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250+ commits behind master.
Matthew Knepley
Merge branch 'knepley/feature-rigid-bodies' into knepley/pylith * knepley/feature-rigid-bodies: Plex: Added declaration
Matthew Knepley
Plex: Added declaration
Matthew Knepley
Merge branch 'knepley/feature-rigid-bodies' into knepley/pylith * knepley/feature-rigid-bodies: (27 commits) windows fixes revert this change as a relavent fix is already in origin/knepley/fix-ex-types regenerate output log for snes_tutorials-ex62_fetidp_3d_tet that got corrupted in 188e10d6f1cffa866ec0197053a0e55fa4e7da41 fix opensolaris build error with --with-log=0 Undefined first referenced symbol in file PetscLogEventGetPerfInfo …
Matthew Knepley
Merge branch 'master' into knepley/feature-rigid-bodies * master: (204 commits) windows fixes revert this change as a relavent fix is already in origin/knepley/fix-ex-types regenerate output log for snes_tutorials-ex62_fetidp_3d_tet that got corrupted in 188e10d6f1cffa866ec0197053a0e55fa4e7da41 fix opensolaris build error with --with-log=0 Undefined first referenced symbol in file PetscLogEventGetPerfInfo arch-opensolaris-…
Matthew Knepley
Merge branch 'knepley/feature-dm-bc-components' into knepley/pylith * knepley/feature-dm-bc-components: (175 commits) Plex: Fix projection when we have a dmAux which is a domain boundary - If we are projecting on a lower dimension thing (effectiveHeight > 0), then we need to get the space and dual space on this subcell - The tabulation needs to be in the right dimension for both dm and dmAux PetscFE: Added height subspaces to PetscFE - Added PetscFEGetHeightSu…
Matthew Knepley
Merge branch 'knepley/feature-rigid-bodies' into knepley/pylith * knepley/feature-rigid-bodies: Plex: Added DMPlexCreateRigidBodies() - Handles disconnected pieces, like sides of a fault DM: Added DMProjectFunctionLabel() Change MPIUni to not immediately abort on operations it cannot perform, instead return error code Add filter for example that can produce 1 different iteration count Example add system calloc, bad formating of %d in print, commented…
Matthew Knepley
Plex: Added DMPlexCreateRigidBodies() - Handles disconnected pieces, like sides of a fault
Matthew Knepley
DM: Added DMProjectFunctionLabel()
Matthew Knepley
Merge branch 'knepley/feature-dm-bc-components' into knepley/feature-rigid-bodies * knepley/feature-dm-bc-components: DM: Fixed problem with setting boundary conditions for selected components - The problem was that projection always set every component of a field, even when the BC was only for a certain component. Now you can pass in masking components. - Added masking components to projections over labels - Changed interface to boundary value insertion
Matthew Knepley
Bad merge
Matthew Knepley
Merge branch 'knepley/fix-dm-blocksize' into knepley/pylith * knepley/fix-dm-blocksize: (146 commits) Plex: Make sure submeshes inherit the right coordinate dimension DM: Fix determination of vector block size when some procs are empty - We need to turn -1 into PETSC_MIN_INT updates to manual page for clarity update help menu for MatRARt() -- MatRARt_mpiaij_mpiaij is supported now, but not efficient. update help menu for MatRARt as suggested by F…
Matthew Knepley
Merge branch 'knepley/feature-dm-bc-components' into knepley/pylith * knepley/feature-dm-bc-components: DM: Fixed problem with setting boundary conditions for selected components - The problem was that projection always set every component of a field, even when the BC was only for a certain component. Now you can pass in masking components. - Added masking components to projections over labels - Changed interface to boundary value insertion Added ignore Plex…
Matthew Knepley
Merge branch 'master' into knepley/pylith * master: (42 commits) PetscDS: Fix print Plex ex19: Output fixes for proper destruction TSMonitorDrawSolutionPhase: Add missing draw pause fix warning with gcc-7.1 Docs+PetscFE: Evaluate() operates in reference space Plex ex7: Added 600 cell test Plex: Added 600-cell for S^3 Math: Add the golden ratio Plex: Handle unused variable Plex ex7: Meshing a sphere Plex: Changed to D…
Matthew Knepley
Merge remote-tracking branch 'origin/jed/config-mpi-hashline' into knepley/pylith * origin/jed/config-mpi-hashline: (36 commits) configure: fix capture of MPICH/OMPI version macros with recent gcc in system paths Bib: Added ref add a citation to petsc.bib Plex: Initialize variables initialize ap as complained by the nightly tests initialize some variables as complained by nightly tests SNES ex12: Mix misnaming Nf --> Nc update tests add tests add MatView_Seq…
Matthew Knepley
Merge branch 'knepley/feature-fe-kernel-scalars' into knepley/pylith * knepley/feature-fe-kernel-scalars: SNES ex56: Update test output
Matthew Knepley
Merge branch 'knepley/feature-fe-kernel-scalars' into knepley/pylith * knepley/feature-fe-kernel-scalars: Plex ex3: Update to new point function API PetscDS: Turn off Fortran bindings for Constants
Matthew Knepley
Merge branch 'knepley/feature-fe-kernel-scalars' into knepley/pylith * knepley/feature-fe-kernel-scalars: Plex tests: Updated to new point function API SNES ex56: Moved tests to new format DM: Allow field projection functions to take an array of scalars - This will allow us to pass in user data to kernels without void *, more efficiency than aux fields PetscDS: Allow point functions to take an array of scalars - This will allow us to pass in user data to ke…
Matthew Knepley
Merge branch 'knepley/fix-plex-init-pointwise' into knepley/pylith * knepley/fix-plex-init-pointwise: (53 commits) PetscFE: Initialize temp array before calling f1 Bib: Added ref Revert "Revert "Merge branch 'hzhang/ts-ex9busdmnetwork'"" typo Reported-by: Fabrice JURADO <fabrice.jurado@univ-pau.fr> Plex: Small doc fix Added link to MFEM to the PETSc Home page Bib: Fixes KSPChebyshev supports right preconditioning Bib: Updated refs Supply quad …
Matthew Knepley
Merge branch 'knepley/feature-plex-project-submesh' into knepley/pylith * knepley/feature-plex-project-submesh: Plex: Fixing insertion of boundary values - If we have a dmAux that is a boundary, we need minHeight = 1, since faces can be mapped from submesh to mesh, but not cells (since they have incomplete cones) - However, in this case the effectiveHeight should be h, whereas when using a boundary as the mesh as well, the effectiveHeight should be h - minHeight - O…
Matthew Knepley
Merge branch 'knepley/feature-plex-boundary-values' into knepley/pylith * knepley/feature-plex-boundary-values: PetscFE: Derivatives for Point class are all zero
Matthew Knepley
Merge branch 'knepley/feature-plex-boundary-values' into knepley/pylith * knepley/feature-plex-boundary-values: Small fixes
Matthew Knepley
Merge branch 'knepley/feature-plex-boundary-values' into knepley/pylith * knepley/feature-plex-boundary-values: TS ex46: Fix sin and cos TS ex18: Fix sin and cos PetscFE: Fixing Point subclass
Matthew Knepley
Merge branch 'knepley/feature-plex-boundary-values' into knepley/pylith * knepley/feature-plex-boundary-values: Plex: Fixed bug with refinement, fixed composed functions for Plex - When we refine, we were calling DMDestroy_Plex(), which wiped out the composed funds, but not calling DMInitialize_Plex() to reinsert them in to the refined mesh
Matthew Knepley
Merge branch 'knepley/feature-plex-boundary-values' into knepley/pylith * knepley/feature-plex-boundary-values: PetscSpacePoint: Fix handling of points
Matthew Knepley
Merge branch 'master' into knepley/pylith * master: (482 commits) Bib: More refs Fixed errors in the manuals and ts_glee source code doc fix bug to enable '-xxx_via [alg]' to showup in '-help' Reported-by: Mark Adams <mfadams@lbl.gov> TS tutorials ex11: remove unused functions TSAdapt: Set TSADAPTNONE as default adapt type DMPlex: missed viewer change in synchronized output Revert "Merge branch 'hzhang/ts-ex9busdmnetwork'" …
Matthew Knepley
Merge branch 'knepley/fix-submesh-orientation' into knepley/pylith * knepley/fix-submesh-orientation: Plex: Remove dead code
Matthew Knepley
Merge branch 'knepley/feature-plex-project-submesh' into knepley/pylith * knepley/feature-plex-project-submesh: Plex: Submeshes should set the embedding dimension DM: DMClone() should propagate the embedding dimension Plex: Point projection functions should be passed the effective height - This makes projection over a boundary mesh work
Matthew Knepley
Merge branch 'knepley/feature-plex-project-submesh' into knepley/pylith * knepley/feature-plex-project-submesh: DMProject: If dmAux is a sub mesh, get correct mapped point corresponding to p
Matthew Knepley
Merge remote-tracking branch 'origin/barry/fix-xsdk-0.2.0-rc2' into knepley/pylith * origin/barry/fix-xsdk-0.2.0-rc2: Add hack to get PETSc with gfortran to work on Apple with xcode 8.3 Conflicts: config/BuildSystem/config/libraries.py
BarryFSmith
Add hack to get PETSc with gfortran to work on Apple with xcode 8.3 Commit-type: bug-fix Funded-by: IDEAS Project: IDEAS/xSDK
Matthew Knepley
Plex: Revert mistaken commit
Matthew Knepley
Merge branch 'knepley/fix-submesh-orientation' into knepley/pylith * knepley/fix-submesh-orientation: Plex: Fix submesh cell reversal (again)
Matthew Knepley
