Complete update to new PetscOptions interface

Begin renaming the PetscOptions objects for the future where PetscOptions will not be a singleton

Merge remote-tracking branch 'petsc/master' into fix-pcgasm-reuse

Merge branch 'master' into knepley/fix-examples-plex

* master: (112 commits)
correct expression for implict ODE/DAE in table 11 of users manual
remove warning about deprecated MPI call in exampl

Merge branch 'master' into knepley/fix-examples-plex

* master: (112 commits)
correct expression for implict ODE/DAE in table 11 of users manual
remove warning about deprecated MPI call in examples
rm variables declared in middle of subroutine
tolerance for equality in PETSc test should depend on machine epsilon
tolerance for acccuracy in test example should depend on machine epsilon
increase convergence tolerance to get same result in single precision as double for convergence history
update no change output for gasm test which had not been properly updated
remove C++ // comment
example mistakenly used MPI_COMM_WORLD as if it was rank in print statement thus producing output only with MPI Uni
grep out name of DM object since on some systems the address printed has extra zeros thus producing a false difference in output
increase tolerance for test example
build: revert el6-4 build to cg - as el6 compilers give link errors
fix error type
insure similar convergence history for single, double, quad
fix ex104.c based on Barry's suggestion
increase example convergence tolerance to get matching convergence history in single and double precision
increase convergence tolerance so that test example has similar convergence history in single and double precisions
changed from cg to gmres for eigenestimator since in single precision cg produced a possible indefinite matrix report
change test example tolerance to depend on machine epsilon so as to give correct results in various precisions
loosen convergence tolerance to have similar convergence history with single, double, quad precisions
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Merge branch 'master' into shri/add-tsevent-to-powergrid-examples

Merge branch 'master' into stefano_zampini/feature-pardiso-schur

Branch got out of sync with master

Merge branch 'barry/add-mpiu_allreduce'

We always start with petsc/master. Trying to fix a bug (submatrix reuse) reported by
Dmitry.
Merge remote-tracking branch 'petsc/master' into fix-pcgasm-reuse

Merge branch 'master' into pr263/PierreBdR/ts-domain-error-in-stage/master

Merge branch 'master' into barry/improve-git-download

Introduce MPIU_Allreduce() to detect cases where all processes that share an MPI comm do not call the same sequence of MPI_Allreduce()
This is a bug that can be difficult to track down.

Suggested-by

Introduce MPIU_Allreduce() to detect cases where all processes that share an MPI comm do not call the same sequence of MPI_Allreduce()
This is a bug that can be difficult to track down.

Suggested-by: Eric Chamberland <Eric.Chamberland@giref.ulaval.ca>
Suggested-by: Patrick Lacasse <placasse@giref.ulaval.ca>

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Split PetscViewerASCIISpinLock into three locks because it was used in nested functions leading to deadlock

Reported-by: Michele De Stefano <MStefano@slb.com>

added SAWs option -saws_port_auto_select to use the new SAWs_Get_Available_Port() to get a new unique port number
so that many PETSc SAWs programs can be running simultaniously. The URL to access SAW

added SAWs option -saws_port_auto_select to use the new SAWs_Get_Available_Port() to get a new unique port number
so that many PETSc SAWs programs can be running simultaniously. The URL to access SAWs is printed in PETSc initialize

Requested-by: Noemi Petra <npetra@ucmerced.edu>

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

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

Merge branch 'master' into tisaac/dmforest

Get 3.6.2 patches

* master: (1360 commits)
remove nasty memory leak with CUDA code when using block Jacobi with multiple blocks per process
print abs

Merge branch 'master' into tisaac/dmforest

Get 3.6.2 patches

* master: (1360 commits)
remove nasty memory leak with CUDA code when using block Jacobi with multiple blocks per process
print abs in Fortran test example in order to have same result with real and complex builds
changed outdate mpirun and -np to mpiexec and -n
force sqrt to be taken in the precision of PetscReal in fortran examples
continuation line too soon for some compilers
stop configure if user selected C++ clanguage, single precision, complex combination since we do not support it
fixes for Fortran examples to compile cleanly in single precision that do not involve complex numbers
fixes to Fortran examples to compile cleanly in single precision complex
fix previous mistake
must cast 1. to PetscScalar before dividing by a PetscScalar (C++ complex class is terrible)
must cast 0.0 to PetscScalar before comparison with a PetscScalar
changed order of suggested locations of downloadable PETSc to Barry's preference
Increase patchlevel to 3.6.2
remove debug print statement from two commits before
remove debug print statements I accidently left in the last commit
PetscDraw: Fix dummy definition of PetscDrawCollective{Begin|End}()
remove cleanupMumps flag from MatDestroy_Mumps() it should always free the memory it allocated Bug detected while adding features to libMesh
improved viewing of fractional counts in xml nested log viewing fixed bug in output of doubles to xml nested log files
chombo: build only libs - not examples
fix typo. 'gcc-4.8 --with-cxx-dialect=C++11' gives a warning with this line - even though its in a #ifdef thats never enabled.
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To add a space to all comments I have made before. Barry pointed out
that a comment without a space right after '/*' may cause bfort to crash

