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madams/sr1
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250+ commits behind master.
Mark Adams
fixed PetscNew error
Mark Adams
Merge branch 'madams/sr1' of bitbucket.org:petsc/petsc into madams/sr1
Mark Adams
fixing parallel bug
Mark Adams
Merge branch 'next' of bitbucket.org:petsc/petsc into madams/sr1
Matthew Knepley
Merge branch 'knepley/feature-plex-hybrid-3d' into next * knepley/feature-plex-hybrid-3d: DMPlex: Fix hybrid bounds in DMPlexCheckFaces() DMPlex ex5: Now all test working - Two faults working correctly DMPlex: Fix for hybrid meshes with multiple surfaces - Move the original hybrid cells to the end of the numbering, so that split+hybrid points are inserted as a block - Use DMPlexShiftPoint_Internal() uniformly SNES ex4: Fix for DMCheckSkeleton()…
BarryFSmith
Merge branch 'barry/remove-strdup' into next fixed bug in previous pushed version of branched that crashed SAWs usage
Mark Adams
merge
Mark Adams
clean up
Peter Brune
Merge branch 'prbrune/fas-gscolorsecant' into next
Peter Brune
Merge branch 'jed/malloc-array' into next
Satish Balay
Merge branch 'master' into next
Satish Balay
Merge branch 'balay/cmake-use_make_j' into next
Matthew Knepley
Merge branch 'knepley/fix-fortran-init-cuda' into next * knepley/fix-fortran-init-cuda: Sys: Fix CUDA init for Fortran
Jed Brown
Merge branch 'jed/malloc-array' into next * jed/malloc-array: Sys: drop explicit type arguments from PetscNew() and PetscNewLog() Sys: add PetscCalloc[1-7] Sys: add PetscMalloc1 macro, array allocation without redundant types PetscMalloc[2-7]: remove type arguments, infer from pointer type SNESComputeJacobianDefaultColor: fix uninitialized variable Conflicts: src/sys/objects/mpinit.c cat > malloc-convert.sh <<EOF git grep -l …
Jed Brown
Merge branch 'knepley/feature-dmda-section' into next * knepley/feature-dmda-section: DMPlex: fix stale docs about DMPlexGetCoordinateSection Conflicts: src/dm/impls/plex/plexinterpolate.c
Matthew Knepley
Merge branch 'knepley/feature-plex-gmsh' into next * knepley/feature-plex-gmsh: DMPlex Gmsh: Fixed integer size problem DMPlex Gmsh: Fixed interface for coordinates
Matthew Knepley
Merge branch 'knepley/feature-plex-hybrid-3d' into next * knepley/feature-plex-hybrid-3d: DMPlex ex4: All non-hybrid refinement test pass (Fuck Yeah) DMPlex: In tet refinement, fixed edge orientation in internal face DMPlex ex4: Correct output after cross-tet edge orientation fix DMPlex: In tet refinement, correct internal tet face orientations DMPlex: In tet refinement, correct internal face cones DMPlex: In tet refinement, correct check f…
Peter Brune
Merge branch 'prbrune/mat-matcolor' into next
BarryFSmith
Merge branch 'barry/fix-mpiint-petscoptionsgetint' into next
Matthew Knepley
Merge branch 'knepley/fix-plex-submesh-parallel' into next * knepley/fix-plex-submesh-parallel: DMPlex: Fixed leak in SF creation for submesh - Changed name of subpointIS to avoid confusion
Matthew Knepley
Merge branch 'knepley/fix-plex-submesh-parallel' into next * knepley/fix-plex-submesh-parallel: DMPlex: Fixed SF creation in hybrid tet refinement, added better check DMPlex: Guard for empty submesh in parallel during subSF creation
Matthew Knepley
Merge branch 'knepley/feature-plex-gmsh' into next * knepley/feature-plex-gmsh: DMPlex ex1: Added test for Gmsh DMPlex: Added Gmsh input Conflicts: config/builder.py
Matthew Knepley
Merge branch 'knepley/feature-plex-hybrid-3d' into madams/sr1 * knepley/feature-plex-hybrid-3d: DMPlex: Fixed split face supports for tet refinement DMPlex: Multiple refinement for hex now working - Fixed face orientations for hexes - Fixed split face orientations - Fixed split face supports - Fixed internal face orientations - Fixed internal edge supports DMPlex: Added GetQuadEdgeInverse_Static() and GetQuadSubfaceInverse_Static() for refinement DMP…
Matthew Knepley
Merge branch 'knepley/feature-plex-hybrid-3d' into next * knepley/feature-plex-hybrid-3d: DMPlex: Fixed split face supports for tet refinement DMPlex: Multiple refinement for hex now working - Fixed face orientations for hexes - Fixed split face orientations - Fixed split face supports - Fixed internal face orientations - Fixed internal edge supports DMPlex: Added GetQuadEdgeInverse_Static() and GetQuadSubfaceInverse_Static() for refinement DMP…
BarryFSmith
Merge branch 'barry/fix-complex-examples' into next
Shrirang Abhyankar
Merge branch 'shri/feature-dm-circuit' into next
Peter Brune
Merge branch 'prbrune/fas-gscolorsecant' into next
BarryFSmith
Merge branch 'barry/fix-more-examples' into next
BarryFSmith
Merge branch 'barry/fix-singleton-viewer' into next
Matthew Knepley
Merge branch 'knepley/fix-plex-submesh-parallel' into next * knepley/fix-plex-submesh-parallel: DMPlex: Make DMPlexCreateCohesiveSubmesh_Interpolated() also create PetscSF