Merge branch 'knepley/fix-submesh-orientation' into knepley/pylith * knepley/fix-submesh-orientation: Plex: Fix submesh cell reversal ]
Matthew Knepley
Merge branch 'knepley/feature-plex-boundary-values' into knepley/pylith * knepley/feature-plex-boundary-values: (131 commits) PetscDS: Added update() function for fields - This is intended to directly update the values at points Plex: DMPlexInsertBoundaryValues() can now be overridden by the user Add all the seealsos for MatZeroRowsXXX() routines. fix a test case MatMUMPS: fix from nightlybuilds update scalable routines remove outdated __FUNCT__ definiti…
Matthew Knepley
Merge branch 'knepley/feature-bc-values-general' into knepley/pylith * knepley/feature-bc-values-general: (71 commits) Plex: Renamed the functions which insert boundary values and made them public update external xSDK packages to use xsdk-0.2.0-rc1 tag fix typo in command line argument of test case PetscStageLogGetStage() returned wrong id, not -1, if requested item was not found blaslapack: make sure both with-blas-lapack-dir and with-blas-lapack-lib get…
Matthew Knepley
Merge branch 'knepley/feature-plex-project-submesh' into knepley/pylith * knepley/feature-plex-project-submesh: Plex: Choose correct dual space for sub meshes
Matthew Knepley
Merge branch 'master' into knepley/pylith * master: Travis-CI: Attempt to solve issues with gfortran Travis-CI: Use newer macOS image clarify damping and other issues related to SNESLINESEARCHBASIC change example in new harness to use simple partitioner so gets consistent output on all systems remove unused function from test file cleanup formatting in example, plus myrank not rank missing - makes the manual page formatting …
Matthew Knepley
Merge branch 'knepley/fix-submesh-orientation' into knepley/pylith * knepley/fix-submesh-orientation: (36 commits) Plex: Fix for submesh orientation - Has not been tested in 3D fix typo and cut and paste error in docs fix warning for ';;' MatLRC: store in the context the parallel matrices rather than the sequential ones Bib: Add ref Error in VecScatterView_MPI() had the meaning of from and to backwards fix build warning as reported by the nightly te…
Matthew Knepley
Merge branch 'knepley/fix-plex-docs' into knepley/pylith * knepley/fix-plex-docs: Plex: Fix declaration
Matthew Knepley
Merge branch 'knepley/fix-plex-docs' into knepley/pylith * knepley/fix-plex-docs: Doc+Plex: Added function docs Doc+Plex: More function docs - Make functions static - Move internal declarations Doc+Plex: More function docs Doc+Plex: Document DMPlexGetOrientedFace() and DMPlexSetSubpointMap() - Make functions static Doc+Plex: Document DMPlexCreateOverlapMigrationSF() - Make functions static Plex: Make functions static - Move internal declarat…
Matthew Knepley
Merge branch 'knepley/fix-plex-interp-parallel' into knepley/pylith * knepley/fix-plex-interp-parallel: (23 commits) SNES+Plex: Fixed bug with point location indexing - I switch to REMOVE, which changes the length of foundCells[] SNES ex2: More tests for interpolation - Fixed test partitioning p4est: use official v2.0 release, update vtk api to match Fixed documentation for -pc_hypre_boomeramg_rtol should be _tol TSSetPreStep: Update documentation fix …
Matthew Knepley
Merge branch 'master' into knepley/pylith * master: (67 commits) Bib: Update years on unpublished stuff fortran: include petscversion.h test: c++ pipeline build fix for d2a797cfef64a79a330b420f01b2d605a8acc690 Extract the submatrices Convert C Null pointer to Fortran in Fortran stub before passing back to user PC Galekin and KSP should properly propagate calls to SetFromOptions to subsolvers Converted Fortran PetscSF to Fort…
Matthew Knepley
Merge branch 'knepley/feature-plex-project-submesh' into knepley/pylith * knepley/feature-plex-project-submesh: Plex: Allow projection to work for submeshes of lower dimension more __FUNCT__ fixes Plex+Gmsh: Allow files with no newline at the end DMPlexTranferVecTree_Inject(): fix indexing for multiple fields
Matthew Knepley
Merge branch 'master' into knepley/pylith * master: (893 commits) Bib: Added ref Doc: Added headers for documentation sections Bib: Small corrections doc: update example makefiles with deleted sourcefile info doc: fix manual build errors doc: fix SOURCEH for some fortran includes that got moved doc: fix broken manualpages - bug introduced by 1b266c9 MatMissingDiagonal() is actually not a collective operation shorten a ur…
Matthew Knepley
Merge branch 'knepley/fix-plex-interp-quad' into knepley/pylith * knepley/fix-plex-interp-quad: (30 commits) Plex: Quad interpolation should default to linear fix the typo in makefile fix one more Barry changed the function names in these example by mistake in commit 3a88037 DMPlexCreateHexBoxMesh(): again, fix initialization for c89 Change Fortran example to use MatSetValue() so compiler does not complain about Error: Rank mismatch in argument 'c'…
Matthew Knepley
Merge branch 'master' into knepley/pylith * master: (1187 commits) Fix typo in manual page TAO: add "chained Rosenbrock" to example PetscPartitioner: fix documentation of PetscPartitionerShellSetPartition fix typos in manual pages phrasing in manual page results in false link and is incomplete. strumpack: add backup url parmetis: fix typo in testsuite Added PETSC_HAVE_ATTRIBUTEALIGNED flag to makefile PCSetUp_SVD() used …
Matthew Knepley
Merge branch 'knepley/fix-logging-reductions' into knepley/pylith * knepley/fix-logging-reductions: Logging: We can only use MPIU_Allreduce where the reduction happens on the same line
Matthew Knepley
Merge branch 'knepley/fix-dm-interpolation-parallel' into knepley/pylith * knepley/fix-dm-interpolation-parallel: Plex: Fix initialization of search array - New point location may return a subset of points add X monitoring of residual norm and true residual norm to example since not currently tested TSAdaptSetType() had no manual page remove a couple of seemingly strange unneeded PetscReturnFunction(ierr) manual page for PetscLogObjectMemory() missing manua…
Matthew Knepley
Merge branch 'knepley/fix-dm-embed-dim' into knepley/pylith * knepley/fix-dm-embed-dim: DM: If no coordinates exist on vertices, set coordinate dimension to PETSC_DEFAULT - If you leave it -1, then you get weird problems with inconsistent dims on different procs tree: workarround bug 'cannot handle multipe #requirespackage listing'. Pragmatic: Bump version configure: improve -fPIC test for ubuntu 16.10 sys: print scanf/PetscInt with --with-clangu…
Matthew Knepley
Merge branch 'master' into knepley/pylith * master: fixes and updates for webclient code missing ierr and CHKERRQ() Configure: Remove spurious dependence of scalarTypes on MPI
Matthew Knepley
Merge branch 'knepley/fix-plex-order' into knepley/pylith * knepley/fix-plex-order: (325 commits) Plex: Fixed bad assumption of sorted Label values Setup Bitbucket Pipelines PCBDDC: fix set but not used warning DMP4est: type fix KSP: SetUp - fix signature typo in error message related to KSP-DM interaction Plex: Fixes for analyzer Bib: Updated refs extra configure or cmake arguments provided by user in command line should be listed AFTER …
Matthew Knepley
Merge branch 'knepley/fix-plex-mat-bs' into knepley/pylith * knepley/fix-plex-mat-bs: Plex: Must check block size in parallel from DMGetLocalToGlobalMapping() - Small format cleanup
Matthew Knepley
Merge remote-tracking branch 'origin/knepley/fix-plex-mf-prec' into knepley/pylith * origin/knepley/fix-plex-mf-prec: Plex: Only compute Jacobian matrix if point wise functions for it are specified - Now we can use -snes_mf_operator with a constructed preconditioned matrix and MF Jacobian action Plex: Added PetscDSHasJacobian() Doc+Plex: Fix note Reported-by: Morten Nobel-Jørgensen <mono@mek.dtu.dk> Plex: Grid hashing only works in 2D
Matthew Knepley
Merge branch 'master' into knepley/pylith * master: Plex: Do not use existing Mat block size when it is 1 There appear to be bugs in VecAssemblyBegin/End_MPI_BTS() [petsc-maint] Undeterministic behaviour in VecSetValuesBlocked SNES ex7: This is hopelessly broken SNES ex7: This is hopelessly broken sowing: update to use the bugfix for docs generated with 'Many br' string all over manualpages Implemented Barry's changes: optiona…
Matthew Knepley
Merge branch 'master' into knepley/pylith * master: (82 commits) Increase patchlevel to 3.7.1 Fix manual page for MatGetTransposeNullSpace() Plex: deal correctly with off-process dof when calculating block size remove unneeded use of PetscContainer to hold iscoloring in SNESComputeNGSDefaultSecant() added SNESView for ngs, added options database to ngs manual page, removed dead routine gcov: enable in mpiuni test incorrect c…
Matthew Knepley
Merge branch 'knepley/feature-ts-mass-matrix' into knepley/pylith * knepley/feature-ts-mass-matrix: Plex: Removed unused variables
Matthew Knepley
Merge branch 'knepley/fix-plex-namespace' into knepley/pylith * knepley/fix-plex-namespace: Plex: Forgot to zero out Jacobian
Matthew Knepley
Merge branch 'knepley/fix-plex-namespace' into knepley/pylith * knepley/fix-plex-namespace: Plex: Changed every *_Internal() function to PETSC_INTERN - Except the residual and Jacobian computation which should not be internal Plex: Fixed declaration for function which produce indices for assembly
Matthew Knepley
