Merge branch 'balay/mpiuni-namespace-fc'

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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mpiuni: namespace fortran interface and remove -with-mpiuni-fortran-binding option

Drawbacks:
- require cpp for fortran includes [so if user .f code uses mpif.h - this will break]
- cpp is case sens

mpiuni: namespace fortran interface and remove -with-mpiuni-fortran-binding option

Drawbacks:
- require cpp for fortran includes [so if user .f code uses mpif.h - this will break]
- cpp is case sensitive - currently providing mapping for MPI_Comm_rank(), MPI_COMM_RANK(), mpi_comm_rank() types

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Merge branch 'maint'

* maint:
mpiuni: c8d2b952 was incomplete wrt change to using MPIUNI_FORTRAN_BINDING
build: fix issue with --with-threadsafety --with-scalar-type=complex

mpiuni: c8d2b952 was incomplete wrt change to using MPIUNI_FORTRAN_BINDING

fixes the following error with --with-mpi=0 --with-mpiuni-fortran-binding=0

/home/balay/petsc/arch-uni/lib/libpetsc.so: un

mpiuni: c8d2b952 was incomplete wrt change to using MPIUNI_FORTRAN_BINDING

fixes the following error with --with-mpi=0 --with-mpiuni-fortran-binding=0

/home/balay/petsc/arch-uni/lib/libpetsc.so: undefined reference to `mpi_init_'

Reported-by: Barry Smith <bsmith@mcs.anl.gov>

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Merge branch 'master' into stefano_zampini/feature-pcbddc-saddlepoint

Conflicts:
src/docs/website/documentation/changes/dev.html
src/ksp/ksp/examples/tutorials/ex59.c
src/ksp/pc/impls/bddc/bddc.c

Merge branch 'master' into stefano_zampini/feature-pcbddc-saddlepoint

Conflicts:
src/docs/website/documentation/changes/dev.html
src/ksp/ksp/examples/tutorials/ex59.c
src/ksp/pc/impls/bddc/bddc.c
src/ksp/pc/impls/bddc/bddcfetidp.c
src/ksp/pc/impls/bddc/bddcprivate.c
src/ksp/pc/impls/bddc/bddcschurs.c
src/mat/impls/is/matis.c
src/mat/impls/is/matis.h

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Merge branch 'knepley/fix-vec-visibility' into knepley/feature-dm-point-location-failure

* knepley/fix-vec-visibility:
Vec: DuplicateVecs_Default and DestroyVecs_Default should be available to the

Merge branch 'knepley/fix-vec-visibility' into knepley/feature-dm-point-location-failure

* knepley/fix-vec-visibility:
Vec: DuplicateVecs_Default and DestroyVecs_Default should be available to the user - This is needed is IBAMR
Fix error in MPI-uni when creating additional MPI communicators did not properly mark them as active
OSX: fix .dmg create script to set PETSC_DIR Also fix paths to work on case sensitive file systems.
Configure: Fix pickling error This is still a problem since it reveals that something is not cleaning up correctly. Configure needs a global rewrite badly
Configure: Silence warning on test compile
Configure: Bump MPFR version
remove multiple the the constructs
cd src/benchmarks/steams should be: cd src/benchmarks/streams
missing seealso for NASM

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Merge branch 'maint'

Fix error in MPI-uni when creating additional MPI communicators did not properly mark them as active

This appear when using sequential MUMPS, which needed its own "dummy" communicator which we obtai

Fix error in MPI-uni when creating additional MPI communicators did not properly mark them as active

This appear when using sequential MUMPS, which needed its own "dummy" communicator which we obtained with our dummy MPI_Comm_dup()

Reported-by: William F Mitchell <william.mitchell@nist.gov>

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Merge branch 'master' into stefano_zampini/feature-pcbddc-saddlepoint

Merge branch 'master' into knepley/feature-plex-handle-func-failure

* master: (378 commits)
SNES ex5: Fix coordinate determination for empty subdomains
fixed petsc.bib entry
p4est: fix syntax

Merge branch 'master' into knepley/feature-plex-handle-func-failure

* 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 options on refined or coarsened meshes
Plex: Add info for grid hashing
Plex: Add logging in interpolator creation
Plex: Correct use of tabs in ASCII viewer
DM: Shorten long event name
Plex ex12: Create boundary label automatically at all levels of mesh hierarchy
Plex ex12: Change PetscViewerSetFormat --> PetscViewerPushFormat - Fix order of SetMode and SetFilename
Plex ex12: Change all functions to static
Since DMDA with periodic boundary conditions does support P0 interpolation remove checks that error out under those conditions
ascem-io.py and amanzi.py need to handle self.hdf5.include being None correctly
fix MPI Uni to recycle communicators so it won't run out like with the petsc4py tests also fix check for location of python shared library on mac to check all cases each time
Switch back to Sherry's version since she accepted by pull request
PetscDraw: Update help messages for -draw_save* options
...