BarryFSmith
Merge branch 'barry/remove-hmpi' into next
BarryFSmith
Merge branch 'barry/fix-examples' into next
BarryFSmith
Merge branch 'barry/fix-complex-examples' into next
BarryFSmith
Merge branch 'barry/fix-complex-examples' into next
BarryFSmith
Merge branch 'barry/fix-complex-examples' into next Conflicts: src/dm/examples/tests/ex15.c src/dm/examples/tutorials/ex3.c
BarryFSmith
Merge branch 'barry/add-complex-svd' into next
Matthew Knepley
Merge branch 'knepley/feature-plex-hybrid-3d' into next * knepley/feature-plex-hybrid-3d: DMPlex: Fix compiler warning in mesh refinement DMPlex: Fix compiler warning in submesh creation Conflicts: src/dm/impls/plex/plexrefine.c
Satish Balay
Merge branch 'master' into next
Jed Brown
Merge branch 'jed/gnumake' into next * jed/gnumake: gmake: pass abspath to the compiler so that error messages contain full paths
Jed Brown
Merge branch 'jed/ex10-nearnull' into next * jed/ex10-nearnull: KSP ex10: add support for -nearnulldim with MatSetNearNullSpace()
Satish Balay
Merge branch 'master' into next
BarryFSmith
Merge branch 'barry/minor-draw-improvements' into next
Jed Brown
Mat HSL: remove file missed by f6389467ca0a699 "Revert HSL MC64AD branch"
Matthew Knepley
Merge branch 'knepley/fix-plex-submesh-parallel' into next * knepley/fix-plex-submesh-parallel: PetscSection: Fix for PetscSectionCreateGlobalSectionCensored() - Offset was wrong DM: Added check in DMCreateDefaultSF() - Check for overrun of largest offset
BarryFSmith
Merge branch 'barry/fix-synchronized-printf' into next Conflicts: src/docs/website/documentation/changes/dev.html
BarryFSmith
Merge branch 'barry/fix-synchronized-printf' into next
Matthew Knepley
Merge branch 'knepley/fix-plex-submesh-parallel' into next * knepley/fix-plex-submesh-parallel: PetscSection: Fixed PetscSectionGetOffsetRange() for empty section
Matthew Knepley
Merge branch 'knepley/feature-dmda-section' into next * knepley/feature-dmda-section: DMDA: Fix compiler warnings DMDA+DMPlex: Fixed preallocation declarations
Matthew Knepley
Merge branch 'knepley/feature-plex-hybrid-3d' into next * knepley/feature-plex-hybrid-3d: DMPlex ex5: Added a 3D hex test for a buried fault DMPlex: Fixed hybrid cell creation in 3D with internal boundaries - Fixed the support of hybrid edges introduced by unsplit vertices - Look for unsplit vertices on a split edge - Allow unsplit edges on a hybrid face - Fixed labeling to split some edges on boundary split faces
BarryFSmith
Merge branch 'barry/hide-fntptr-conversion' into next
BarryFSmith
Merge branch 'barry/fix-solaris' into next
BarryFSmith
Merge branch 'barry/draw-popup-prefix' into next
Matthew Knepley
Merge branch 'knepley/feature-dmda-section' into next * knepley/feature-dmda-section: DMDA: c89 fix DMDA: Forgot to add new source file DMPlex: Fix merge from master DMDA: Add a matrix preallocation routine that works with PetscSection DMDA: Add transitive closure - Only working in 2D DMDA: Add preallocation center dim for using PetscSection Conflicts: src/dm/impls/plex/plex.c src/dm/impls/plex/plexinterpolate.c
Matthew Knepley
Merge branch 'knepley/fix-fem-bd-integrate' into next * knepley/fix-fem-bd-integrate: SNES ex12: Fix Neumann tests - Now using normal from f0, f1 - Turned on 3D test DMPlex: DMPlex: Fix 1D face geometry in DMPlexComputeGeometryFVM_1D_Internal() - Normalize vector DMPlex: DMPlex: Fix 1D face geometry in DMPlexComputeGeometryFVM_1D_Internal() - Used inward pointing normal DMPlex: Fix 1D face geometry in DMPlexComputeProjection2Dto1D_Internal() …
Jed Brown
Merge branch 'jed/feature-mat-orderings' into next Should fix C++ build failure. http://ftp.mcs.anl.gov/pub/petsc/nightlylogs/archive/2013/11/23/build_next_arch-osx-10.6-cxx-pkgs-opt_petsc-mini.mcs.anl.gov.log * jed/feature-mat-orderings: MatOrdering WBM: need extern "C" for mc64ad_
Mark Adams
working in 2D, but in 3D
BarryFSmith
Merge branch 'barry/fix-fnt-ptr-compare' into next
BarryFSmith
Merge branch 'barry/rm-unused-variables-dmplex' into next
BarryFSmith
Merge branch 'barry/configure-test-complex' into next
BarryFSmith
Merge branch 'barry/fix-hypre-superlu-64bitindex-casts' into next
Matthew Knepley
Merge branch 'knepley/fix-plex-closure-index' into next * knepley/fix-plex-closure-index: DMPlex: Fixed two bugs with DMPlexCreateClosureIndex() - Must make index for entire DM chart - Need to update cloff when no fields are present
Jed Brown
Merge branch 'jed/feature-mat-orderings' into next * jed/feature-mat-orderings: MatOrdering: Dead simple dense spectral partitioner MatOrdering: Added Weighted Bipartite Matching MatOrdering: fix Fortran declaration for AMD
Jed Brown
Merge branch 'knepley/feature-mat-orderings' into next * knepley/feature-mat-orderings: Revert HSL MC64AD branch
Jed Brown
Revert HSL MC64AD branch The HSL license does not allow redistribution under the PETSc license.
