge branch 'knepley/fix-plex-closure' into next * knepley/fix-plex-closure: DMPlex: Fix VecGetClosure() when the array is input Conflicts: config/builder.py src/dm/impls/plex/plexgeometry.c src/dm/impls/plex/plexsubmesh.c src/snes/examples/tutorials/output/ex12_10.out src/snes/examples/tutorials/output/ex12_11.out src/snes/examples/tutorials/output/ex12_5.out src/snes/examples/tutorials/output/ex12_6.out src/snes/examples/tutorials/o…
Matthew Knepley
Merge branch 'knepley/fix-hybrid-distribution' into next * knepley/fix-hybrid-distribution: DMPlex: Better fix for distribution of hybrid bounds - Bounds are now computed from the reordering at distribution time - Still incomplete since we need to compute the interpolated bounds after interpolation DMPlex: Temporary fix for handling hybrid meshes in parallel - Try to compute the hybrid structure - Should really send it out with Distribute() Conflic…
Matthew Knepley
Merge branch 'knepley/fix-dm-clone' into next * knepley/fix-dm-clone: DMPlex: clones are already setup Conflicts: src/dm/impls/plex/plexcreate.c
Matthew Knepley
Merge branch 'knepley/fix-plex-orient' into next * knepley/fix-plex-orient: DMPlex: Fixed bug with mesh orientation - flipped marker must be a boolean for ^ operation - Final check needs a mismatch as well DMInterpolation: Fixed declarations DMPlex: Added declaration
Matthew Knepley
Merge branch 'knepley/submesh-declarations' into next * knepley/submesh-declarations: DMInterpolation: Fixed declarations DMPlex: Added declaration Conflicts: include/petscdm.h
Matthew Knepley
Merge branch 'knepley/feature-plex-refine-3d' into next * knepley/feature-plex-refine-3d: DMPlex: Test output fixes
Matthew Knepley
Merge branch 'knepley/feature-plex-refine-3d' into next * knepley/feature-plex-refine-3d: DMPlex ex4: Now passes all tests, added 2D simplex test - Only check symmetry for non-hybrid meshes right now (need to fix support of cohesive edges) - Took out hacky code for hybrid distribution - Added new test output DMPlex: Fix creation of SF in 3D uniform refinement DMPlex: Fix support of edges in 2D uniform refinement DM: Fixed initialization - Sys b…
Jed Brown
Merge branch 'jed/avoid-getpwuid' into next * jed/avoid-getpwuid: cleanup includes that are no longer needed. Also remove check for _fullpath() as the corresponding code is removed.
Jed Brown
Merge branch 'jed/avoid-getpwuid' into next The file path routines were broken because the current directory was placed in front of the given path before checking for leading ~ or ~user. This is now fixed, along with the removal of getpwuid (a liability on BG/Q and Cray). We still attempt to use getpwnam when encountering ~user. * jed/avoid-getpwuid: Sys: fix PetscGetFullPath expansion of ~ and ~user, ensure NULL termination Sys: …
Jed Brown
Merge branch 'master' into next
Jed Brown
Merge branch 'jed/remove-dynamic-loading-option' into next * jed/remove-dynamic-loading-option: Remove --with-dynamic-loading / PETSC_USE_DYNAMIC_LIBRARIES
Jed Brown
Merge branch 'master' into next * master: Sys: revert packed PetscMalloc to PetscMallocN in PetscCommBuildTwoSided_Allreduce
Matthew Knepley
Merge branch 'knepley/feature-dt-fem' into next * knepley/feature-dt-fem: PetscFE: OpenCL is hardcoded for P0 coefficients right now
Matthew Knepley
Merge branch 'knepley/feature-dt-fem' into next * knepley/feature-dt-fem: SNES ex12: Added test cases for variable coefficient Laplace - The P1 tests reproduce the analytic linear coefficient PetscFE: Added auxiliary fields to PetscFEIntegrateJacobian() - Hooked it up to DMPlexComputeJacobian() SNES ex12: Removed code generation SNES ex12: Small fix SNES ex12: Fixed test output Conflicts: config/builder.py
Peter Brune
Merge branch 'prbrune/snes-jacobiancolormgfix' into next Conflicts: src/ts/examples/tutorials/makefile