Merge branch 'knepley/fix-plex-bs' into knepley/pylith * knepley/fix-plex-bs: Plex: Fix default partition weighting Plex: Fix support for ADD_BC_VALUES Plex: Allow incoming blocksize in DMCreateMatrix() Plex: Fix for blocksize in preallocation
Matthew Knepley
Merge branch 'knepley/fix-plex-bs' into knepley/pylith * knepley/fix-plex-bs: Plex: Fix blocksizes determination in ltog mapping
Matthew Knepley
Merge branch 'knepley/fix-petscfe-kernels-ts' into knepley/pylith * knepley/fix-petscfe-kernels-ts: Plex+SNES: Fixed kernels for Jacobian action
Matthew Knepley
Merge branch 'knepley/fix-petscfe-kernels-ts' into knepley/pylith * knepley/fix-petscfe-kernels-ts: Bib: Added ref -random_view caused error because PetscRandomView() was not provided in PetscRandomCreate() Update the xSDKTrilinos test message to use interactive session and ctest gcc6: fix comple warnings with -Wmisleading-indentation bugfix for MatTransposeMatMultSymbolic_MPIAIJ_MPIAIJ_nonscalable() bugfix of MatDuplicate for mpiaij matrix product R…
Matthew Knepley
Merge remote-tracking branch 'origin/knepley/fix-petscfe-kernels-ts' into knepley/pylith * origin/knepley/fix-petscfe-kernels-ts: Plex+SNES+TS: Pass time and shift down into residual and Jacobian kernels, and the boundary kernels - Added time into ComputeRHS/IFunction
Matthew Knepley
Merge branch 'knepley/fix-plex-bs' into knepley/pylith * knepley/fix-plex-bs: (58 commits) Plex: Set block size regardless of whether the Mat has block storage fix compile warning minor formatting cleanup of gamg.c add ml example to tutorials page for xsdk The deprecated -log_summary_exclude was still being used when it should have been -log_exclude cpardiso: requires mkl_blacs so check for that. Also common code to detect MKL for both par…
Matthew Knepley
Merge branch 'knepley/feature-ts-mass-matrix' into knepley/pylith * knepley/feature-ts-mass-matrix: TS ex32: Added a heat equation example - Not yet working, but checking mass matrix now Plex+SNES: Added DMPlexSNESComputeJacobianActionFEM() - And an internal version
Matthew Knepley
Merge branch 'master' into knepley/pylith * master: (331 commits) Support -ts_monitor_lg_solution_variables when the variables are not explicitly named revert sources to dev - reset PETSC_VERSION_RELEASE - reset changes/dev.html - enable cuda in configure release: set v3.7 strings TS: Mention changes and additions update the alquimia version downloaded to 1.0.2 update the alquimia version downloaded to 1.0.2 Examples: Add…
Matthew Knepley
Merge branch 'master' into knepley/pylith * master: (118 commits) Communicator passed to VecCreateSeq should be PETSC_COMM_SELF PCMG man page: fix typo in options name Bib: Added refs Metis tries to use backtrace which requires -lexecinfo on some systems such as freebsd Remove -lexecinfo from freebsd configure files since it is only needed by metis add alternative output that occurs on some systems due to use of random number ge…
Matthew Knepley
Merge branch 'master' into knepley/pylith * master: (39 commits) Plex ex3: remove bad const qualifiers remove output of number of function evaluations since it varies by machine/compiler updated to latest hypre prelease version PetscDraw: Use 'int' for pixel coordinates fix a9fd68dbf4c59964d6668725c66a5c1530f3bdee nightlybuilds: disable superlu_dist build on opensolaris thats crashing.. Toby used an MPIU_MAX with an MPIU_INT…
Matthew Knepley
Merge branch 'knepley/feature-plex-handle-func-failure' into knepley/pylith * knepley/feature-plex-handle-func-failure: Plex: Protected more user functions Plex: Looks like array restore was in the wrong place Conflicts: src/dm/impls/plex/plexfem.c
Matthew Knepley
Merge branch 'master' into knepley/pylith * master: (378 commits) SNES ex5: Fix coordinate determination for empty subdomains fixed petsc.bib entry p4est: fix syntax error with error message SNES ex5: Correct Jacobian handling on patches SNES ex5: Stupid complex fixes DMP4est: fix transfer of labels to parents petsc4py: update to latest snapshot. Fixes da example breakage in petsc4py test suite Plex: Correct setting of opt…
Matthew Knepley
Merge branch 'knepley/feature-plex-handle-func-failure' into knepley/pylith * knepley/feature-plex-handle-func-failure: Plex: If user function fails, put back array
Matthew Knepley
Merge branch 'master' into knepley/pylith * master: (373 commits) superlu_dist: install target should first make sure prefix/[include,lib] dirs exist - similar to superlu dm: add DMRemoveLabel() fortran interface nightlybuilds: allocate more time to run arch-linux-xsdk-dbg build... Remove superfluous information messages Cannot have rank 1 print before parallel print since it may end up before or after the print from process 0. …
Matthew Knepley
Merge branch 'master' into knepley/pylith * master: mpiuni: do not build somempifort.F when configured with -with-mpiuni-fortran-binding=0 fix: typo introduced in bfd7a005b57e6c6f0db1f4135172d2c8bfa5168c - breaks compiles
Matthew Knepley
Merge branch 'master' into knepley/pylith * master: (44 commits) Plex: Fix memory leak in natural-to-global In the manual page, http://www.mcs.anl.gov/petsc/petsc-current/docs/manualpages/KSP/MatGetSchurComplement.html#MatGetSchurComplement towards the bottom, when discussing using PetscObjectCompose() to provide a user method to compute the Schur complement, the string which is queried should be docs: replace os.popen('ls') with os…
Matthew Knepley
Merge branch 'knepley/fix-dm-clone-coord-section' into knepley/pylith * knepley/fix-dm-clone-coord-section: (137 commits) DM: When cloning, need to propagate the coordinate DM section mpich: default to using ver 3.2 on OSX/ElCapitan as 3.1.3 does not build on Barry's laptop Revert "mpich: update version to mpich-3.2" superlu/dist: disable build on freebsd - as this test is with bsdmake [and superlu requires gnumake] superlu/dist: enable in complex nightly …
Matthew Knepley
Merge branch 'master' into knepley/pylith * master: (88 commits) DT ex3: The test should check the number of digits requested DT ex3: One test fails in single precision Plex: Do not automatically create a default section if no fields are defined Plex: DMPlexCopyCoordinates() needs to create the coordinate section if it is missing superlu: no longer requires xerbla slamch dlamch ? superlu: update to v5.1 skip MatSolve() if ma…
Matthew Knepley
Merge branch 'knepley/fix-dm-clone-coordinates' into knepley/pylith * knepley/fix-dm-clone-coordinates: DM: Clone the coordinate DM instead of reusing in Clone()
Matthew Knepley
Merge branch 'knepley/fix-dm-clone-coordinates' into knepley/pylith * knepley/fix-dm-clone-coordinates: (62 commits) DM: Clone() should also copy the coordinate DM Tests: Run CUDA tests with datafiles only when using double precision. Tests: Reverted KSP ex10 with CuSparse to use ILU. Tests: Fixed wrong reference output for KSP tutorial 10 with cusparse. fix: 620d467- split checkDownload and move only download_cygwin part to configure() Fixes build error…
Matthew Knepley
Merge branch 'master' into knepley/pylith * master: (22 commits) Bib: Added new PETSc app pubs generate errors for ctetgen build options it does not support Older Windows systems do not have tan and tanh for complex C++ add #if to avoid usage; still need to add checks for existance replace printf() with appropriate PETSc construct Different Fortran compilers print a different number of columns per row producing different ou…
Matthew Knepley
Merge branch 'master' into knepley/pylith * master: (63 commits) update jenkins script win32: compile fix yaml: fix issues with PetscOptions change SNES ex69: Updated to new function API, fixed test output SNES ex75: Fixed for new function API add fortran stub for TSMonitorLGSetTransform() and fix TSMonitorLG for multiple fields but no names provided for fields add -binary_write_double so __float128 precision can save as dou…
Matthew Knepley
Merge branch 'knepley/feature-plex-add-time' into knepley/pylith * knepley/feature-plex-add-time: TS ex18: Fixed function API and test output
Matthew Knepley
Merge branch 'knepley/feature-plex-add-time' into knepley/pylith * knepley/feature-plex-add-time: Plex ex3: Use new function API SNES ex62: Use new function API SNES ex12: Use new function API Plex: Fixed unused options in examples Plex+DMDA: Add time to signatures Plex+SNES+TS: Changed all of the callback function to take time as an argument SNES ex12: Fix silly missing argument Error message should say use negative threshold value to prevent f…
Matthew Knepley
Merge branch 'knepley/fix-plex-e12-3d' into knepley/pylith * knepley/fix-plex-e12-3d: SNES ex12: Fixed 3D MMS solution and updated test output
Matthew Knepley
Merge branch 'master' into knepley/pylith * master: DMPlex: Silence overzealous compiler warnings SNES ex12: Naming mistake in tests SNES ex62: Fixed test output for decimal change, no nullspace in KSP Plex ex17: Fixed test output for decimal change Plex ex16: Fixed test output for decimal change Plex ex15: Fixed test output for decimal change Plex ex13: Fixed test output for decimal change Plex ex12: Fixed test output for…
Matthew Knepley
