Sys: drop explicit type arguments from PetscNew() and PetscNewLog()

git grep -l 'PetscNew\(Log\)\?(' -- $1 | xargs perl -pi -e '
s@PetscNew\([^,;()]+ *, *@PetscNew(@;
s@PetscNewLog\(([^,;()]+) *,[^,

Sys: drop explicit type arguments from PetscNew() and PetscNewLog()

git grep -l 'PetscNew\(Log\)\?(' -- $1 | xargs perl -pi -e '
s@PetscNew\([^,;()]+ *, *@PetscNew(@;
s@PetscNewLog\(([^,;()]+) *,[^,;()]+, *@PetscNewLog($1,@'

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Sys: add PetscCalloc[1-7]

Replace lots of places where PetscMemzero is called immediately after
allocation.

Sys: add PetscMalloc1 macro, array allocation without redundant types

The type is inferred from the pointer return type. This patch is
automated via the following script:

git grep -l 'PetscMalloc(

Sys: add PetscMalloc1 macro, array allocation without redundant types

The type is inferred from the pointer return type. This patch is
automated via the following script:

git grep -l 'PetscMalloc(.*sizeof' src | xargs perl -pi -e 's@PetscMalloc\(([^,;]*[^,; ]) *\* *sizeof\([^,;()]+\),@PetscMalloc1($1,@'

This commit contains an additional bug-fix in csrperm.c, fixing pointer
arity. The code was introduced in 2006, but the allocation could not
have been correct at any time. This probably means that
MatDuplicate_SeqAIJPERM has never been tested.

a54129beb540034ba105796c682d589e7e1111f2
Richard Tran Mills <rmills@ornl.gov>

Added MATSEQCSRPERM support for MatDuplicate() and conversion to/from
MATSEQAIJ. Note that these changes are not quite debugged.

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PetscMalloc[2-7]: remove type arguments, infer from pointer type

This change can be performed almost entirely by this script:

git grep -l PetscMalloc[2-7] $1 | xargs perl -pi \
-e '
s@PetscMalloc

PetscMalloc[2-7]: remove type arguments, infer from pointer type

This change can be performed almost entirely by this script:

git grep -l PetscMalloc[2-7] $1 | xargs perl -pi \
-e '
s@PetscMalloc2\(([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+)\)@PetscMalloc2($1,$3,$4,$6)@;
s@PetscMalloc3\(([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+)\)@PetscMalloc3($1,$3,$4,$6,$7,$9)@;
s@PetscMalloc4\(([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+)\)@PetscMalloc4($1,$3,$4,$6,$7,$9,$10,$12)@;
s@PetscMalloc5\(([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+)\)@PetscMalloc5($1,$3,$4,$6,$7,$9,$10,$12,$13,$15)@;
s@PetscMalloc6\(([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+)\)@PetscMalloc6($1,$3,$4,$6,$7,$9,$10,$12,$13,$15,$16,$18)@;
s@PetscMalloc7\(([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+),([^,;()]+)\)@PetscMalloc7($1,$3,$4,$6,$7,$9,$10,$12,$13,$15,$16,$18,$19,$21)@;
'

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PetscSection: Fix for PetscSectionCreateGlobalSectionCensored()
- Offset was wrong

added FILE* argument to PetscSynchronizedFlush() so it knows where to flush the off process values

Previously if process 0 did not call PetscSynchronizedFPrintf() then it output the off process valu

added FILE* argument to PetscSynchronizedFlush() so it knows where to flush the off process values

Previously if process 0 did not call PetscSynchronizedFPrintf() then it output the off process values
to stdout even if the file was not stdout. Also affected PetscViewerASCIISynchronizeFlush()

Reported-by: Randall Mackie <rlmackie862@gmail.com>

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PetscSection: Fixed PetscSectionGetOffsetRange() for empty section

PetscSection: Doc fix for permutation

Merge branch 'knepley/feature-plex-reordering'

* knepley/feature-plex-reordering:
doc: update makefile with order.h -> ../../../include/petsc-private/matorderimpl.h rename
DMPlex: Fixed bug with

Merge branch 'knepley/feature-plex-reordering'

* knepley/feature-plex-reordering:
doc: update makefile with order.h -> ../../../include/petsc-private/matorderimpl.h rename
DMPlex: Fixed bug with DMPlexPermute - Fixed label permutation
DMPlex: Check whether default section exists to be reordered
DMPlex: Fixed compiler warning
DMPlex ex10: Fixed test output
DMPlex: Added missing declarations
DMPlex: Fixed misuse of PetscObjectSetName()
MatComputeBandwidth: use PetscInt instead of PetscMPIInt
Mat: Fixed declaration
Mat: Changed MatCalcBandwidth() to MatComputeBandwidth() - Added Fortran interface
DMPlex ex10: This tests reordering of meshes
DMPlex: Added DMPlexGetOrdering() and DMPlexPermute()
PetscSection: Added PetscSectionPermute()
DMLabel: Added DMLabelPermute()
DMPlex: Added DMPlexCreateDoublet()
DMPlex: Added DMPlexCopyLabels()
Mat: Added MatCalcBandwidth()
MatOrdering: Moved private header into petsc-private - Fix to pointer checks in sorder.c

