| d0892670 | 17-Oct-2013 |
Matthew G. Knepley <knepley@gmail.com> |
DMDA: Added functions which emulate DMPlex functionality |
| e42e3c58 | 17-Oct-2013 |
Matthew G. Knepley <knepley@gmail.com> |
DMDA: Now DMDAGetNumCells() returns the cells in each direction as well |
| 170be9ae | 16-Oct-2013 |
Matthew G. Knepley <knepley@gmail.com> |
Merge branch 'master' into knepley/feature-dmda-section
* master: (397 commits)
PetscSynchronizedFGets: fix deadlock at EOF
Compiler: Fix warnings from MPI impls which do not initialize outputs
Merge branch 'master' into knepley/feature-dmda-section
* master: (397 commits)
PetscSynchronizedFGets: fix deadlock at EOF
Compiler: Fix warnings from MPI impls which do not initialize outputs
Increase patchlevel to 3.4.3
SNES: Now work vectors come from the DM
SNES ex62: Remove code generation
SNES: Move setup involving snes->vec_sol from SNESSetUp() to SNESolve()
Compiler: Fix warnings from MPI impls which do not initialize outputs
DMPlex ex7: Added missing test output
SNES ex52: Removed old Jacobian stuff, and fixed call to DMPlexProjectFunction() - Fixed calls for new element handling
SNES ex12: Added a performance profiling mode
DMPlex ex8: Fixed leak
PetscSection: Must reset the section when changing the number of fields
DMPlex ex7: Fixed test output - Corrected orientations in interpolation
DMPlex ex1: Fixed test output - Uniform refinement for quads changed
DMPlex: Fix overagressive checks
PC: Removed support graph PC
configure: both downloadonWindows and worksonWindows refer to MS compilers. Also fix isWindows() -> isWindows(CC).
MatXAIJSetPreallocation: use array[] notation to help out Fortran
__float128: when blas/lapack is not found instruct using f2cblaslapack
Configure: Package.downloadonWindows is supposed to mean that Windows compilers work. not Cygwin - Also changed doc for Package.worksonWindows, which does refer to Cygwin
...
Conflicts:
src/dm/impls/da/dalocal.c
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| 29a5cbdc | 10-Oct-2013 |
Matthew G. Knepley <knepley@gmail.com> |
Compiler: Fix warnings from MPI impls which do not initialize outputs
(cherry picked from commit d892089bd4a83d5450f25ac15dd2b0a661537089) |
| d892089b | 10-Oct-2013 |
Matthew G. Knepley <knepley@gmail.com> |
Compiler: Fix warnings from MPI impls which do not initialize outputs |
| 93cf2482 | 02-Oct-2013 |
Jed Brown <jedbrown@mcs.anl.gov> |
Merge branch 'barry/dmvecmattypes'
The MatType argument is removed from DMCreateMatrix(), you can use
DMSetMatType() to indicate the type you want used with a DM, defaults to
MATAIJ.
* barry/dmvecm
Merge branch 'barry/dmvecmattypes'
The MatType argument is removed from DMCreateMatrix(), you can use
DMSetMatType() to indicate the type you want used with a DM, defaults to
MATAIJ.
* barry/dmvecmattypes:
DMPlex ExodusII: fix dm->vectype pointer syntax
removed use of VecSetFromOptions() all over the placed, instead use MatGetVecs() or use dm->vectype to determine type added DMGetVecType() and DMGetMatTYpe()
removed MatType argument from DMCreateMatrix() and DMCreateColoring() since information is obtained from DM
Conflicts:
src/dm/impls/da/fdda.c
src/dm/impls/plex/plex.c
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| 25a75388 | 01-Oct-2013 |
Jed Brown <jedbrown@mcs.anl.gov> |
Merge branch 'jed/remove-dynamic-loading-option'
Option --with-dynamic-loading has been removed. Similar functionality
is available via the run-time option -dynamic_library_preload.
* jed/remove-d
Merge branch 'jed/remove-dynamic-loading-option'
Option --with-dynamic-loading has been removed. Similar functionality
is available via the run-time option -dynamic_library_preload.
* jed/remove-dynamic-loading-option:
Sys: PetscContainerCreate must call PetscSysInitializePackage
Remove --with-dynamic-loading / PETSC_USE_DYNAMIC_LIBRARIES
Conflicts:
src/dm/impls/mesh/mesh.c
src/dm/interface/dlregisdmdm.c
src/docs/website/documentation/changes/dev.html
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| e5c84f05 | 25-Sep-2013 |
Jed Brown <jedbrown@mcs.anl.gov> |
doc: restore functions in PETSc zero their arguments
This is done to prevent accidental misuse. In general, one can pass
NULL for the pointer argument to keep the pointer around for longer, but
use
doc: restore functions in PETSc zero their arguments
This is done to prevent accidental misuse. In general, one can pass
NULL for the pointer argument to keep the pointer around for longer, but
use of arrays after restoration is invalid.