Merge branch 'master' into knepley/pylith * master: (189 commits) fix formatting error in previous commit [broke nightlybuilds] fix formating of TSTHETA manual page and add missing command line option run hwloc with MPIEXEC and binding so it runs on the correct machine fix: memory leaks [in valgrind test] added MPI_BINDING variable for running streams and display exact options used to run streams  elemental: build with optio…
Matthew Knepley
Merge branch 'knepley/fix-examples-plex' into knepley/pylith * knepley/fix-examples-plex: (44 commits) Plex: Require Pragmatic for coarsening tests Plex ex12: New output Plex: New GAMG defaults Plex: New MSM output Plex: New printing for examples builds: migrate from petsc-mini to ipro builds: migrate from bb to frog Split PetscViewerASCIISpinLock into three locks because it was used in nested functions leading to deadlock Fix print statem…
Matthew Knepley
Merge branch 'knepley/fix-plex-point-location' into knepley/pylith * knepley/fix-plex-point-location: Plex: Some grid hash generalization for hex cells Plex: Grid hash must not hash hybrid cells Plex: Put in a flag for grid hash point location - Responds to -dm_plex_hash_location cmake: rename PETScConfig.cmake to PETScBuildInternal.cmake to avoid confusion as <Package>Config.cmake generally refers to the cmake config mode file for <Package> cmake: fix …
Matthew Knepley
Merge branch 'master' into knepley/pylith * master: (78 commits) Bib: Added many references update manual pages for context set and get routines regarding use from Fortran and defining interface for them Fortran examples that use the interface definitions need to take array arguments for row, column, and value entries for XXSetValues() otherwise an error about inconsistent types is generated. call MPI_Wait on MPI_Isend hopefully t…
Matthew Knepley
Merge branch 'knepley/fix-configure-ml' into knepley/pylith * knepley/fix-configure-ml: SNES ex3: Corrected docs and fixed crash in post_check_iterates Reported-by: Cyrill Vonplanta <cyrill.von.planta@usi.ch> Configure: The Apple Clang 6.0 has an annoying warning that breaks configure Configure+ML: ML needs the math library
Matthew Knepley
Merge branch 'knepley/feature-ds-copy' into knepley/pylith * knepley/feature-ds-copy: PetscDS: Added PetscDSCopyEquations() chombo: build only libs - not examples fix typo. 'gcc-4.8 --with-cxx-dialect=C++11' gives a warning with this line - even though its in a #ifdef thats never enabled. cleanup bugfix as reported by the nightly tests add more tests for pipes1 rename MyDMNetworkMonitorTS -> TSDMNetworkMonitor add example pipes1.c add D…
Matthew Knepley
Merge branch 'master' into knepley/pylith * master: (718 commits) builds: do not list /usr/lib path for libraries cuda: update error message with url to using petsc develoment version doc: fix typo 'threads' FOPTFLAGS not FCOPTFLAGS remove test example that really didn't test anything useful but generated false positive on many systems fix typo for MatRARtNumeric reported by Boris enable changing matrix type at runtime for …
Matthew Knepley
Merge branch 'knepley/feature-plex-ordering-group' into knepley/pylith * knepley/feature-plex-ordering-group: (142 commits) Plex ex10: Now has a test for grouping with reordering Plex: Added an optional argument to DMPlexGetOrdering() to allow grouping doc: add in tao handson.html from http://www.mcs.anl.gov/research/projects/tao/tutorials/atpesc/handson.html remove outdated version header in tutorials/HandsOnExercise.html - and let it be autogeneated in tarb…
Matthew Knepley
Merge remote-tracking branch 'origin/knepley/fix-plex-l2diff' into knepley/pylith * origin/knepley/fix-plex-l2diff: (410 commits) Plex: Fixed arguments to pointwise function DMPlexComputeL2Diff() Bib: Added ref Need to dely attachment of null spaces from IS to matrices inside fieldsplit until after the matrices are available removed eig est unused stuff removed unused var checkBuilds: remove bad code. checkBuilds: fix Mark's e-mail removed dead datastructure for…
Matthew Knepley
Merge remote-tracking branch 'origin/knepley/fix-dtfe-allow-null-residual-func' into knepley/pylith * origin/knepley/fix-dtfe-allow-null-residual-func: DTFE: Now allow f0, f1 to be NULL Plex: Documentation on FV geometry Bib: Added reference Includegraph: Updated for compatibility with new folder layout. TSEvent: PETSc blame digest (next) 2015-05-19 fix => PetscOptionsBegin needs CHKERRQ(ierr) TSEvent: PETSc blame digest (next) 2015-05-19 fix => Cast to TSEventStatus TSEvent: Updat…
Matthew Knepley
Merge remote-tracking branch 'origin/knepley/feature-plex-bc' into knepley/pylith * origin/knepley/feature-plex-bc: TS: Take out unnecessary declaration XDMF: Allow missing time dimension MatSchur: Better check for missing D matrix TAO ex1: Updated to new Plex interface Plex: Fixed bug for FV BCs in DMCreateSection_Plex() Plex+TS: FIxed DMPlexTSCheckFromOptions() Plex: Changed the signature of pointwise input functions - Now the spatial dimension and number of fie…
Matthew Knepley
Merge branch 'knepley/fix-dm-default-section-null' into knepley/pylith * knepley/fix-dm-default-section-null: (141 commits) DM: Allow the default section to be set to NULL Add SNESLineSearchReason to fortran includes Also truncate names to fit 32 char fortran limit fix compile warnings /usr/home/balay/petsc.clone-2/src/vec/vec/interface/vector.c:1944: warning: division by zero in '1.0e+0 / 0.' /usr/home/balay/petsc.clone-2/src/ksp/ksp/interface/itfunc.c:508: wa…
Matthew Knepley
Merge branch 'knepley/feature-composable-callbacks' into knepley/pylith * knepley/feature-composable-callbacks: TS ex28: Updated to new kernel interface SNES ex62: Updated to new kernel interface SNES ex12: Updated to new kernel interface Plex ex3: Updated to new kernel interface PetscDS: Added NfAux argument to FE kernels
Matthew Knepley
Merge branch 'knepley/feature-plex-assembly-cellrange' into knepley/pylith * knepley/feature-plex-assembly-cellrange: (23 commits) Plex: DMPlexComputeJacobian_Internal() defined - Give both t and X_tShift arguments - Give cell range - Put in declaration Plex: Now DMPlexComputeResidual_Internal() explicitly takes [cStart, cEnd) rebase output file based on changes to example to make it run faster fix a costintegral bug in rk adjoint removed tests from makefile th…
Matthew Knepley
Merge branch 'knepley/feature-composable-callbacks' into knepley/pylith * knepley/feature-composable-callbacks: PetscDS: Change signature of Jacobian functions to include the shift a for dF/dU_t PetscDS: Cleanup - Removed silly consts - Removed unused vars - Fixed declarations
Matthew Knepley
Merge branch 'knepley/feature-composable-callbacks' into knepley/pylith * knepley/feature-composable-callbacks: (642 commits) TS: Took extra space out of default monitor TS ex18: Updated Riemann and pointwise interface TS ex11: Updated Riemann interface PetscDS: Added dimension and num fields to Riemann interface PetscDS: Added missing declarations SNES ex62: Updated to new pointwise interface PetscMalloc: Fix handling of zero-sized allocations add not…
Matthew Knepley
Merge branch 'knepley/fix-label-leak' into knepley/pylith * knepley/fix-label-leak: (216 commits) DMLabel: Allocation mismatch Bib: More supercapacitor refs PCBDDC: fix for 64bit indices in PCBDDCSubsetNumbering CUSP: Fix VecMDot_SeqCUSP for the case where local size is zero fixes for readonly vectors Bib: Added bio refs Don't print SAWs URL since it disturbs all the test output missing (double) cast in print statement don't output to t…
Matthew Knepley
Merge branch 'knepley/fix-plex-submesh-section' into knepley/pylith * knepley/fix-plex-submesh-section: DM: Fix FUNCT
Matthew Knepley
Merge branch 'knepley/fix-plex-submesh-section' into knepley/pylith * knepley/fix-plex-submesh-section: DM: Fixed naming of utility function
Matthew Knepley
Merge branch 'knepley/fix-plex-submesh-section' into knepley/pylith * knepley/fix-plex-submesh-section: (166 commits) Plex: Fixed array reuse bug in PetscSectionCreateGlobalSectionCensored() DM+Plex: Added sanity checking for global sections received from user Plex: Unified interpolated submesh creation - Now both versions create an SF - Moved DMPlexFilterPoint_Internal() - DMPlexMarkCohesiveSubmesh_Interpolated() now takes a DMLabel instead of a string Pl…
Matthew Knepley
Merge branch 'knepley/fix-veclock-fftw' into knepley/pylith * knepley/fix-veclock-fftw: DM: Fix more Vec lock issues FFTW: Updated for vector locking
Matthew Knepley
Merge branch 'knepley/fix-vec-readonly' into knepley/pylith * knepley/fix-vec-readonly: Plex: Added read-only Vec fixes for point location and interpolation Mat: Added read-only Vec fixes for MATDENSE removed dead link from installation page fixes for manual pages for TSSetRHSJacobian() SNES ex48: Fixed prototypes Doc: Fixed DMDASNESSetJacobianLocal() optimized memory usage of DMCreateMatrix_DA_Xd_MPIAIJ_Fill() for memory usage for setting ze…
Matthew Knepley
Merge branch 'knepley/fix-plex-orient-1d' into knepley/pylith * knepley/fix-plex-orient-1d: Plex: Fix orientation in 1D - Forgot to include flipping check in 1D code Plex: Rename orientation variable Plex: Rationalize orientation debugging bddc: c89 fixes. [triggered by b7d87ab19e1e95173f67f3da509587a15b2e6ae1] fix that was missed in manual merge for MPAIJ function pointer table Doc: Fixed bad doc comment added MatFindOffBlockDiagonalEntries() …
Matthew Knepley
