Merge branch 'psanan/dmswarm-namespacing' [PR #904]

* psanan/dmswarm-namespacing:
This attempts to namespace many of the internally-used components of DMSwarm.

DMSwarm: namespacing and symbol hiding

DataBucket --> DMSwarmDataBucket
DataEx --> DMSwarmDataEx
DataField --> DMSwarmDataField
DEObjectState --> DMSwarmDEObjectState
DATA_BUCKET_XXX --> DMSWARM_DAT

DMSwarm: namespacing and symbol hiding

DataBucket --> DMSwarmDataBucket
DataEx --> DMSwarmDataEx
DataField --> DMSwarmDataField
DEObjectState --> DMSwarmDEObjectState
DATA_BUCKET_XXX --> DMSWARM_DATA_BUCKET_XXX
DATAFIELD_XXX --> DMSWARM_DATAFIELD_XXX
StringInList/StringFindInList --> DMSwarmDataFieldStringInList/DMSwarmDataFieldStringFindInList
__DATATFIELD_XXX --> DMSWARM_DATAFIELD_XXX

Mark DMSwarmDataBucket and DMSwarmDataEx functions PETSC_INTERN

Update test output with new names DMSwarmDataEx and DMSwarmDataBucket

Fix alignment as needed, and perform other minor formatting fixes.

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Merge branch 'barry/add-ftn-linfinity-conv-test' of bitbucket.org:petsc/petsc into barry/add-ftn-linfinity-conv-test

incorrect handling of PetscMPIInt in prints, treated as if PetscInt

Commit-type: bug-fix, portability-fix
Reported-by: nightly tests

Merge branch 'master' into scott/ksp-ksp-tutorials

Merge branch 'barry/all-new-test-harness-branches'

filter atomic size from swarm output because it depends on size of PetscInt

Commit-type: portability-fix, testing-fix
Reported-by: nightly builds

swarm always requires real and double! Remove dead test example

use size for size, not freaking nproc or any random crap name you make up

Commit-type: testing-fix,style-fix
Reported-by: nightly te

swarm always requires real and double! Remove dead test example

use size for size, not freaking nproc or any random crap name you make up

Commit-type: testing-fix,style-fix
Reported-by: nightly tests

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Converted a directory over to the new test harness

Includes adding missing tests and fixing the incorrect formating of several examples source code

Commit-type: testing-fix,style-fix,example

Merge remote-tracking branch 'origin/stefano_zampini/fix-dmwswarm-includes-andothers'

DMSwarm: remove unneded inclusion of petsc.h that was triggering recompilation when any of petscts.h etc was modified

Merge branch 'dmay/swarm-pic-tools-v3.8'

Fix conflict in makefile when merging dmay/swam-pic-tools into master

Merge branch 'master' into knepley/feature-plex-sphere-mesh

* master: (2633 commits)
Bib: Added ref
SNES ex56: Update test output
add a citation to petsc.bib
Plex: Initialize variables
ini

Merge branch 'master' into knepley/feature-plex-sphere-mesh

* master: (2633 commits)
Bib: Added ref
SNES ex56: Update test output
add a citation to petsc.bib
Plex: Initialize variables
initialize ap as complained by the nightly tests
Plex ex3: Update to new point function API
initialize some variables as complained by nightly tests
SNES ex12: Mix misnaming Nf --> Nc
update tests
add tests
add MatView_SeqXAIJ_ASCII_structonly(); enable A->structure_only in MatSetValuesBlocked_SeqBAIJ
typo
fill-in some references
Bib: Fixed ref
Plex: Added PLY to file support
Plex: Adding PLY support
PetscDS: Turn off Fortran bindings for Constants
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
...

Conflicts:
config/builder.py
include/petscdmplex.h
src/dm/impls/plex/examples/tests/ex1.c
src/dm/impls/plex/plexcreate.c
src/dm/impls/plex/plexgmsh.c
src/snes/examples/tutorials/ex63.c

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DMSwarm event logging:
* Log events related to data movement between MPI-ranks

Merge branch 'master' into knepley/feature-plex-pragmatic-parallel

* master: (1379 commits)
Minor fixes for tchem examples due to changes in PETSc infrastructure
update webpage about API changes