Matthew Knepley
Merge branch 'knepley/fix-plex-reorder-empty' into next * knepley/fix-plex-reorder-empty: DMPlex: Allow preallocation to cope with a non-distributed mesh at the cost of a reduction
Matthew Knepley
Merge branch 'knepley/fix-plex-label-hash' into next * knepley/fix-plex-label-hash: DMLabel: Fix bug in clearing value for array representation
Matthew Knepley
Merge branch 'knepley/fix-plex-submesh-parallel' into next * knepley/fix-plex-submesh-parallel: DMPlex: Small doc fix for DMPlexConstructCohesiveCells()
Jed Brown
Merge branch 'jed/mat-convert-preallocate' into next * jed/mat-convert-preallocate: MatConvert_Basic(): preallocate for DENSE
Matthew Knepley
Merge branch 'knepley/fix-fem-bd-integrate' into next * knepley/fix-fem-bd-integrate: SNES ex12: Fixed bug in 3D P2 test cases - I was not marking boundary edges, so these variables were unconstrained SNES ex12: Fixed newline at the end of test output
BarryFSmith
Merge branch 'barry/fix-ftn-func-pointers' into next
Matthew Knepley
Merge branch 'knepley/fix-plex-submesh-parallel' into next * knepley/fix-plex-submesh-parallel: DMPlex: Protect another instance of empty IS
BarryFSmith
Merge branch 'barry/fix-hypre-superlu-64bitindex-casts' into next
BarryFSmith
Merge branch 'barry/configure-test-complex' into next
Matthew Knepley
Merge branch 'knepley/fix-fem-bd-integrate' into next * knepley/fix-fem-bd-integrate: SNES ex12: Now complete the boundary label in all circumstances - The boundary integration ignores non-faces DMPlex: Added determination of the normal for boundary faces DMPlex: Only allow boundary integration on faces
Matthew Knepley
Merge branch 'knepley/fix-plex-submesh-parallel' into next * knepley/fix-plex-submesh-parallel: DMPlex: Protect submesh selection when some procs have empty labels
Matthew Knepley
Merge branch 'knepley/fix-plex-label-hash' into next * knepley/fix-plex-label-hash: DMLabel: Fixed warning - Damn damn damn, messed up line selection
Matthew Knepley
Merge branch 'knepley/fix-plex-label-hash' into next * knepley/fix-plex-label-hash: DMLabel: Added PetscHashIDelKey() - Fixed bug where I was passing a point for an iterator DMLabel: PetscHashIGetKeys() was made a function - It now accepts a NULL argument
Matthew Knepley
Merge branch 'knepley/fix-plex-reorder-empty' into next * knepley/fix-plex-reorder-empty: DMPlex: Fix reordering for empty meshes
Matthew Knepley
Merge branch 'knepley/fix-plex-submesh-parallel' into next * knepley/fix-plex-submesh-parallel: DMPlex: Turn off check for cells bordering a cohesive face - In parallel, the negative side cell for a cohesive face can be on another process - We might want to consider communicating these nightlylogs: eliminate some known warnings from the dashboard count doc: add errorcheck when processing badly formatted makefiles nightlylogs: add different dashboa…
Matthew Knepley
Merge branch 'knepley/feature-mat-orderings' into next * knepley/feature-mat-orderings: MatOrdering: Fix MS complex compile
Matthew Knepley
MatOrdering: Fix MS complex compile
Jed Brown
Merge branch 'jed/stdint.h' into next * jed/stdint.h: Sys: configure test for MPI_INT64_T, it need not be a macro
BarryFSmith
Merged in barry/fix-quad-c++ (pull request #111) __float128 does not compile with clanguage c++ fix
BarryFSmith
Merged in jed/stdint.h (pull request #123) Use standard int64_t
Satish Balay
Merge branch 'barry/fix-solaris' into next
Satish Balay
memmove: requires string.h
Satish Balay
Revert "solaris has sys/ddi.h location for prototype for memmove" This reverts commit 3fbe6efad015e07d7fa21254e77c163c61d71cbf.