Merge branch 'knepley/feature-partitioner-simple' into knepley/pylith * knepley/feature-partitioner-simple: (50 commits) Partitioner: Added tests for simple partitioner Plex: Added a simple partitioner fix manual, reported by Fabian Gabel removed the PETSC_HAVE_PCBDDC nonsense. You are either part of the PETSc repository or not! Now it is always built and tested squash -Wmaybe-uninitialized ml: update to use tarball with build fix for osx (old versions)…
Matthew Knepley
Merge branch 'master' into knepley/pylith * master: (93 commits) fixes and improvements to a variety of manual pages fixes for SNESSetJacobian and friend manual pages to use SNESJacobianFunction to provide calling sequence of callback Mumps.py --prefix installer did not create include file before copying to it therefor in --prefix cases where mumps was the first package needing the include file the install of mumps would fail. imp…
Matthew Knepley
Merge branch 'knepley/fix-dm-df-local-copy' into knepley/pylith * knepley/fix-dm-df-local-copy: Plex: Fix local to global section correspondence - This needs to go in the documentation somewhere
Matthew Knepley
Merge branch 'knepley/fix-dm-df-local-copy' into knepley/pylith * knepley/fix-dm-df-local-copy: Plex+SF: Local copy should ignore points with no global dogs
Matthew Knepley
Merge branch 'knepley/fix-dm-coord-sf' into knepley/pylith * knepley/fix-dm-coord-sf: Plex: With new distribute code, we have to set the SF for the coordinate DM explicitly raise error flg if superlu_dist is not installed when it is tested fix build warnings when ex52 is built without superlu, only with superlu, only mumps etc
Matthew Knepley
Merge branch 'master' into knepley/pylith * master: (113 commits) Plex: Fix printf Bib: Added two references in CFD nightlybuild: delete externalpackages properly Plex: Use DMGetCoordinateDim() instead of a calculation Plex: Added routine to view geometry TS ex18: Added new tests TS ex18: Updated test output TS ex18: Add support for functionals TS ex18: Global field offsets depend on the point since we allow constraints …
Matthew Knepley
Merge branch 'master' into knepley/pylith * master: (261 commits) call conference a Workshop in PETSc home page instead of conference to match other documents unstall now deletes petsc specific directories created by PETSc also don't use exists() so that softlinks to libraries are also deleted do not copy over install.py gmakegen.py or sowing to --prefix location did not include proper quotes for files to exclude in installation d…
Matthew Knepley
Merge branch 'knepley/fix-plex-orient' into knepley/pylith * knepley/fix-plex-orient: Plex: Fix serial orientation TetGen: Syntax fix
Matthew Knepley
Merge branch 'knepley/fix-plex-orient' into knepley/pylith * knepley/fix-plex-orient: Plex: Fix MPI type for orientation Plex: Small orientation fix
Matthew Knepley
Merge branch 'knepley/fix-plex-orient' into knepley/pylith * knepley/fix-plex-orient: (169 commits) Plex ex13: Orientation now working for flipped connected components Plex: Reworked orientation to respect connected components on each process Plex ex13: Check in initial output Plex: Now mark initial cell as seen - Changes the outcome slightly Plex: Added DMPlexCheckFace_Internal() - This checks a face in the mesh for orientation consistency Pl…
Matthew Knepley
Merge branch 'knepley/fix-dm-subdm' into knepley/pylith * knepley/fix-dm-subdm: DM: Protect access of IS in DMCreateSubDM() fix formatting of some manual pages specifically remove use of $ from the middle of parameter or options lists Doc: Added reference bad merge I missed shortened variable name, but forgot to fix in declaration PCBDDC; MatGetVecs is now deprecated ML does not depend on having a Fortran compiler, why was this in here …
Matthew Knepley
Merge branch 'knepley/fix-cohesive-intersection' into knepley/pylith * knepley/fix-cohesive-intersection: (91 commits) Plex: Fix for cohesive labeling - We now allow two cohesive patches to touch directly - This seems to allow hybrid cells to be in the star of fault vertices for other faults, but we have not reproduced this on a small enough example to check - I just filter out hybrid points when labeling Doc: Fix someone's bib screwups DMPlex: Removed contin…
Matthew Knepley
Merge branch 'master' into knepley/pylith * master: (329 commits) Plex+Label: Fix logic for label distribution - It is restrictive now, but doing it right would mean a ton of infrastructure I think Plex ex12: Fix output after label distribution fix Plex: Only call SetFromOptions() after Distribute, since we cannot avoid it TS ex11: Since DMPlexDistribute() calls SetFromOptions(), do not call it again, and cleaned up tests Plex+F…
Matthew Knepley
Merge branch 'knepley/fix-submesh-crossedge' into knepley/pylith * knepley/fix-submesh-crossedge: (153 commits) Plex: Do not check hybrid cells when classifying sides of a mesh split - This is not strictly necessary I think, but is true Plex: Loop edges cannot be cross edges - Loop edges have the same endpoint twice and exist on the endpoints of clamped edges add tests for matconvert() from dense or aij to elemental typo fix in KSPFCG manpage Need to …
Matthew Knepley
Merge branch 'master' into knepley/pylith * master: (44 commits) Nightlysummary: Incomplete builds are now included in the summary. Added libhdf5hl_fortran.a to library searches when using a Fortran compiler We already added the non-hl Fortran library don't put references in the comments, put them in the manual pages started schedule for petsc-20 Plex: Allow zero-size partition in refinement Plex: Fixed simplicial refinement S…
Matthew Knepley
Merge remote-tracking branch 'origin/jed/fix-checkpointer-char' into knepley/pylith * origin/jed/fix-checkpointer-char: (61 commits) Sys: PetscCheckPointer PETSC_CHAR checks char*, not char** Sys: PetscCheckPointer for PETSC_CHAR checks char*, not char** configure: x is autoenabled so if its not found - configure continues. However if user specifies --with-x=1 and its not found - give an error message. KSPSetSupportedNorm: simplify priority logic around KSP_NORM_NONE KS…
Matthew Knepley
Merge branch 'master' into knepley/pylith * master: (296 commits) don't warn on deprecated or superceeded Updates for OpenMPI checking mpi.h against configured version At configure time determine if MPICH_NUMVERSION or OMPI_MAJOR/MINOR_VERSION or MPI-Uni, then at compile time make sure versions match to determine if incorrect mpi.h is being included cite for ParalleX bib: add moose-web-page petsc4py.py should check /usr/lib an…
Matthew Knepley
Merge branch 'knepley/fix-dm-composition' into knepley/pylith * knepley/fix-dm-composition: DM: Removed code to uncompose nullspace/pmat - This was to prevent reference cycles, which happen with MatNullSpace using DM Vecs, but its fragile - My current solution is to strip out DM from Vecs in a MatNullSpace, but that sucks too. Need a better solution updated downloaded elemental to be valgrind clean version petsc4py: update to use a dev snapshot tarball…
Matthew Knepley
Merge branch 'knepley/fix-plex-submesh-intersection' into knepley/pylith * knepley/fix-plex-submesh-intersection: (266 commits) DMPlex: Fix bug with intersecting submeshes - The label for clamped vertices for a given submesh can get extraneous points from an adjacent submesh - We filter these out before checking for cross-edges petsc4py: update tarball to compatible version fixup (and undo revert): fix rpath encoded in libpetsc.so so that does not refer to .so fi…
Matthew Knepley
Merge branch 'master' into knepley/pylith * master: Sys: Got guard logic reversed
Matthew Knepley
Merge branch 'master' into knepley/pylith * master: Sys: The #define guard for PetscMalloc*() must match the one for PetscFree*() PetscFV: I hate fucking complex
Matthew Knepley
Merge branch 'master' into knepley/pylith * master: (218 commits) PetscFV: Another complex fix DMPlex+TS: Fixing types PetscFV: Straighten out complex types TS ex11: Fix casts and remove unused variable PetscFV: Fix Fortran define PetscObjectUseFortranCallbackXXX() already has PetscFunctionReturn() so remove redundant return 0; from numerious stubs ISColoring: Fix ISColoringView PetscFV: Complex fixes bugfix of src/mat…
Matthew Knepley
Merge branch 'knepley/fix-pylith-parallel' into knepley/pylith * knepley/fix-pylith-parallel: DMPlex: In refinement, merge hybrid and non-hybrid SF creation (should be done for everything) - If missing, define *Max as *End - Fixed bound on hybrid 2D simplicial hybrid cell refinement - Fixes bug in which wrong remote point number was calculated if local process had no hybrid cells, but remote process did so refiners were mismatched
Matthew Knepley
Merge branch 'knepley/fix-pylith-parallel' into knepley/pylith * knepley/fix-pylith-parallel: DMPlex: Fix for hybrid refinement - Must correct offsets when neighbor process has no hybrid points
Matthew Knepley
Merge branch 'knepley/fix-pylith-parallel' into knepley/pylith * knepley/fix-pylith-parallel: DMPlex: Fix hex hybrid refinement SF - Fixed offset - Fixed number of cell faces - Fixed missing edge offset - Fixed number of cells faces - FIxed missing edge offset PetscSection: Must initialize remoteOffsets
Matthew Knepley
