Merge branch 'master' into knepley/feature-dm-bc-components

* master: (320 commits)
fix compile warning: /sandbox/petsc/petsc.clone/src/snes/examples/tests/ex2.c:250:8: warning: ‘pointsAllProcs’ m

Merge branch 'master' into knepley/feature-dm-bc-components

* master: (320 commits)
fix compile warning: /sandbox/petsc/petsc.clone/src/snes/examples/tests/ex2.c:250:8: warning: ‘pointsAllProcs’ may be used uninitialized in this function [-Wmaybe-uninitialized] ierr = DMInterpolationSetUp(interpolator, dm, pointsAllProcs);CHKERRQ(ierr);
migrate 'build requires: !mpiuni' to new format
migrate 'build requires: !complex' to new format
workarround 'division by zero' compiler warning on windows C:\cygwin64\home\petsc\PETSC~3.CLO\src\ts\examples\TUTORI~1\ex11.c(416): warning #39: division by zero if (uL->h < 0 || uR->h < 0) {for (i=0; i<1+dim; i++) flux[i] = 0./0.; return;} /* SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Reconstructed thickness is negative"); */
dos2unix to prevent warnings on opensolaris "/export/home/petsc/petsc.clone/src/ksp/ksp/examples/tests/ex53.c", line 6: warning: invalid white space character in directive
fix output file - corresponding to code changes in efd4aadf157bf1ba2d80c2be092fcf4247860003
disable test on windows
update log from opensolaris so that the diff is clean on linux aswell
update grep in sync with change in efd4aadf157bf1ba2d80c2be092fcf4247860003
Fixed code that did not correctly set current color for block insertion
Update output files that did not get fixed after previous merges
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 out code
Always use (void) for functions that take no arguments, never ()
always need to caste PetscReal variables to (double) in print statements
updates to manual page for clarity
update help menu for MatRARt() -- MatRARt_mpiaij_mpiaij is supported now, but not efficient.
fix nightlybuild error with c1cbb1def3f8ddca04c3998b9c06618fd1ffef35 on arch-linux-IPL64 src/ksp/pc/examples/tests ex5_1
output has changed with e6d0a238963c2a97dd04845ea512b529992c7cdb so update the output file
...

show more ...

Merge remote-tracking branch 'origin/barry/consistent-formating-ascii-solver-viewers'

KSPFETIDP/PCBDDC: allow using a single matrix for deluxe when the change of basis context is of type QR

KSPFETIDP: use PCFIELDSPLIT for preconditioning

PCFETIDP: use single kernel for PCApply and PCApplyTranspose

MATFETIDP: use a single kernel for MatMult and MatMultTranspose

KSPFETIDP/PCBDDC: compute non-pde-harmonic Schur complement for deluxe if requested

KSPFETIDP: rename iP in iV as it should be, since they are velocity dofs

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

show more ...

KSPFETIDP/PCBDDC: allow using a single matrix for deluxe when the change of basis context is of type QR

Merge branch 'stefano_zampini/enhancements-fetidp-saddlepoint' into stefano_zampini/feature-fetidp-ex69

KSPFETIDP: use PCFIELDSPLIT for preconditioning

PCFETIDP: use single kernel for PCApply and PCApplyTranspose

MATFETIDP: use a single kernel for MatMult and MatMultTranspose

KSPFETIDP/PCBDDC: compute non-pde-harmonic Schur complement for deluxe if requested

KSPFETIDP: rename iP in iV as it should be, since they are velocity dofs

Merge branch 'knepley/fix-plex-example-logging' into knepley/feature-plex-torus

* knepley/fix-plex-example-logging: (151 commits)
Plex ex12: Added logging stages
Plex ex1: Added logging stages

Merge branch 'knepley/fix-plex-example-logging' into knepley/feature-plex-torus

* knepley/fix-plex-example-logging: (151 commits)
Plex ex12: Added logging stages
Plex ex1: Added logging stages
update to latest hypre tag on github
fix 'inf' vs 'Inf' diff wrt vec_vec_utils_tagger_tutorials-ex1_8,9,18,19
MatSetOption(mat,MAT_IGNORE_ZERO_ENTRIES,PETSC_TRUE) no longer applies to zero values set or added to the matrix diagonal, they are now not ignored and are included in the matrix nonzero structure. This is useful for Jacobians passed to TS.
replace use/mention of depreciated -log_summary in many places
add extchem.py which was written years ago but never put in the distribution (hence it is broken).
petsc4py: update to snapshot with MatGetSubMatrices -> MatCreateSubMatrices etc API changes
Minor fixes for tchem examples due to changes in PETSc infrastructure
update webpage about API changes
add help menu for MatCreateSubMatricesMPI()
PetscCMPLX: assume type punning is safe
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
...

Conflicts:
src/dm/impls/plex/examples/tests/ex1.c
src/dm/impls/plex/examples/tests/ex12.c

show more ...

Merge branch 'knepley/fix-plex-example-logging' into knepley/feature-plex-tests-new

* knepley/fix-plex-example-logging: (151 commits)
Plex ex12: Added logging stages
Plex ex1: Added logging stag

Merge branch 'knepley/fix-plex-example-logging' into knepley/feature-plex-tests-new

* knepley/fix-plex-example-logging: (151 commits)
Plex ex12: Added logging stages
Plex ex1: Added logging stages
update to latest hypre tag on github
fix 'inf' vs 'Inf' diff wrt vec_vec_utils_tagger_tutorials-ex1_8,9,18,19
MatSetOption(mat,MAT_IGNORE_ZERO_ENTRIES,PETSC_TRUE) no longer applies to zero values set or added to the matrix diagonal, they are now not ignored and are included in the matrix nonzero structure. This is useful for Jacobians passed to TS.
replace use/mention of depreciated -log_summary in many places
add extchem.py which was written years ago but never put in the distribution (hence it is broken).
petsc4py: update to snapshot with MatGetSubMatrices -> MatCreateSubMatrices etc API changes
Minor fixes for tchem examples due to changes in PETSc infrastructure
update webpage about API changes
add help menu for MatCreateSubMatricesMPI()
PetscCMPLX: assume type punning is safe
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
...

Conflicts:
src/dm/impls/plex/examples/tests/ex12.c

show more ...

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
...

show more ...

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

Merge remote-tracking branch 'origin/hzhang/rename_matgetsubmats'

rename MatGetSubMat -> MatCreateSubMat

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>

show more ...

Merge branch 'stefano_zampini/feature-pcbddc-saddlepoint'

Conflicts:
src/mat/impls/aij/mpi/mpiaij.c
src/mat/impls/is/matis.c

Modified ex23.c for the API change of the function CheckMat