Mark Adams
super small cleanup
Mark Adams
small cleanup
BarryFSmith
Merge branch 'knepley/remove-cxx-logging' into next
Mark Adams
cleaned up ex33, started adding high order in ex98
BarryFSmith
Merge branch 'knepley/remove-cxx-logging' into next
BarryFSmith
Merge branch 'knepley/remove-cxx-logging' into next
BarryFSmith
Merge branch 'barry/fix-deprecated-check' into next
Satish Balay
Merge branch 'barry/fix-struct-initialization' into next
BarryFSmith
Merge branch 'barry/fix-struct-initialization' into next
BarryFSmith
Merge branch 'barry/update-external' into next
BarryFSmith
Merge branch 'barry/remove-strdup' into next
Lisandro Dalcin
Merge branch 'dalcinl/dsymutil' into next
BarryFSmith
Merge branch 'barry/fix-solaris' into next
BarryFSmith
solaris has sys/ddi.h location for prototype for memmove
BarryFSmith
Merge branch 'barry/fix-struct-initialization' into next
Jed Brown
Merge branch 'master' into next
Matthew Knepley
Merge branch 'knepley/fix-hash-scaling' into next * knepley/fix-hash-scaling: PetscSF: Register logging events
Matthew Knepley
Merge branch 'knepley/fix-mat-zero-rows' into next * knepley/fix-mat-zero-rows: Mat: Replaced communication in MatZeroRows_MPIBAIJ() with PetscSF - Tested with Mat ex12
Matthew Knepley
Merge branch 'knepley/fix-hash-scaling' into next * knepley/fix-hash-scaling: PetscSF: Added logging
Matthew Knepley
Merge branch 'knepley/fix-plex-partition-overlap' into next * knepley/fix-plex-partition-overlap: DMPlex: When partitioning with overlap, make sure no points from the original partition can be owned by another process
Mark Adams
Merge branch 'next' of bitbucket.org:petsc/petsc into madams/sr1
BarryFSmith
Merge branch 'barry/fix-parmetis-64bitindices' into next
BarryFSmith
Merge branch 'barry/fix-superlu-dist-64bitindices' into next
BarryFSmith
Merge branch 'barry/saws-update' into next
BarryFSmith
Merge branch 'barry/saws-update' into next
Matthew Knepley
Merge branch 'knepley/fix-hash-scaling' into next * knepley/fix-hash-scaling: DMPlex: Bug fix for interpolated adjacency formation
Matthew Knepley
Merge branch 'knepley/fix-hash-scaling' into next * knepley/fix-hash-scaling: DMPlex: Fast adjacency graph construction for interpolated meshes
Matthew Knepley
Merge branch 'knepley/fix-hash-scaling' into next * knepley/fix-hash-scaling: DMPlex: Fixed error in new events
Matthew Knepley
Merge branch 'knepley/fix-hash-scaling' into next * knepley/fix-hash-scaling: DMPlex: More events for distribution
Matthew Knepley
Merge branch 'knepley/fix-hash-scaling' into next * knepley/fix-hash-scaling: DMPlex: Fixed allocation bug in reordering
Jed Brown
Merge branch 'jed/mat-adj-getrow' into next * jed/mat-adj-getrow: MatGetRow_MPIAdj: return actual values if requested MatGetRow_MPIAdj: simplify expression for idx
Jed Brown
Merge branch 'jed/mat-convert-preallocate' into next * jed/mat-convert-preallocate: MatConvert_Basic: preallocate for AIJ, BAIJ, and SBAIJ Sys signal: fix typo
Matthew Knepley
Merge branch 'knepley/fix-builder-launch' into next * knepley/fix-builder-launch: Builder: More portable hosts option for mpiexec
Jed Brown
Merge branch 'knepley/feature-plex-hybrid-3d' into next Provides missing function GetTriSubfaceInverse_Static that was accidentally already used by 'next' via mistake with 'knepley/feature-plex-refine-3d'. * knepley/feature-plex-hybrid-3d: DMPlex ex4: New test output after changing refinement of hybrid cells for 3D simplex DMPlex: In refinement, fixed correspondence between hybrid cells and faces DMPlex: In refinement, added GetTriEdgeInverse_St…
Matthew Knepley
Merge branch 'knepley/fix-hash-scaling' into next * knepley/fix-hash-scaling: DMPlex: Fixed mismatched Malloc2 in reordering
Mark Adams
added version of ex32 (ex98) with a 9-point stencil and a non-constant coeficient convergance test problem
Matthew Knepley
Merge branch 'knepley/fix-hash-scaling' into next * knepley/fix-hash-scaling: DMLabel: Split Malloc3 into Malloc2 and Malloc
Matthew Knepley
Merge branch 'knepley/fix-dm-label-fortran' into next * knepley/fix-dm-label-fortran: DMPlex ex1F90: Added test of DMLabel bindings DMLabel: Moved custom bindings to zplexlabel.c - Added DMPlexGetLabel() binding - Added DMLabelGet/Set/ClearValue() bindings
Matthew Knepley
Merge branch 'knepley/feature-plex-refine-3d' into next * knepley/feature-plex-refine-3d: DMPlex: For 3d simplicial refinement, fixes hybrid faces in support of hybrid face edges DMPlex: For 3d simplicial refinement, fixes hybrid faces in support of interior face edges
Satish Balay