Merge branch 'knepley/fix-pylith-parallel' into knepley/pylith * knepley/fix-pylith-parallel: DMPlex: Fixed cohesive cell creation for clamped boundaries - Explicitly tag cross-edges (edges with two clamped endpoints) with 2 in boundary label - Add cross-edge to vertices when looking for things that need split points replaced - Remove extra check for boundary vertices
Matthew Knepley
Merge branch 'knepley/fix-pylith-parallel' into knepley/pylith * knepley/fix-pylith-parallel: DMPlex: Fixes for marking cohesive submesh - Do not mark points as split which are in the boundary label - Mark boundary points from label as unsplit
Matthew Knepley
Merge branch 'knepley/fix-pylith-parallel' into knepley/pylith * knepley/fix-pylith-parallel: DMPlex: Changing meaning of boundary label in DMPlexLabelCohesiveComplete() - Now it marks vertices already present in the original label - We mark these as unsplit, and ignore their stars - Remove old code
Matthew Knepley
Merge branch 'knepley/fix-pylith-parallel' into knepley/pylith * knepley/fix-pylith-parallel: DMPlex: Fixed stupid typo DMPlex: Fixed refinement to respect embedded manifolds
Matthew Knepley
Merge branch 'knepley/fix-pylith-parallel' into knepley/pylith * knepley/fix-pylith-parallel: DMPlex: Fixed types in DMPlexOrient() DMPlex: Fixed initialization in DMPlexLabelCohesiveComplete()
Matthew Knepley
Merge branch 'knepley/fix-pylith-parallel' into knepley/pylith * knepley/fix-pylith-parallel: DMPlex: Fixed logic in hybrid cell tagging and added missing declaration
Matthew Knepley
Merge branch 'knepley/fix-pylith-parallel' into knepley/pylith * knepley/fix-pylith-parallel: DMPlex Fixed huge error with last change set - Default cellHeight is 0
Matthew Knepley
Merge branch 'knepley/fix-pylith-parallel' into knepley/pylith * knepley/fix-pylith-parallel: DMPlex: Allow cellHeight argument for DMPlexMarkBoundaryFaces()
Matthew Knepley
Merge branch 'knepley/fix-pylith-parallel' into knepley/pylith * knepley/fix-pylith-parallel: DMPlex: Added blabel argument to DMPlexLabelCohesiveComplete() - Lets user designate the boundary of a dividing surface - Added GetSurfaceSize_Static()
Matthew Knepley
Merge branch 'knepley/fix-pylith-parallel' into knepley/pylith * knepley/fix-pylith-parallel: DMPlex: Fix for DMPlexOrient() - I was not symmetrizing the orientation graph on processes DMPlex: Added DMPlexAddConeSize() DMPlex: Fixed memory overwrite at depth 0 for viewing PC+Doc: Fixed FieldSplit doc
Matthew Knepley
Merge branch 'knepley/fix-pylith-parallel' into knepley/pylith * knepley/fix-pylith-parallel: Sys: Replace Malloc1() in multiple mallocs (fix size)
Matthew Knepley
Merge branch 'knepley/fix-pylith-parallel' into knepley/pylith * knepley/fix-pylith-parallel: (149 commits) PetscSection: Better check when creating global section Sys: Replace Malloc1() in multiple mallocs since PETSc cannot view factored matrices, generate an error rather than display the wrong stuff (this was really bad) outdated example that doesn't match coding style removed and buggy petscversion.h: workaround ifort -cpp lack of referential tr…
Matthew Knepley
Merge branch 'knepley/fix-dm-vec-blocksize' into knepley/pylith * knepley/fix-dm-vec-blocksize: DMPlex: Fix variable init DMPlex: Fix coordinate blocksize in uniform refinement Vec: Fix blocksize determination with VecGetSubVector()
Matthew Knepley
Merge branch 'knepley/fix-dm-vec-blocksize' into knepley/pylith * knepley/fix-dm-vec-blocksize: (84 commits) DM: Handle empty vectors correctly for blocksize determination SNES & TS: remove stale comments about DMDAComputeFunction DMPlex: Fixed #ifdef for HDF5 DMPlex ex2: Added an example that checks a mesh DMPlex: #ifdef support functions for HDF5 DMPlex: Damn this branch to Hell Doc: Bib fix Doc: Added tutorial TS: Fix output sequence DMP…
Matthew Knepley
DM: Handle empty vectors correctly for blocksize determination
Matthew Knepley
Merge branch 'knepley/fix-plex-refine-unsplit' into knepley/pylith * knepley/fix-plex-refine-unsplit: DMPlex: Fixed refinement of hybrid hex cells - Copied code from the tet case
Matthew Knepley
Merge branch 'master' into knepley/pylith * master: (179 commits) SNESQN: Fix manual for SNESQNSetRestartType removed "data points" from perfect scaling plot of streams remove traceback from python error make sure that streams benchmark actual speedup takes at least one third of the y axis use ${PYTHON} process.py instead of ./process.py in makefiles Barry is an idiot, forgot to put back try except in plotting streams remove…
Matthew Knepley
Merge branch 'master' into knepley/pylith * master: example used PETSC_NULL_INTEGER in place that REQUIRED MatFactorInfo object. DTGaussQuadrature: fix weight averaging for npoints=2 and output Increase patchlevel to 3.4.4 dense: fix overflow with int32*int32 during malloc() initial arrays that are published to SAWs, otherwise SAWs may access them before PETSc code has put correct values into them KSP: MatSchur fixes for preco…
Matthew Knepley
Merge branch 'knepley/fix-plex-refine-unsplit' into knepley/pylith * knepley/fix-plex-refine-unsplit: DMPlex: In hybrid face construction, orientation was wrong for faces from unsplit edges tests: move ex151 out of complex tests to avoid compile errors on windows Microsoft C++ compiler needs extra care with complex numbers and casting DMPlex: C++ has fucking namespaces, use them assholes Field has 3 components therefor need to initialize three component…
Matthew Knepley
Merge branch 'master' into knepley/pylith * master: VecView_MPI_DA: fix gsizes bug (bad conversion in parent commit) Make SNESJacobianFunction docs & code consistent. IS: Fix comm for ISLocalToGlobalMappingApplyIS() Reported-by: Vincent Frans Maria De Groof <Vincent.De-Groof@uibk.ac.at> TSARKIMEX: needs equation type to be specified when not mass matrix remove all use of configuretime make petscconfigureruntime not static so c…
Matthew Knepley
Merge remote-tracking branch 'origin/knepley/feature-plex-fas' into knepley/pylith * origin/knepley/feature-plex-fas: DMPlex: Removed unused variable DMPlex: Fix for C++ build, small fix for PetscFE
Matthew Knepley
Merge branch 'knepley/fix-plex-submesh-edge' into knepley/pylith * knepley/fix-plex-submesh-edge: DMPlex: Removed unused variable in refinement DMPlex: Also mark hybrid cells with unsplit vertices
Matthew Knepley
DMPlex: Also mark hybrid cells with unsplit vertices
Matthew Knepley
DMPlex: Removed unused variable in refinement
Matthew Knepley
Merge branch 'knepley/fix-plex-submesh-edge' into knepley/pylith * knepley/fix-plex-submesh-edge: DMPlex: Docs for preallocation DMPlex: Fix for parallel refinement - PetscSF needs the leaves in sorted local order for it to get SFGather correct
Matthew Knepley
Merge remote-tracking branch 'origin/knepley/feature-plex-fas' into knepley/pylith * origin/knepley/feature-plex-fas: (60 commits) DMPlex: Removed leak from Triangle SNES ex12: Two working unstructured FAS solves for the unregularized p-Laplacian DMPlex: Cleaned up some memory issues DMPlex: Implement injection - I don't think this should be required DMPlex: DM interpolation requires the scaling vector for FAS DMPlex: Can now create a map from coarse to fine vertices…
Matthew Knepley
Merge branch 'knepley/fix-plex-submesh-edge' into knepley/pylith * knepley/fix-plex-submesh-edge: DMPlex: Label hybrid cells with unsplit edges during submesh creation - I don't like this completely since we have to use -(cell number) to avoid aliasing vertices in the original mesh
Matthew Knepley
Merge branch 'knepley/fix-plex-submesh-edge' into knepley/pylith * knepley/fix-plex-submesh-edge: DMPlex: Fixed submesh boundary in 3D - Correct support for unsplit edges - Correct support for hybrid faces from unsplit edges - Added checks DMPlex: Now DMPlexCheclSymmetry() also checks multiple cone/support entries
Matthew Knepley
Merge branch 'jed/plex-Wmaybe-uninitialized' into knepley/pylith * jed/plex-Wmaybe-uninitialized: DMPlex: Need to protect this Free()
Matthew Knepley
Merge branch 'knepley/fix-plex-submesh-edge' into knepley/pylith * knepley/fix-plex-submesh-edge: (837 commits) DMPlex: Fix unsplit vertex support in submeshes - Assumed only a single split edge, which is true in 2D DMPlex: Fixing marking of unsplit vertices - Check for presence in label was wrong (has to be exactly -1) - Check for incidence was wrong (was also getting unsplit marker) mpich: use latest mpich tarball with gcov but use '--enable-coverage' m…
Matthew Knepley
Merge branch 'knepley/fix-plex-orient-parallel' into knepley/pylith * knepley/fix-plex-orient-parallel: DMPlex: Added braindead simple parallel orientation solver - This gathers the graph to proc 0, solves, and scatters the answer - Need to store neighbor ranks and matches for each neighbor - This should be replaced with a parallel BFS DMPlex: For 1D orientation, you have to use cone position rather than face orientation
Matthew Knepley
Merge branch 'knepley/fix-plex-orient-parallel' into knepley/pylith * knepley/fix-plex-orient-parallel: DMPlex: Fixed some small mistakes - Initialize var - Declare at the top of the block - Added cone size call # Please enter a commit message to explain why this merge is necessary, # especially if it merges an updated upstream into a topic branch. # # Lines starting with '#' will be ignored, and an empty message aborts # the commit.