Suggested-by: Wolfgang Bangerth <bangerth@math.tamu.edu>
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| 01f69807 | 19-Sep-2013 |
Barry Smith <bsmith@mcs.anl.gov> |
Merge branch 'master' into barry/dmvecmattypes
possible some messed up manual merges!
Conflicts:
src/dm/impls/mesh/examples/tutorials/ex4f90.F
src/dm/impls/mesh/mesh.c
src/dm/impls/mesh/meshcreat
Merge branch 'master' into barry/dmvecmattypes
possible some messed up manual merges!
Conflicts:
src/dm/impls/mesh/examples/tutorials/ex4f90.F
src/dm/impls/mesh/mesh.c
src/dm/impls/mesh/meshcreate.c
src/dm/impls/mesh/section.c
src/snes/examples/tutorials/ex10.c
src/snes/examples/tutorials/ex12.c
src/snes/examples/tutorials/ex52.c
src/snes/examples/tutorials/ex62.c
src/snes/utils/mesh/dmmeshsnes.c
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| 554c65c0 | 15-Sep-2013 |
Barry Smith <bsmith@mcs.anl.gov> |
DMCreateMatrix_DA_1d_MPIAIJ_Fill() needs at least 2 points per grid point |
| 114749ab | 15-Sep-2013 |
Matthew G. Knepley <knepley@gmail.com> |
Merge branch 'knepley/feature-fem-dgspace' into knepley/fix-fem-0d
* knepley/feature-fem-dgspace:
PetscFE: Fixed quadrature names for OpenCL
PetscSpace: Added a DG space - Defined on a set of qu
Merge branch 'knepley/feature-fem-dgspace' into knepley/fix-fem-0d
* knepley/feature-fem-dgspace:
PetscFE: Fixed quadrature names for OpenCL
PetscSpace: Added a DG space - Defined on a set of quadrature points - Need tests
PetscQuadrature: Revamped - Removed basis tabulation - Shortened names - Added PetscQuadratureView()
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| 0acb5beb | 11-Sep-2013 |
Barry Smith <bsmith@mcs.anl.gov> |
added support for dfill for DMCreateMatrix_1d_MPIAIJ for DMDA |
| a4b60ecf | 05-Sep-2013 |
Matthew G. Knepley <knepley@gmail.com> |
DMDA: Fix DMDACreateSection()
- Fix setting the default section
- Fix setting pointSF |
| c38c1269 | 05-Sep-2013 |
Matthew G. Knepley <knepley@gmail.com> |
DMDA: Fix DMCreateSubDM_DA()
- Cannot call DMClone() since we want to change the number of fields
- DMDA needs to be fixed to separate dof and topology |
| a9811db3 | 05-Sep-2013 |
Matthew G. Knepley <knepley@gmail.com> |
DMDA: Must call DMSetUp() inside DMClone() |
| f9fd7fdb | 04-Sep-2013 |
Matthew G. Knepley <knepley@gmail.com> |
PetscQuadrature: Revamped
- Removed basis tabulation
- Shortened names
- Added PetscQuadratureView() |
| cc85fe4d | 04-Sep-2013 |
Barry Smith <bsmith@mcs.anl.gov> |
Merge branch 'barry/dmvecmattypes' into barry/saws
Needed to work with version of PETSc that did not have constant calls to VecSetFromOptions() etc
Conflicts:
src/ksp/ksp/interface/ams/kspams.c
s
Merge branch 'barry/dmvecmattypes' into barry/saws
Needed to work with version of PETSc that did not have constant calls to VecSetFromOptions() etc
Conflicts:
src/ksp/ksp/interface/ams/kspams.c
src/snes/impls/composite/snescomposite.c
src/snes/impls/gs/snesgs.c
src/snes/impls/nasm/nasm.c
src/snes/impls/ngmres/snesngmres.c
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| c0dedaea | 03-Sep-2013 |
Barry Smith <bsmith@mcs.anl.gov> |
removed use of VecSetFromOptions() all over the placed, instead use MatGetVecs() or use dm->vectype to determine type
added DMGetVecType() and DMGetMatTYpe() |
| b412c318 | 03-Sep-2013 |
Barry Smith <bsmith@mcs.anl.gov> |
removed MatType argument from DMCreateMatrix() and DMCreateColoring() since information is obtained from DM |
| 0b45a142 | 01-Sep-2013 |
Barry Smith <bsmith@mcs.anl.gov> |
cannot malloc inside xxxxSetFromOptions() when using GUI for setting values because memory does not get freed properly later |
| 48fe7c28 | 31-Aug-2013 |
Matthew G. Knepley <knepley@gmail.com> |
Merge branch 'knepley/plex-speed-tests'
* knepley/plex-speed-tests:
DMPlex: Remove unused variables
DMPlex: Fixed bug in special case for DMPlexVecGetClosure() - Need to set outgoing size if arr
Merge branch 'knepley/plex-speed-tests'
* knepley/plex-speed-tests:
DMPlex: Remove unused variables
DMPlex: Fixed bug in special case for DMPlexVecGetClosure() - Need to set outgoing size if array is passed in
DMPlex: Added special case for DMPlexVecSetClosure() - Could add more modes
DMPlex: Optimizations for DMPlexVecGetClosure() - Removed branch (seems to have little effect) - Removed calculation of size when array is provided (profiled for 20% effect)
DMPlex: Forgot one init for DMPlexVecGetClosure()