Merge branch 'balay/hdf5-use_make_j' into next
Satish Balay
Merge branch 'jed/gnumake' into next
Satish Balay
Merge branch 'balay/fix-retrieval-permissions' into next
Jed Brown
Merge branch 'jed/snes-ex12-output' into next * jed/snes-ex12-output: SNES ex12: disable -show_solution (was on by default for -run_type full) SNES ex12: remove manual VTK output Conflicts: src/snes/examples/tutorials/ex12.c
Jed Brown
Merge branch 'master' into next * master: Doc: Fixed configure doc SNES ex12: Added a 'none' bc type and fix the run types SNES ex52: Fix leaks and name mesh
Jed Brown
Merge branch 'jed/use-coptflags' into next * jed/use-coptflags: compilerOptions.py: use -O0 with gcc when in debug mode
Jed Brown
Merge branch 'knepley/fix-mat-zero-rows' into next * knepley/fix-mat-zero-rows: Mat: Cast to remove warning
Matthew Knepley
Merge branch 'knepley/fix-fem-opencl' into next * knepley/fix-fem-opencl: PetscFe+OpenCL: Removed N_c variable PetscFE+OpenCL: Removed redundant numQuadraturePoints, numBasisFunctions, and numBasisComponents
Matthew Knepley
Merge branch 'knepley/fix-hash-scaling' into next * knepley/fix-hash-scaling: Hash+DMPlex: Changed PetscHashIPut() to eliminate pass-by-ref - Jed can sleep soundly tonight
Matthew Knepley
Merge branch 'knepley/fix-plex-geometry-hex' into next * knepley/fix-plex-geometry-hex: DMPlex: If “vtk” label has no cells, do not use it
Jed Brown
Merge branch 'jed/ctetgen-deps' into next * jed/ctetgen-deps: ctetgen: update git version to close memory leaks ctetgen: require OpenMP to ensure that compiler flags are set OpenMP: passing -fopenmp three times is excessive
Matthew Knepley
Merge branch 'knepley/fix-hash-scaling' into next * knepley/fix-hash-scaling: DMPlex: Use PetscHashIHasKey() to check for membership Hash; Added PetscHashIHasKey() - PetscHashIMap does not match the documentation
Matthew Knepley
Merge branch 'knepley/feature-plex-hybrid-3d' into next * knepley/feature-plex-hybrid-3d: DMPlex: Fix DMPlexCheckSkeleton() for submeshes
Matthew Knepley
Merge branch 'knepley/fix-hash-scaling' into next * knepley/fix-hash-scaling: DMPlex: Added simple DMLabel test DMPlex: Fix missing restore Reported-by: Jed Brown <jedbrown@mcs.anl.gov> DMPlex: Use DMLabelDistribute() in DMPlexDistribute() DMPlex: Use DMLabelGetStrautmBounds() in DMPlexGetDepth/HeightStratum() DMPlex: Added DMLabelDistribute() DMPlex: Added DMLabelGetStratumBounds() DMPlex: Fixed quadratic behavior of DMLabel insert…
Mark Adams
start of box stencil
BarryFSmith
Merge branch 'barry/rm-strncmp' into next
Matthew Knepley
Merge branch 'knepley/fix-plex-geometry-hex' into next * knepley/fix-plex-geometry-hex: DMPlex: DMPlexCreateCohesiveSubmesh() must also extract orientations DMPlex: Add 1D code for DMPlexCheckSkeleton() DMPlex: Cleanup code for VTK output - Removed diagnostic print - Use DMLabel interface
Matthew Knepley
Merge branch 'knepley/fix-hash-scaling' into next * knepley/fix-hash-scaling: DMPlex: Redo interpolation with new PetscHashIJKL interface Hash: Vast simplification of PetscHashIJKL and redo interface
BarryFSmith
Merge branch 'barry/protect-logging' into next
Matthew Knepley
Merge branch 'knepley/fix-hash-scaling' into next * knepley/fix-hash-scaling: DMPlex: Expand logging Sys ex26: Jed is right that this is much faster PetscHash: Added test for scalability Conflicts: include/petsc-private/dmpleximpl.h
Jed Brown
Merge branch 'jed/fix-mat-header-replace-log' into next * jed/fix-mat-header-replace-log: MatHeaderReplace: fix duplicate call to PetscLogObjectDestroy
BarryFSmith
Merge branch 'barry/fix-fortran-error-handler-example' into next
Mark Adams
Merge branch 'next' of bitbucket.org:petsc/petsc into madams/sr1
Mark Adams
added start of new SR driver
Matthew Knepley
Merge branch 'knepley/fix-plex-reorder-coords' into next * knepley/fix-plex-reorder-coords: DMPlex: Fixed bug in coordinate permutation PetscSection: Doc fix for permutation
Matthew Knepley
Merge branch 'knepley/fix-plex-geometry-hex' into next * knepley/fix-plex-geometry-hex: DMPlex: Change geometry check to support interpolated meshes - This all has to be replaced anyway Bib: Added Top500 and fixed entry
Matthew Knepley
Merge branch 'knepley/fix-fem-opencl' into next * knepley/fix-fem-opencl: SNES ex12: Added uniform refinement
Matthew Knepley
Merge branch 'knepley/fix-fem-opencl' into next * knepley/fix-fem-opencl: PetscFE: Fixed syntax bug
Matthew Knepley