Matthew Knepley
Merge branch 'knepley/fix-plex-orient-parallel' into knepley/pylith * knepley/fix-plex-orient-parallel: DMPlex: Added parallel stage to DMPlexOrient() - The coarse solver is not implemented, so only works for p=2 PetscBT: Added PetscBTNegate()
Matthew Knepley
Merge branch 'knepley/fix-plex-refine-sf' into knepley/pylith * knepley/fix-plex-refine-sf: SF: Added additional checking DMPlex: Fixed SF created during refinement - Remote edge had wrong starting point - Forgot an entry for hybrid edge ignore another silly Fortran compiler warning message added citations for TS and SNES papers Web: Moved tutorial to previous, and added slides KSP: Fixed Fortran enum definition - I cannot see how this did not co…
Matthew Knepley
Merge branch 'knepley/fix-str-leak' into knepley/pylith * knepley/fix-str-leak: Sys: Have to check for all zero sizes in PetscMalloc*() - Produced a leak in optimized mode DMPlex: Replaced a PetscMalloc3() with PetscMalloc1()s - Fieldsplit was freeing these individually
Matthew Knepley
Merge branch 'knepley/fix-str-leak' into knepley/pylith * knepley/fix-str-leak: (52 commits) Sys: Fix memory leak in PetscStrreplace() PetscViewerGetSingleton() does not work in parallel for binary viewers DMPlex: Fix missing declaration Bib: New reference DMPlex: Documentation and declaration for creation functions SNES ex62: Fix syntax for test output PetscFE: Fix loop order for Jacobian calculation PetscFE: Correct sizes for f0, f1 a…
Matthew Knepley
Merge branch 'knepley/fix-hybrid-tet-refinement' into knepley/pylith * knepley/fix-hybrid-tet-refinement: DMPlex ex4: Fixed test output for hybrid tet refinement DMPlex: Fix for 3d hybrid simplicial refinement - Fixed the order in which hybrid faces are attached to the cell
Matthew Knepley
Merge branch 'knepley/fix-hybrid-tet-refinement' into knepley/pylith * knepley/fix-hybrid-tet-refinement: DMPlex: Fix hybrid 2d simplex refinement - If hybrid end face is inverted, flip the new hybrid cells created - Fix supports for this flip
Matthew Knepley
Merge branch 'knepley/malloc-0size-null' into knepley/pylith * knepley/malloc-0size-null: Sys: More from the grimy underbelly of text substitution
Matthew Knepley
Merge branch 'knepley/malloc-0size-null' into knepley/pylith * knepley/malloc-0size-null: Sys: Fuck Macros and their Unholy Enabler, The Preprocessor
Matthew Knepley
Merge branch 'knepley/malloc-0size-null' into knepley/pylith * knepley/malloc-0size-null: Sys: Fixed PetscFree to account for some NULL pointers
Matthew Knepley
Merge branch 'knepley/malloc-0size-null' into knepley/pylith * knepley/malloc-0size-null: Sys: Always return NULL for a 0 size allocation PetscCalloc7: fix bad copy/modify DMPlex: mark two unused functions to quash -Wunused-functions MatAIJ ASCII_MATLAB: fix nofinalvalue case MatAIJ ASCII_MATLAB: conform to documented spconvert interface for complex
Matthew Knepley
Merge branch 'master' into knepley/pylith * master: (85 commits) missing } in source mprint.c: fix typo '$%' -> '%%' bug fix, generated error with %%F or %%G in PetscPrintf output bib: add TChem Doc: Fixed MG Galerkin docs to note that different restriction and interpolation are possible Reported-by: Torquil Macdonald Sørensen <torquil@gmail.com> petscmpiexec: should work when PETSCVALGRIND_OPTIONS is not set fuck git %D f…
Matthew Knepley
Merge branch 'knepley/fix-plex-closure-index' into knepley/pylith * knepley/fix-plex-closure-index: DMPlex: Small fix
Matthew Knepley
Merge branch 'knepley/fix-plex-closure-index' into knepley/pylith * knepley/fix-plex-closure-index: PetscSection: Added PetscSectionGetField()
Matthew Knepley
Merge branch 'knepley/fix-plex-closure-index' into knepley/pylith * knepley/fix-plex-closure-index: DMPlex: Reorganization of closure operations - Rename DMPlexVecGetClosure_Static() —> DMPlexVecGetClosure_Depth1_Static() - Added special cases with/out fields - Removed the need for field offsets by interchanging loops over points and fields - Fixed bug where field offsets were not calculated if an array was passed in - Made all local functions static - Using S…
Matthew Knepley
Merge branch 'knepley/fix-plex-closure-index' into knepley/pylith * knepley/fix-plex-closure-index: DMPlex: Optimization for Get/SetClosure - Only need field offsets if there is more than one field
Matthew Knepley
Merge branch 'knepley/fix-hybrid-tet-refinement' into knepley/pylith * knepley/fix-hybrid-tet-refinement: DMPlex ex4: Added test for hybrid quads DMPlex: Added in hybrid quad refinement - Strange merge in the middle for some reason DMPlex: Cleanup and fix for SF construction in refinement - Had wrong numbering for vertices in quads
Matthew Knepley
Merge branch 'knepley/remove-petscsyshh' into knepley/pylith * knepley/remove-petscsyshh: Sys: Added missing header - The C++ Saga continues
Matthew Knepley
Merge branch 'knepley/fix-hybrid-tet-refinement' into knepley/pylith * knepley/fix-hybrid-tet-refinement: (29 commits) DMPlex: Bug fix for hybrid tet refinement - The new edges for hybrid faces do not depend on the cap face orientation - This happens because we are not attaching hybrid faces in an order dependent on the cap face orientation. Maybe we should. DMPlex: Bug fix for hybrid tet refinement - The orientation that we get for hybrid faces depends on both…
Matthew Knepley
Merge branch 'knepley/remove-petscsyshh' into knepley/pylith * knepley/remove-petscsyshh: Sys: God let this be the last checkin
Matthew Knepley
Merge branch 'knepley/remove-petscsyshh' into knepley/pylith * knepley/remove-petscsyshh: Sys: Wherein Matt gives up on C++, and eradicates it from error handling
Matthew Knepley
Merge branch 'knepley/fix-plex-closure-index' into knepley/pylith * knepley/fix-plex-closure-index: PetscSection: Change clIndices member to clPoints - Added some docs
Matthew Knepley
Merge branch 'knepley/remove-petscsyshh' into knepley/pylith * knepley/remove-petscsyshh: Sys: Removed ref to PETSc::Exception
Matthew Knepley
Merge branch 'knepley/remove-petscsyshh' into knepley/pylith * knepley/remove-petscsyshh: Sys: Fixed missing include
Matthew Knepley
Merge branch 'knepley/fix-plex-closure-index' into knepley/pylith * knepley/fix-plex-closure-index: SNES ex12: Use ViewFromOptions correctly DMPlex: Use closure index in DMPlexVecSetClosure() and DMPlexMatSetClosure() - Moved depth 1 optimization to static function
Matthew Knepley
Merge branch 'knepley/fix-plex-closure-index' into knepley/pylith * knepley/fix-plex-closure-index: DMPlex: Reorgnized closure index - Now index stores points and orientations instead of offsets, so it can be used for updates as well - Moved index creation to plexindices.c - Moved optimization for depth 1 mesh to a static function Conflicts: src/dm/impls/plex/makefile src/dm/impls/plex/plex.c
Matthew Knepley
Merge branch 'knepley/remove-petscsyshh' into knepley/pylith * knepley/remove-petscsyshh: (106 commits) Sys: Removed petscsys.hh Microsoft very picky about complex number conversion from real another unused variable in example declararitions must come before source allow struct initialization with c99 standard in examples and remove warning example with unused variables example with unused variables and missing CHKERRQ() etc incorrect C code…
Matthew Knepley
Merge branch 'knepley/feature-fem-gradients' into knepley/pylith * knepley/feature-fem-gradients: Test context passing in dm plex test ex3 Add a void *ctx argument to PetscDualSpaceApply and friends
Matthew Knepley
Merge branch 'knepley/feature-fem-gradients' into knepley/pylith * knepley/feature-fem-gradients: DMPlex ex3: Fix derivative for quadratic test DMPlex ex3: Fixed bug setting dimension (again) - Updated test output DMPlex ex3: Put in gradient check - There seems to be a problem with tests 2 and 5 DMPlex: Added DMPlexComputeL2GradientDiff() - I was not sure what to do with BC SNESGS: Fix for uninitialized variable warning in gssecant.c SNESGS: Fixed b…
Matthew Knepley
Merge branch 'knepley/feature-plex-gmsh' into knepley/pylith * knepley/feature-plex-gmsh: DMPlex: Fix for orientation in Gmsh files - Fixed test output do not use C99 struct initialization code in PETSc Nightly Summary: Added time taken to each of the tests in the dashboard. ASCII printing of floating point numbers must cast to (double) to support quad precision configure: check fortranDatatypes only when fortran is enabled [this fixes configure c…
Matthew Knepley
Merge branch 'knepley/feature-plex-refine-hex' into knepley/pylith * knepley/feature-plex-refine-hex: (72 commits) DMPlex: Fixes for ViewFromOptions - Passes regression DM: Moved ViewFromOptions into DMSetUp_DA() DMPlex: Interface fix in refinement PetscFE: Fixed leak from bad merge DMPlex: More fixup from bad rebase, moved to DMGet/SetCoordinateSection() DM: Added DMGet/SetCoordinateSection() Fuckup: Fix for merge that is still untangling bad rebas…
Matthew Knepley
Merge branch 'knepley/feature-plex-refine-hex' into knepley/pylith * knepley/feature-plex-refine-hex: DMPlex: DMPlexCheckSkeleton() now handles hybrid cells
Matthew Knepley
Merge branch 'knepley/feature-plex-refine-hex' into knepley/pylith * knepley/feature-plex-refine-hex: DMPlex ex4: All refinement tests passing DMPlex: Added hybrid hex refinement DMPlex: Bug fix for hybrid tet refinement - Wrong offset DMPlex: Fixed errors in hybrid tet refinement - Use fMax instead of fStart for offset - Use p instead of fEnd for point value - 2 faces are created from each hybrid face, not 4 DMPlex: Corrected refinement coordinates for…
Matthew Knepley
Merge branch 'knepley/feature-plex-refine-hex' into knepley/pylith * knepley/feature-plex-refine-hex: DMPlex ex4: Hybrid tet refinement now working DMPlex: Propagate fixes from tet refinement to hybrid tet refinement
Matthew Knepley