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

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Merged petsc/petsc into master

fix MPI Uni to recycle communicators so it won't run out like with the petsc4py tests
also fix check for location of python shared library on mac to check all cases each time

Reported-by: Lisandro D

fix MPI Uni to recycle communicators so it won't run out like with the petsc4py tests
also fix check for location of python shared library on mac to check all cases each time

Reported-by: Lisandro Dalcin <dalcinl@gmail.com>

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Merge branch 'master' into stefano_zampini/feature-pcbddc-saddlepoint

Conflicts:
src/ksp/pc/impls/bddc/bddc.c
src/ksp/pc/impls/bddc/bddcgraph.c
src/ksp/pc/impls/bddc/bddcprivate.c
src/ksp/pc/imp

Merge branch 'master' into stefano_zampini/feature-pcbddc-saddlepoint

Conflicts:
src/ksp/pc/impls/bddc/bddc.c
src/ksp/pc/impls/bddc/bddcgraph.c
src/ksp/pc/impls/bddc/bddcprivate.c
src/ksp/pc/impls/bddc/bddcscalingbasic.c
src/ksp/pc/impls/bddc/bddcschurs.c
src/mat/impls/is/matis.c

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Merge branch 'tisaac/dmforest' of bitbucket.org:petsc/petsc into tisaac/dmforest

Merge branch 'master' into tisaac/dmforest

* master: (136 commits)
Make error message specific to exactly what matrix is supported
Prevent fblaslapack or f2cblaslapack from being compiled with t

Merge branch 'master' into tisaac/dmforest

* master: (136 commits)
Make error message specific to exactly what matrix is supported
Prevent fblaslapack or f2cblaslapack from being compiled with the -no-prec-dev Intel compiler option since it can produce incorrect results
Fix for PCReset_HYPRE to make it reentrant.
replace default superlu_dist '-mat_superlu_dist_colperm METIS_AT_PLUS_A' with MMD_ATA to avoid different random numbers for nightly tests
fixes for merge from maint patch
Added PCReset_HYPRE() so it may be used with SNESVI solvers
remove Microsoft compiler message for paste macros used for handling Blas/Lapack macro name mangling for example
Increase the number of PetscViewerPushFormat() possible to 25 and use a macro PETSCVIEWERFORMATPUSHESMAX for the value
Configure: Remove redundant logging
Bib: Added ref
nightlybuids: fix permissions of script
MatRegisterDestroy() does not exist but it is listed in manual pages
externalpackages-git: save local changes if any - in git stash - before 'git checkout -f' Useful incase --with-package-commit=HEAD option was msissing [perhaps due to a typo]
nightlybuilds: add xsdk builds
Add architectures for testing xsdk package downloads (Trilinos, Hypre, SuperLU)
create another version of TurnForward() for adaptive time stepping specifically
Configure: Give proper default if HOME is missing from the environment
fix abbreviation
allow zeropivot for MatSOR_SeqAIJ_Inode, node size=1
add test case using adpative time stepping for checkpointing type 'NONE'
...

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Merge branch 'maint'

Merge branch 'balay/to-maint-add-mpiuni_mpi_in_place' into maint

mpiuni: do not build somempifort.F when configured with -with-mpiuni-fortran-binding=0

[switch to using MPIUNI_FORTRAN_BINDING instead of MPIUNI_AVOID_MPI_NAMESPACE
to be consistant with the option

mpiuni: do not build somempifort.F when configured with -with-mpiuni-fortran-binding=0

[switch to using MPIUNI_FORTRAN_BINDING instead of MPIUNI_AVOID_MPI_NAMESPACE
to be consistant with the option -with-mpiuni-fortran-binding - and to be
able to selectively build somempifort.F]

Reported-by: Dominic Meiser <dmeiser@txcorp.com>

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Merge branch 'master' into tisaac/dmforest

* master: (177 commits)
DT ex3: The test should check the number of digits requested
DT ex3: One test fails in single precision
Plex: Do not automati

Merge branch 'master' into tisaac/dmforest

* master: (177 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 matrix factorization fails
replacing SETERRQ with error output info and continue execution
SNES ex12: Added parallel tests - These test parallel, unstructured interpolation/restriction using FAS
Plex+SNES: Now in DMPlexComputeJacobian_Internal(), we also form the Jacobian preconditioner matrix
FE: Now we can form either the Jacobian or the Jacobian preconditioned matrix using a flag
DS: Now have point wise function slots for the Jacobian preconditioned matrix - This will allow us to form the "right" operator for preconditioning, like M in the (2,2) block for Stokes
Plex: When swapping Plexes, also swap point SF
Plex: Fix parallel error in Injector
Mat+Plex: Added MatPreallocator which can be called with MatSetValues() and preallocates another Mat - This could have been another "mode" of Mat, but I thought this was cleaner - Use MatPreallocator to preallocator Plex interpolators
DT ex3: Change tolerance and eliminate tests which need MPFR from regular runs
superlu: fix complex build
superlu: update to using 5.0 tarball with the fix for -Werror=format-security
superlu: update to use tarball with -Werror=format-security fix
DM: Clone the coordinate DM instead of reusing in Clone()
...

Conflicts:
config/builder.py
src/dm/impls/plex/plexcreate.c

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Merge branch 'master' into hongzh/checkpointing

Manual merges for a couple of PetscOptions changes in master

Merge branch 'master' into pr391/zianekhodja/lilia/tsirm/master

Merge branch 'master' into knepley/fix-plex-general-interp

* master:
snesvi should only use DM to compute bounds if it can compute bounds fixes for shashi example, converges to some degree with rs

Merge branch 'master' into knepley/fix-plex-general-interp

* master:
snesvi should only use DM to compute bounds if it can compute bounds fixes for shashi example, converges to some degree with rs method
declare everything in example
nontrivial nonlinear problem arising from reaction
Bib: Many more refs
fix maximum number of iterations in test example to produce similar convergence history with double and __float128 precision
mpiuni: fix build with --with-mpi=0 --with-fc=0

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

Merge branch 'maint'