Merge branch 'knepley/fix-fem-opencl' into next * knepley/fix-fem-opencl: PetscFE: Removed offset members that were used once PetscFE: Use correct flags for code inclusion for auxiliary fields in OpenCL SNES ex12: Fix run type options
Jed Brown
Merge branch 'jed/fix-pcview-fieldsplit-early' into next * jed/fix-pcview-fieldsplit-early: PCView_FieldSplit_Schur: fix crash on view before setup
Matthew Knepley
Merge branch 'knepley/fix-fem-opencl' into next * knepley/fix-fem-opencl: DMPlex: Fix section creation when depth == 1
Satish Balay
Merge branch 'master' into next
Matthew Knepley
Merge branch 'knepley/fix-mat-zero-rows' into next * knepley/fix-mat-zero-rows: Mat: Fix MatZeroRows_MPIAIJ() - Must initialize local rows with -1 instead of 0
Jed Brown
Merge branch 'knepley/fix-mat-zero-rows' into next * knepley/fix-mat-zero-rows: MatZeroRows_MPIAIJ: add missing PetscSFReduceEnd
Jed Brown
Merge branch 'stefano_zampini/pcbddc-reusebddc' into next * stefano_zampini/pcbddc-reusebddc: PCBDDC: remove unneeded code to check nearnullspace PCBDDC: remove trailing whitespaces from source PCBDDC: solved compilation error with complex build PCBDDC: introduce a new variable in PCBDDC data stucture to store the actual number of current vertices (corners with constraints with basis changed) PCBDDC: make BtoNmap a member of bddc data struct (c…
Jed Brown
Merge branch 'master' into next * master: bib: rename ref with duplicate key Webpage: Corrected '-dm_mat_type cusp' to 'dm_mat_type aijcusp'.
Hong Zhang
Merge branch 'hzhang/mat-fixCreateSeqAIJFromTriple' into next
Matthew Knepley
Merge branch 'knepley/fix-fem-opencl' into next * knepley/fix-fem-opencl: DMPlex: Fixed flop calculation for OpenCL evaluator - The old version had (2+2)*dim*N_comp, but I think this should only be 2*dim, which is a 5% effect
BarryFSmith
Merge branch 'barry/saws' into next
BarryFSmith
Merge branch 'barry/saws' into next
Lisandro Dalcin
Merge branch 'dalcinl/mat-seqsbaij-prealloc-csr' into next Add MatSeqSBAIJSetPreallocationCSR()
Lisandro Dalcin
Merge branch 'dalcinl/mat-getblocksize' into next Allow calling MatGetBlockSize[s]() before matrix preallocation
Matthew Knepley
Merge branch 'knepley/feature-plex-hybrid-3d' into next * knepley/feature-plex-hybrid-3d: DMPlex ex5: Added second fault for quad test DMPlex: Fix setting of hybrid bounds for multiple faults DMPlex ex5: Turn on second fault in quad test
Shrirang Abhyankar
Merge branch 'shri/feature-dm-circuit' into next
Matthew Knepley
Merge branch 'knepley/feature-mat-orderings' into next * knepley/feature-mat-orderings: MatOrdering: Removed compiler warnings for complex MatOrdering: Removed log() from f2c code MatOrder: Changed abs --> fabs in f2c code
Matthew Knepley
MatOrdering: Removed compiler warnings for complex
Matthew Knepley
MatOrdering: Removed log() from f2c code
Matthew Knepley
MatOrder: Changed abs --> fabs in f2c code
Peter Brune
Merge branch 'prbrune/snes-linesearchnormfix' into next
BarryFSmith
Merge branch 'barry/saws' into next Conflicts: src/docs/website/documentation/changes/dev.html
Peter Brune
Merge branch 'prbrune/snes-qnscaling' into next
Peter Brune
Merge branch 'prbrune/mat-matcolor' into next
Matthew Knepley
Merge branch 'knepley/fix-mat-zero-rows' into next * knepley/fix-mat-zero-rows: Mat: Rewrote MPIAIJ MatZeroRows() to use PetscSF - Passes test ex12
Matthew Knepley
Merge branch 'knepley/feature-plex-hybrid-3d' into next * knepley/feature-plex-hybrid-3d: DMPlex: Removed compiler warnings DMPlex ex5: Cleaned up 2D tensor tests to rely on interpolation DMPlex ex5: Cleaned up 2D simplex tests to rely on interpolation
Matthew Knepley
Merge branch 'knepley/feature-mat-orderings' into next * knepley/feature-mat-orderings: MatOrdering: Removed compiler warnings DMPlex: Added doc for DMPlexGetHybridBounds()
Matthew Knepley
MatOrdering: Removed compiler warnings
Matthew Knepley
Merge branch 'master' into knepley/feature-mat-orderings * master: (142 commits) DMPlex: Added doc for DMPlexGetHybridBounds() DMPlex: Fix label creation for 3D simplicial refinement DMPlex ex4: Added another 2D simplex hybrid test DMPlex ex4: Reworked 2D simplex hybrid test DMPlex: Fixed Fortran binding for DMPlexSetPreallocationCenterDimension() DMPlex: Fixed bug for label creation in hex refinement Fix for fortran compile error with SN…
Matthew Knepley
Merge branch 'knepley/feature-dmda-section' into next * knepley/feature-dmda-section: DMDA: Added declaration for DMDAGetCellPoint()
Satish Balay
Merge branch 'balay/move-externalpackages-dir' into next
Satish Balay
Merge branch 'balay/remove-archIndependent' into next
Satish Balay