Conflicts:
include/petscdmplex.h

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optimize ISLocalToGlobalMappingCreateIS() to reuse indices created in call to ISGetIndices()
for the case where they are immediately freed anyways no need to copy

PetscSection: Must reset the section when changing the number of fields

Merge branch 'knepley/fix-plex-preallocation'

* knepley/fix-plex-preallocation:
PetscSF: Fixed PetscSFCreateEmbeddedSF() - We were using sf->nleaves for the leaf buffer, which is completely wrong.

Merge branch 'knepley/fix-plex-preallocation'

* knepley/fix-plex-preallocation:
PetscSF: Fixed PetscSFCreateEmbeddedSF() - We were using sf->nleaves for the leaf buffer, which is completely wrong. We have to use the largest thing in sf->mine[]
DMPlex: Fix completely broken code in PetscSFCreateRemoteOffsets() - Non-broken example was in PetscSFDistributeSection()
DMPlex: Fix leaks in preallocation debugging
DMPlex: Put in guard for preallocation sections which are smaller than the SF

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Merge branch 'knepley/feature-closure-cache'

* knepley/feature-closure-cache:
DMPlex: Added declaration of DMPlexCreateClosureIndex()
SNES ex62: Use closure index
DMPlex: Use closure index if

Merge branch 'knepley/feature-closure-cache'

* knepley/feature-closure-cache:
DMPlex: Added declaration of DMPlexCreateClosureIndex()
SNES ex62: Use closure index
DMPlex: Use closure index if available for DMPlexVecGetClosure()
DMPlex: Added DMPlexCreateClosureIndex() - Uses a PetscSection+IS and stashes in the original Section
PetscSection: Added an index for optimization of closure queries - Added PetscSectionGet/SetClosureIndex() - The index is keyed to the DM which built it (use PetscObject) - Only use a single key for now since a lot of checking would be slow

Conflicts:
src/snes/examples/tutorials/ex62.c

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PetscSection: Added PetscSectionPermute()

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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DMPlex: Fix completely broken code in PetscSFCreateRemoteOffsets()
- Non-broken example was in PetscSFDistributeSection()

Merge branch 'maint'

* maint:
Fix for accidentally duplicated refcount decrement in dm->x
PetscLayoutCreate doc: format code block and list

fixes to ex10.c Jacobian
fixes to PetscFGets()
revert attempt to inline ISLocalToGlobalApply()

PetscLayoutCreate doc: format code block and list

PetscSection: Added an index for optimization of closure queries
- Added PetscSectionGet/SetClosureIndex()
- The index is keyed to the DM which built it (use PetscObject)
- Only use a single key for

PetscSection: Added an index for optimization of closure queries
- Added PetscSectionGet/SetClosureIndex()
- The index is keyed to the DM which built it (use PetscObject)
- Only use a single key for now since a lot of checking would be slow

show more ...

Merge branch 'knepley/fix-plex-parallel'

* knepley/fix-plex-parallel:
DMPlex: Fixed creation of global sections - The size of neg[] must be all of nroots instead of pEnd-pStart
DMPlex: Fixed coh

Merge branch 'knepley/fix-plex-parallel'

* knepley/fix-plex-parallel:
DMPlex: Fixed creation of global sections - The size of neg[] must be all of nroots instead of pEnd-pStart
DMPlex: Fixed cohesive submesh SF - I misclassified points which were not owned in the original mesh, but are owned in the submesh
DMPlex: Fixed bug with cohesive submesh SF - Needed to put in owned subpoints since they do not come from leaves OR from the original mesh
DMPlex: Fix out of bounds access for empty mesh
DMPlex: Fixed creation of PetscSF in DMPlexCreateCohesiveSubmesh_Uninterpolated() - Could not assume that original owner of subvertex owned it in submesh because it might have no subcells - Needed to redetermine ownership of subpoints
Plex VTK: Handle missing submesh pieces in parallel
DMPlex: Initializeremote locations when calculating SF for submesh
DMPlex: FIxed hang in DMPlexCreateCohesiveSubmesh()
DMPlex: Added PetscSF creation to DMPlexCreateCohesiveSubmesh_Uninterpolated() - Added DMPlexFilterPoint_Internal() - Still need this for the interpolated variant
DMPlex: Remove dead code
DMPlex: Removed aggressive checks for cohesive cells - How should we handle extraction in parallel?
PetscSection: PetscSectionCreateSubmeshSection() now can take an empty IS
DMPlex: Allow submesh creation with empty mesh and empty label
DMPlex: Allow DMPlexOrient() of empty mesh

Conflicts:
src/dm/impls/plex/plexsubmesh.c

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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.

show more ...