DMPlex: Must initialize argument to DMPlexVecGetClosure()
DMPlex ex9: Added ability to reuse array in VecGetClosure()
DMPlex: Allow DMPlexVecGetClosure() to take an input array
DMPlex: Fix bug in specialization of DMPlexVecGetClosure()
DMPlex: Bug fix for special case in DMPlexVecGetClosure()
DMPlex: Added optimization for depth 1 DMPlexVecGetClosure()
DMPlex ex9: Does not fail by default - Will turn back on failure once we calculate variance
SNES ex12: Cleaning up in preparation for speed testing
DMPlex: Added ex9 to test performance, put in depth 1 special case for TransitiveClosure
Conflicts:
config/builder.py
src/dm/impls/plex/plexgeometry.c
src/snes/examples/tutorials/output/ex12_5.out
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| aa2d57e9 | 30-Aug-2013 |
Jed Brown <jedbrown@mcs.anl.gov> |
Remove --with-dynamic-loading / PETSC_USE_DYNAMIC_LIBRARIES
This option was mostly redundant because normal shared libraries satisfy
all the same needs. This commit adds the run-time option
-dynami
Remove --with-dynamic-loading / PETSC_USE_DYNAMIC_LIBRARIES
This option was mostly redundant because normal shared libraries satisfy
all the same needs. This commit adds the run-time option
-dynamic_library_preload that can be used to load/initialize all the
packages in advance, as used to be done when --with-dynamic-loading.
The PetscDLLibraryRegister_petscxxx functions have been kept, but are
not called unless -dynamic_library_preload is used. The petsc-dev
discussion, "Why --with-dynamic-loading?" did not reach consensus about
whether this was ever useful, so it may also be removable.
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| c0c93d0e | 28-Aug-2013 |
Matthew G. Knepley <knepley@gmail.com> |
Merge branch 'master' into knepley/feature-dmda-section
* master: (287 commits)
Mat ex170: Comments
VTK: Small fix to error message (.vts to .vtu)
VTK: Small fix to error message
Fixed bib e
Merge branch 'master' into knepley/feature-dmda-section
* master: (287 commits)
Mat ex170: Comments
VTK: Small fix to error message (.vts to .vtu)
VTK: Small fix to error message
Fixed bib entries
Bib: Updates
AO: fix erroneous processing of -ao_view and factor into AOViewFromOptions
doc: fix named argument in {Vec,Mat,DM}ViewFromOptions
Sys: add PetscDataTypeFromString() and test code
Mat: Should say that it has a nullspace in MatView()
parms: update tarball with fix for namespace conflict with metis
fix citation 'Golub_Varga_1961'
parmetis: update tarball to parmetis-4.0.2-p5 which fixes an install issue with cygwin
Sys Logging: revert parent traversal
fixed hdf5.py so that if self.libraries.compression is None the code still runs correctly
DMDA: fix bad cast of DM_DA to PetscObject
MatClique: follow DistMultiVec API changes
MatClique: remove unused variables
config cmakeboot: add C++ flags any time compiler is available
config OpenMP: check for C++ flag any time the compiler is available
replaced all left-over uses of a single PetscMalloc() to allocated multiple arrays: replaced with PetscMallocN() The only ones left are when the second array is set into the first array and one ugly usage in the MUMPS interface that cannot be easily fixed
...
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| 86bfadb5 | 28-Aug-2013 |
Matthew G. Knepley <knepley@gmail.com> |
Merge branch 'knepley/feature-dm-clone'
* knepley/feature-dm-clone:
DMPlex: Removed unused variables
DM: Dammit, forgot declaration
DM: Small fix to DMClone for DMPlex
DM: Added specializati
Merge branch 'knepley/feature-dm-clone'
* knepley/feature-dm-clone:
DMPlex: Removed unused variables
DM: Dammit, forgot declaration
DM: Small fix to DMClone for DMPlex
DM: Added specialization for DMCreateSubDM() with a PetscSection - Replace DMPlex implementation - Is used by DMDA when a section is defined
DM: Fix DMDA clone - Made it work for all dimensions (which makes DMCreateSubDM() work) - Removed DMSetUp() which should be called by caller
DM: Added DMClone() which makes a shallow copy - This is very useful for DM since it can have a lot of associated data and is used as a building block for different problems - This replaces DMPlexClone()
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| 3a0e354c | 20-Aug-2013 |
Jed Brown <jedbrown@mcs.anl.gov> |
Merge branch 'barry/improve-memory-logging'
* barry/improve-memory-logging:
DMDA: fix bad cast of DM_DA to PetscObject |