Merge branch 'balay/error-with-winzip' into next
Matthew Knepley
Merge branch 'knepley/fix-fem-opencl' into next * knepley/fix-fem-opencl: DMPlex: Fix FEM bug with initialization of auxiliary coefficient array
Matthew Knepley
Merge branch 'knepley/fix-plex-regression' into next * knepley/fix-plex-regression: Builder: Added parsing of L2 error to test parser SNES ex62: Use new parsing for numerical output, and added missing output SNES ex12: Added missing output DMPlex ex4: Added missing output DMPlex ex9: Make tests run in a reasonable time DMPlex ex10: Fix interface and add missing output DMPlex ex9: Fix leaks PetscInitialize: Replicate CUBLAS behavior o…
Matthew Knepley
Merge branch 'knepley/feature-plex-refine-3d' into next * knepley/feature-plex-refine-3d: DMPlex: Fix label creation for 3D simplicial refinement DMPlex ex4: Added another 2D simplex hybrid test DMPlex ex4: Reworked 2D simplex hybrid test DMPlex: Fixed bug for label creation in hex refinement Conflicts: src/dm/impls/plex/examples/tests/ex4.c
Matthew Knepley
Merge branch 'knepley/example-ts-friction' into next * knepley/example-ts-friction: TS ex34: Now reproducing plots from Berkeley paper - Fixed coordinate DM screwups DMDA: Fixed bug with 1D DMDAGetRay() TS: Allow the DMDARay viewer to operator in LG mode - Added TSMonitorLGDMDARay() activated by -ts_monitor_lg_dmda_ray - Added TSMonitorLGCtx to TSMonitorDMDARayCtx DMDA: Allow DMDAGetRay() to work in 1D TS: Make TSMonitorLGCtx visible to ot…
Matthew Knepley
Merge branch 'knepley/example-ts-friction' into next * knepley/example-ts-friction: TS: Added an example of DR friction
Matthew Knepley
Merge branch 'knepley/feature-dmda-section' into next * knepley/feature-dmda-section: DMDA: Added DMDAGetCellPoint() DMPlex: Added documentation
Matthew Knepley
Merge branch 'master' into next * master: DMPlex: Fixed Fortran binding for DMPlexSetPreallocationCenterDimension()
Karl Rupp
Merge branch 'paulmullowney/cusp-vector-scatter-with-fix' into next
BarryFSmith
Merge branch 'barry/fix-pcredistribute-memory-leak' into next
BarryFSmith
Merge branch 'barry/fix-petscbagview' into next
BarryFSmith
Merge branch 'next' of bitbucket.org:petsc/petsc into next
Matthew Knepley
Merge branch 'knepley/feature-mat-orderings' into next * knepley/feature-mat-orderings: MatOrdering: Must check for multiple components in the matrix
BarryFSmith
Merge branch 'barry/reduce-dmsetup-da-memoryusage' into next
Matthew Knepley
Merge branch 'barry/reduce-dmsetup-da-memoryusage' into next * barry/reduce-dmsetup-da-memoryusage: Hypre: Fix cast for DMDAGetGlobalIndices()
Matthew Knepley
MatOrdering: Must check for multiple components in the matrix
Matthew Knepley
Merge branch 'knepley/feature-mat-orderings' into next * knepley/feature-mat-orderings: MatOrdering: Fixed logic
Matthew Knepley
MatOrdering: Fixed logic
Matthew Knepley
Merge branch 'knepley/feature-mat-orderings' into next * knepley/feature-mat-orderings: MatOrdering: Add declaration
Matthew Knepley
MatOrdering: Add declaration
Peter Brune
Merge branch 'prbrune/mat-matcolor' into next
Matthew Knepley
Merge branch 'knepley/feature-mat-orderings' into next * knepley/feature-mat-orderings: MatOrdering: Fixes for complex
Matthew Knepley
MatOrdering: Fixes for complex
Jed Brown
Merge branch 'madams/sr-driver4' into next * madams/sr-driver4: added new gold ex33 output and reduced ex33 size. TS ex33: start segmental refinement example SNESComputeJacobianDefaultColor: allow vec_sol NULL Semantic conflict: perl -pi -e 's,DMPlex([SG]etCoord),DM$1,' src/ts/examples/tutorials/ex33.c
Matthew Knepley
Merge branch 'knepley/feature-mat-orderings' into next * knepley/feature-mat-orderings: MatOrdering: Fix Fortran binding for spectral MatOrdering: Fix compiler warnings for WBM
Matthew Knepley
MatOrdering: Fix Fortran binding for spectral
Matthew Knepley
MatOrdering: Fix compiler warnings for WBM
Matthew Knepley
Merge branch 'knepley/feature-mat-orderings' into next * knepley/feature-mat-orderings: MatOrdering: Fix makefile MatOrdering: Dead simple dense spectral partitioner - Should eventually use SLEPc with TraceMin MatOrdering: Added Weighted Bipartite Matching - Did f2c of HCL MC64 Conflicts: include/petsc-private/matorderimpl.h src/mat/order/makefile
Matthew Knepley
MatOrdering: Fix makefile
Matthew Knepley
MatOrdering: Dead simple dense spectral partitioner - Should eventually use SLEPc with TraceMin
Matthew Knepley
MatOrdering: Added Weighted Bipartite Matching - Did f2c of HCL MC64
Mark Adams
added new gold ex33 output and reduced ex33 size.