Merge branch 'master' into knepley/feature-plex-pragmatic-parallel

* master: (1379 commits)
Minor fixes for tchem examples due to changes in PETSc infrastructure
update webpage about API changes
add help menu for MatCreateSubMatricesMPI()
rename struct Mat_SubMat -> Mat_SubSppt
add a little information to the manual about using tchem
rename MatCreateSubMatrixComposite -> MatCreateSubMatrixVirtual; Mat_SubMatrix -> Mat_SubVirtual
need to protect the \ passed on the makefile on my Mac
Bib: Updated ref
update src/mat/examples/tests/output/ex23_#.out
rename MatGetSubMat -> MatCreateSubMat
Mark MatCreateMPIAIJWithSplitArrays() and MatMPIAIJSetPreallocationCSR() with MAT_NO_OFF_PROC_ENTRIES
superlu: libray is installed in PREFIX/lib64 - fix this to use PREFIX/lib
backport fixes cc105cc3 2b35c90a - required for 3bf428d - that was backported from master - 80c96bb
'echo -n' fails on opensolaris/osx - so avoid using it.
fix diffs in nightlybuilds due to options in ~/.petscrc
add Kelley03 to src/docs/tex/petsc.bib
build: determine moudles, mpi.h used during buildtime and print in 'info'
fix analyzer warnings
fix build failure on opensolaris - where -lm from flibs is removed due to -lm in cxxlibs. But then - only flib gets used for some configure tests [blaslapack, parms]
config: prefer __restrict over C99 restrict keyword
...

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Merge branch 'barry/remove-funct'

Remove the use and definition of __FUNCT__ throughout the code

Since all modern C/C++ compilers provide this functionality we no longer need to provide it manually in PETSc
Time: 1.5 hours
Thanks-t

Remove the use and definition of __FUNCT__ throughout the code

Since all modern C/C++ compilers provide this functionality we no longer need to provide it manually in PETSc
Time: 1.5 hours
Thanks-to: Andreas Mang <andreas@ices.utexas.edu>

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Merge branch 'master' of bitbucket.org:petsc/petsc

analyzer fixes

Merge branch 'master' into tisaac/dmplex-feature-real-to-ref

I need updated PetscFE interfaces in what I'm going to do

* master: (603 commits)
parmetis: fix typo in testsuite
Added PETSC_HAVE_A

Merge branch 'master' into tisaac/dmplex-feature-real-to-ref

I need updated PetscFE interfaces in what I'm going to do

* master: (603 commits)
parmetis: fix typo in testsuite
Added PETSC_HAVE_ATTRIBUTEALIGNED flag to makefile
PCSetUp_SVD() used incorrect matrix for matrix size in parallel, also need to skip LAPACK call if matrix size is zero
strumpack: update to latest version 1.0.4
Remove valgrind warning about MPI_Allreduce() with uninitialized data
sed for test output that has atol convergence with quad precision
updated ex1_nest tests
fixed incorrect key value
fix: bad merge a69d34a
test: move runex78 to TESTEXAMPLES_C_NOTSINGLE
build: fix warnings
sys: update test to produce same result - irrespective of debug/opt build - and presence of ~/.petscrc
sys: src/sys/examples/tests/ex30.c -> src/sys/examples/tests/ex32.c to avoid conflict in master
Sed output, since quad precision reduces below atol on these tests
remove automatically generated matrix names from test output files since can be different
Fixes for MatMPIXXXSetPreallocation(), they were not reentrant, since they kept the information used for matrix-vector products
GAMG: fix PCView_GAMG() format - and update output/ex56_0.out
superlu_dist: 64-bit-indices fix https://github.com/xiaoyeli/superlu_dist/issues/4
Add SNESSetDivergenceTolerance / -snes_divergence_tolerance.
fixed unit read in Plex
...

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Merge branch 'stefano_zampini/feature-convert-matnest-matis' into stefano_zampini/feature-pcbddc-saddlepoint

I have to merge it here, since there's an API addition for MatIS in stefano_zampini/featu

Merge branch 'stefano_zampini/feature-convert-matnest-matis' into stefano_zampini/feature-pcbddc-saddlepoint

I have to merge it here, since there's an API addition for MatIS in stefano_zampini/feature-pcbddc-saddlepoint
that prevents me to smoothly merge stefano_zampini/feature-convert-matnest-matis into next.

This will also facilitate merging stefano_zampini/feature-pcbddc-saddlepoint into master

Conflicts:
src/docs/website/documentation/changes/dev.html

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Merge branch 'barry/fix-ignore-returns'

Merge branch 'dmay/dmswarm-fixes' into barry/fix-ignore-returns

Replaced Dave's (void) casting with the if () testing I had already added

DMSwarm - DataExchanger:
* Do not use SETERRQ as a one-liner statement inside {}