Matthew Knepley
Merge branch 'knepley/fix-plex-parmetis' into next * knepley/fix-plex-parmetis: DMPlex: ParMetis now working - Ridiculous stub partition up front removed - Metis does not return 0 on success, so fixed call
Matthew Knepley
Merge branch 'knepley/fix-plex-parmetis' into next * knepley/fix-plex-parmetis: DMPlex: Changed DMPlexCreatePartition() to take the partitioner name PetscSection: Added docs for Fortran binding for VecSetValuesSection() Vec: Removed old F90 binding for PetscSection
Satish Balay
Merge branch 'knepley/feature-dt-fem' into next
Jed Brown
Merge branch 'knepley/feature-plex-metis' into next * knepley/feature-plex-metis: DMPlex: remove unused variable
Matthew Knepley
Merge branch 'knepley/feature-plex-refine-3d' into next * knepley/feature-plex-refine-3d: DMPlex: Fix array length Conflicts: include/petscdmplex.h
Matthew Knepley
Merge branch 'knepley/feature-dt-fem' into next * knepley/feature-dt-fem: DMPlex+PetscFE: Fix compile errors for complex - LAPACK calls still broken Conflicts: config/builder.py src/dm/impls/plex/plexgeometry.c src/snes/examples/tutorials/ex12.c
Satish Balay
Merge branch 'balay/fix-deadlock-on-bgq' into next
Jed Brown
Merge branch 'master' into next Compatibility fixes after Matt merged to 'master', plus some docs. * master: DMPlex: change order of assignment to appease -Wmaybe-initialized (gcc-4.8.1) DMPlex: Fix 64-bit int problem in VTK Mat: Fix for PetscSparseDenseMaxDot() for complex Vec: Correct VecUniqueEntries() for 64-bit indices MatSeqAIJGetArrayF90: add man pages and fix typo in MatDense version SF docs: add link to sum…
Jed Brown
Merge branch 'knepley/fix-configure-package' into next * knepley/fix-configure-package: Configure: Fixed logic when using --with-package-lib when the package has no includes
Jed Brown
Merge branch 'knepley/reordering' into next * knepley/reordering: Mat ex170: Comments Mat ex170: Test for MatMult() using max instead of plus - Finds the number of connected components in parallel - Can still optimize better in parallel Mat: Added stuff to let me do (max, mult) algebra things for reordering - Added MatMultMax_SeqAIJ() and MatMultAddMax_SeqAIJ() - Added PetscSparseDenseMaxDot() Vec: Added VecUniqueEntries() - This is…
Matthew Knepley
Merge branch 'knepley/feature-plex-refine-3d' into next * knepley/feature-plex-refine-3d: DMPlex: Fixed view
Matthew Knepley
Merge branch 'knepley/feature-dt-fem' into next * knepley/feature-dt-fem: SNES ex12: Added Neumann output SNES ex12: Fixed test output, now all tests except Exodus run DMPlex+PetscFE: Looks like boundary integration is working - DMComputeResidualFEM() checks for feBd, and does bd integral if present - Normals are still not being calculated - Added PetscFEIntegrateBdResidual() and a basic implementation - Added normals to PetscCellGeometry…
Matthew Knepley
Merge branch 'knepley/feature-plex-refine-3d' into next * knepley/feature-plex-refine-3d: DMPlex: Add plexrefine.c to makefile DMPlex ex4: Had to turn off re-interpolation check for uniform refinement DMPlex: Fix check in refinement for tet face edges that intersect the cross-tet edge - My re-interpolation test still does not work DMPlex: Fix array restore in DMPlexGetFaces_Internal() DMPlex: Now DMView_Plex() uses the DM name DMPlex: Added…
Matthew Knepley
Merge branch 'knepley/feature-dt-fem' into next * knepley/feature-dt-fem: SNES ex12: Added 3D Dirichlet test output SNES ex12: Dirichlet BC tests working with PetscFE PetscDualSpace: Added 1D reference element PescFE: Corrected spelling, Fixed pointer check PetscFE: Remove Quadrature from PetscFEM, added boundary elements Conflicts: config/builder.py src/snes/examples/tutorials/ex12.c src/snes/examples/tutorials/output/ex12_10.out…
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