Mark Adams
Merge branch 'knepley/fix-plex-ghost-cells' of bitbucket.org:petsc/petsc into madams/sr-driver4
Peter Brune
Merge branch 'prbrune/snes-qnscaling' into next
Matthew Knepley
Merge branch 'knepley/fix-plex-ghost-cells' into next * knepley/fix-plex-ghost-cells: DMLabel: Fixed index for ranges with nonzero lower limit
Matthew Knepley
Merge branch 'knepley/feature-plex-refine-3d' into next * knepley/feature-plex-refine-3d: DMPlex: Fixed compiler warnings
Mark Adams
TS ex33: start segmental refinement example This is a simplified version of ts/ex11 that solves a Lapacian in 2D with a 5-point stencil. It has a synthetic solution and a convergence test. It uses SNES to construct a differencing Jacoabian without a solve. This is intened to be the start of an extreme scale solver driver.
Mark Adams
SNESComputeJacobianDefaultColor: allow vec_sol NULL This is necessary to assemble a Jacobian without calling SNESSolve.
Satish Balay
Merge branch 'balay/add-newline-between-stdout-stderr' into next
Satish Balay
Merge branch 'balay/configure-winpython-check' into next
Mark Adams
Merge remote-tracking branch 'origin/knepley/fix-plex-ghost-cells' into madams/sr-driver4
Peter Brune
Merge branch 'prbrune/snes-qnscaling' into next
Satish Balay
Merge branch 'shri/feature-dm-circuit' into next
Satish Balay
Merge branch 'master' into next
Satish Balay
Merge branch 'shri/ts-dae-semi-explicit' into next
Satish Balay
doc: fix LOCDIR
BarryFSmith
Merged in barry/reduce-dmsetup-da-memoryusage (pull request #107) reduce memory usage of DMSetUp_DA()
Peter Brune
Merge branch 'prbrune/mat-matcolor' into next
Satish Balay
Merge branch 'knepley/feature-plex-reordering' into next
Peter Brune
Merge branch 'prbrune/snes-qnscaling' into next Conflicts: src/snes/impls/qn/qn.c
Jed Brown
Merge branch 'jed/check-pointer-runtime' into next * jed/check-pointer-runtime: Sys: add PetscCheckPointerSetIntensity -check_pointer_intensity Sys: add PetscFunctionBeginHot to switch to cheaper pointer checks PetscStack: use same definitions for PetscStack functions PetscStack: declare types regardless of debug vs. optimized
Jed Brown
Merge branch 'jed/gnumake' into next * jed/gnumake: gmakegen.py: actually fix symlink translation
Satish Balay
Merge branch 'prbrune/sf-sfbasicops' into next
Jed Brown
Merge branch 'jed/gnumake' into next * jed/gnumake: gmakegen.py: fix relative paths when PETSC_DIR contains symlink
Satish Balay
Merge branch 'knepley/fix-configure-dll' into next
Matthew Knepley
Merge branch 'knepley/feature-plex-refine-3d' into next * knepley/feature-plex-refine-3d: DMPlex: Fix uniform refinement for empty mesh DMPlex: Fixed creation of hybrid submesh - No more Lagrange flag, just check for proper prism hybrid cells
Satish Balay
Merge branch 'jed/gnumake' into next
Jed Brown
Merge branch 'jed/mat-setvalues-col-bs' into next * jed/mat-setvalues-col-bs: Check column block size in MatSetBlockSizes
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
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…
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 next * knepley/fix-plex-ghost-cells: DMPlex: Fixed DMPlexConstructGhostCells() to filter out non-faces from the label DMPlex: Added DMLabelFilter() Conflicts: include/petscdmplex.h
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