Merge branch 'master' into knepley/pylith * master: (29 commits) DMPlex: Missed malloc conversion config ctetgen: upgrade for PetscMalloc[1-7] API change PetscFE: Upgraded to new malloc interface FFTW: Removed spurious cast Nightly summary: Examples now report number of possible problems rather than warnings and errors. Nightly summary: Dashboard order is now 'Make', 'Examples', 'Configure' comment code to make sure malloc a…
Matthew Knepley
Merge branch 'knepley/feature-plex-hybrid-3d' into knepley/pylith * knepley/feature-plex-hybrid-3d: DMPlex ex5: Check faces on all meshes DMPlex ex5: Fix consistency of original meshes - Fix orientations of tet meshes - Redo hex test to automatically interpolate - Replaced output DMPlex ex5: Check original meshes for consistency DMPlex: make non-namespaced CellRefiner functions static
Matthew Knepley
Merge branch 'knepley/feature-plex-hybrid-3d' into knepley/pylith * 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()…
Matthew Knepley
Merge branch 'knepley/feature-plex-hybrid-3d' into knepley/pylith * 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…
Matthew Knepley
Merge branch 'knepley/fix-plex-submesh-parallel' into knepley/pylith * 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 knepley/pylith * 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 knepley/pylith * knepley/feature-plex-gmsh: (49 commits) DMPlex ex1: Added test for Gmsh DMPlex: Added Gmsh input require PETSC_USE_COMPLEX for PetscScalar to be complex for PetscOptionsStringToScalar() fix PetscOptionsStringToScalar() for missing complex Nightly Summary: No longer create filtered log file for examples. added PetscOptionsGetScalarArray() fixed a variety of examples with problems for …
Matthew Knepley
Merge branch 'knepley/feature-plex-hybrid-3d' into knepley/pylith * 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/fix-plex-submesh-parallel' into knepley/pylith * knepley/fix-plex-submesh-parallel: DMPlex: Make DMPlexCreateCohesiveSubmesh_Interpolated() also create PetscSF
Matthew Knepley
Merge branch 'knepley/feature-plex-hybrid-3d' into knepley/pylith * 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
Matthew Knepley
Merge branch 'knepley/fix-plex-submesh-parallel' into knepley/pylith * knepley/fix-plex-submesh-parallel: PetscSection: Fix for PetscSectionCreateGlobalSectionCensored() - Offset was wrong DM: Added check in DMCreateDefaultSF() - Check for overrun of largest offset
Matthew Knepley
Merge branch 'knepley/fix-plex-submesh-parallel' into knepley/pylith * knepley/fix-plex-submesh-parallel: PetscSection: Fixed PetscSectionGetOffsetRange() for empty section
Matthew Knepley
Merge branch 'knepley/feature-plex-hybrid-3d' into knepley/pylith * 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 DMPlex ex4: New test output afte…
Matthew Knepley
Merge branch 'knepley/fix-plex-closure-index' into knepley/pylith * 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
Matthew Knepley
Merge branch 'knepley/fix-plex-reorder-empty' into knepley/pylith * 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 knepley/pylith * knepley/fix-plex-label-hash: DMLabel: Fix bug in clearing value for array representation
Matthew Knepley
Merge branch 'knepley/fix-plex-submesh-parallel' into knepley/pylith * knepley/fix-plex-submesh-parallel: DMPlex: Small doc fix for DMPlexConstructCohesiveCells()
Matthew Knepley
Merge branch 'knepley/fix-plex-submesh-parallel' into knepley/pylith * knepley/fix-plex-submesh-parallel: DMPlex: Protect another instance of empty IS
Matthew Knepley
Merge branch 'knepley/fix-plex-submesh-parallel' into knepley/pylith * 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 knepley/pylith * 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 knepley/pylith * 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 knepley/pylith * knepley/fix-plex-reorder-empty: DMPlex: Fix reordering for empty meshes
Matthew Knepley
Merge branch 'knepley/fix-plex-submesh-parallel' into knepley/pylith * 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
Matthew Knepley
Merge branch 'master' into knepley/pylith * master: (31 commits) nightlylogs: eliminate some known warnings from the dashboard count forgot to remove C++ petsc logging in plog.c doc: add errorcheck when processing badly formatted makefiles start blacklist for compiler error messages since currently BuildSystem ignores ALL output! nightlylogs: add different dashboards for each of the branches nightlybuilds: add with-serialize-f…
Matthew Knepley
Merge branch 'knepley/remove-cxx-logging' into knepley/pylith * knepley/remove-cxx-logging: (129 commits) need to remove the include of petsclog.hh also Logging: Removed C++ wrappers for logging need to caste to idx_t * from PetscInt * for Parmetis fix incorrect caste to superlu_dist int_t type when using 64 bit indices Builder: More portable hosts option for mpiexec DMPlex ex1F90: Added test of DMLabel bindings DMLabel: Moved custom bindings t…
Matthew Knepley
Merge branch 'knepley/fix-hash-scaling' into knepley/pylith * knepley/fix-hash-scaling: DMPlex: Bug fix for interpolated adjacency formation
Matthew Knepley
Merge branch 'knepley/fix-hash-scaling' into knepley/pylith * knepley/fix-hash-scaling: DMPlex: Fast adjacency graph construction for interpolated meshes DMPlex: Fixed error in new events DMPlex: More events for distribution
Matthew Knepley
Merge branch 'knepley/fix-hash-scaling' into knepley/pylith * knepley/fix-hash-scaling: DMPlex: Fixed allocation bug in reordering
Matthew Knepley
Merge branch 'knepley/fix-hash-scaling' into knepley/pylith * knepley/fix-hash-scaling: DMPlex: Fixed mismatched Malloc2 in reordering
Matthew Knepley
Merge branch 'knepley/fix-hash-scaling' into knepley/pylith * knepley/fix-hash-scaling: DMLabel: Split Malloc3 into Malloc2 and Malloc
Matthew Knepley
Merge branch 'knepley/feature-plex-refine-3d' into knepley/pylith * 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
Matthew Knepley
DMPlex ex4: New test output after changing refinement of hybrid cells for 3D simplex
Matthew Knepley
DMPlex: In refinement, fixed correspondence between hybrid cells and faces
Matthew Knepley
DMPlex: In refinement, added GetTriEdgeInverse_Static() and GetTriSubfaceInverse_Static()
Matthew Knepley
DMPlex: Whitespace change
Matthew Knepley
Merge branch 'knepley/fix-hash-scaling' into knepley/pylith * 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 knepley/pylith * knepley/fix-plex-geometry-hex: DMPlex: If “vtk” label has no cells, do not use it
Matthew Knepley
Merge branch 'knepley/fix-hash-scaling' into knepley/pylith * 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 knepley/pylith * knepley/feature-plex-hybrid-3d: DMPlex: Fix DMPlexCheckSkeleton() for submeshes
Matthew Knepley
Merge branch 'knepley/fix-hash-scaling' into knepley/pylith * 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…
Matthew Knepley
Merge branch 'knepley/fix-plex-geometry-hex' into knepley/pylith * 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-plex-geometry-hex' into knepley/pylith * knepley/fix-plex-geometry-hex: DMPlex: Change geometry check to support interpolated meshes - This all has to be replaced anyway
Matthew Knepley
Merge branch 'knepley/fix-plex-reorder-coords' into knepley/pylith * knepley/fix-plex-reorder-coords: (23 commits) DMPlex: Fixed bug in coordinate permutation PetscSection: Doc fix for permutation Bib: Added Top500 and fixed entry fun3d: update PetscMallocValidate() usage bib: rename ref with duplicate key Webpage: Corrected '-dm_mat_type cusp' to 'dm_mat_type aijcusp'. Allow calling MatGetBlockSize[s]() before matrix preallocation SNESLINESEARCHB…
Matthew Knepley
Merge branch 'knepley/feature-plex-hybrid-3d' into knepley/pylith * knepley/feature-plex-hybrid-3d: (29 commits) 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 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 DMPlex: Added doc for DMPlex…
Matthew Knepley
Merge branch 'knepley/feature-plex-refine-3d' into knepley/pylith * knepley/feature-plex-refine-3d: DMPlex: Fix label creation for 3D simplicial refinement
Matthew Knepley
Merge branch 'knepley/example-ts-friction' into knepley/pylith * knepley/example-ts-friction: (144 commits) 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…
Matthew Knepley
Merge branch 'knepley/feature-plex-refine-3d' into knepley/pylith * knepley/feature-plex-refine-3d: DMPlex ex4: Added another 2D simplex hybrid test DMPlex ex4: Reworked 2D simplex hybrid test
Matthew Knepley
Merge branch 'knepley/feature-plex-refine-3d' into knepley/pylith * knepley/feature-plex-refine-3d: DMPlex: Fixed bug for label creation in hex refinement
Matthew Knepley
Merge branch 'knepley/fix-plex-ghost-cells' into knepley/pylith * knepley/fix-plex-ghost-cells: (114 commits) DMLabel: Fixed index for ranges with nonzero lower limit DMPlex: Fixed DMPlexConstructGhostCells() to filter out non-faces from the label DMPlex: Added DMLabelFilter() TS ex31: fix Jacobian destruction TSRK: remove TSRKSetTolerance because we now use TSAdapt __SDIR__: remove remaining traces and document in changes.html Added a post-stage…
Matthew Knepley
Merge branch 'knepley/feature-plex-refine-3d' into knepley/pylith * knepley/feature-plex-refine-3d: DMPlex: Fixed compiler warnings
Matthew Knepley
Merge branch 'knepley/feature-plex-refine-3d' into knepley/pylith * knepley/feature-plex-refine-3d: DMPlex: Fix uniform refinement for empty mesh
Matthew Knepley
Merge branch 'knepley/feature-plex-reordering' into knepley/pylith * knepley/feature-plex-reordering: DMPlex: Fixed bug with DMPlexPermute - Fixed label permutation
Matthew Knepley
Merge branch 'knepley/feature-plex-refine-3d' into knepley/pylith * knepley/feature-plex-refine-3d: DMPlex: Fixed creation of hybrid submesh - No more Lagrange flag, just check for proper prism hybrid cells
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