Merge remote-tracking branch 'petsc/master' into fixed-c

To add a space to all comments I have made before. Barry pointed out
that a comment without a space right after '/*' may cause bfort to crash

Merge remote-tracking branch 'petsc/master' into fixed-comment-space

Conflicts:
include/petsc/finclude/petscmat.h
include/petscmat.h
src/mat/examples/tests/makefile
src/mat/impls/aij/mpi/mpiaij.h

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Merge branch 'pr329/master/Fande-Kong/matpartitioning-hierarch' into pr361/master/Fande-Kong/pcgasm-increaseoverlap: need hierarch to build GASM subdomains.

Conflicts:
src/mat/examples/tests/makefi

Merge branch 'pr329/master/Fande-Kong/matpartitioning-hierarch' into pr361/master/Fande-Kong/pcgasm-increaseoverlap: need hierarch to build GASM subdomains.

Conflicts:
src/mat/examples/tests/makefile
src/mat/impls/aij/mpi/mpiaij.h

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Merge branch 'master' into knepley/feature-label-empty-stratum

* master: (151 commits)
moved PCTELESCOPE comment into users manual since no one will see the comment
message in makefile about hyp

Merge branch 'master' into knepley/feature-label-empty-stratum

* master: (151 commits)
moved PCTELESCOPE comment into users manual since no one will see the comment
message in makefile about hypre bugs causing test crashes
remove use of some unitialized variables, remove use of "dummy" entries in Vec and IS since Dave May thought they could not be of size zero. Now three telescope tests give no valgrind errors
code sent unitialized data via MPI and allocated too large space for creating indices
Force generateetags.py to use /usr/local/bin/ctags before using ctags because the ctags provided with Apple XCode gets confused by function usage in .tex files and does not make proper tags for TSSolve() and many many others
Optimized version of snes/examples/tutorials/ex1f.F produced incorrect results when lx_v() and lf_v() were declared as of dimension 1 with optimzed builds only. Cannot explain exactly why this happens but since we are using VecGetArray() from Fortran we are gambling with the compiler regardless
make the PetscRandom object used in GAMG to be a public object that can be controlled via the options database. This allows the same example to produce the same results with real and complex numbers by using the option -pc_gamg_random_no_imaginary_part
added parallel tester for examples. Crude but it reduces a basic alltests on my laptop from 25 minutes to 7 1/2 minutes.
remove unneccessary if
fix the problem for ex9 which involves multiple TSSolve calls
shortened the time of several test examples
decrease dramatically the time used by several test examples that take more than a minute on may machine with debug mode
Some of the vectors created in MatNullSpaceCreateRigidBody() were not normalized to 1
fix strange PCTelescope struct name of P which caused duplicate symbol error on some systems cleanup use of PetscMalloc and PetscFree for telescope for modern PETSc standards replace semiredundat to telescope in makefile that runs test examples
SNESUpdateCheckJacobian: make relative norm output syntactically correct
DMCompositeGetGlobalISs: document Fortran interface
fix warnings on bsd. Also fix usage of PetscFunctionBegin/Return
Making an even bigger mess, I cannot explain why this is not in the branch
hypre: update with "Bug fix for Parasails; src/ksp/ksp/examples/tutorials/ex10.c runex10_16"
decrease duration of ex22 by factor of 10 to decrease testing time
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Merge branch 'jed/mat-assembly-perf' of bitbucket:petsc/petsc

VecAssembly and MatAssembly now use a scalable exchange pattern based on
PetscCommBuildTwoSided. This feature can be controlled with th

Merge branch 'jed/mat-assembly-perf' of bitbucket:petsc/petsc

VecAssembly and MatAssembly now use a scalable exchange pattern based on
PetscCommBuildTwoSided. This feature can be controlled with the options

-vec_assembly_bts 0 or 1 (default 0)
-matstash_bts 0 or 1 (default 0)

The rationale is that the new implementation with scalable data
structures can be slightly slower than the old version at small process
counts. The default here could be changed to depend on the process
count (leading to possibly-confusing scaling performance diagnostics) or
the implementation could learn to take a fast path.

* 'jed/mat-assembly-perf' of bitbucket:petsc/petsc: (49 commits)
MatStash: fix -Wsign-compare by using size_t for loop index when max is also size_t
Sys BuildTwoSided test: fix for non-POD std::complex
MatStash: cast to satisfy non-structural MPI type tag check
mpiuni: fix compile error /sandbox/petsc/petsc.clone-2/arch-linux-uni/lib/libpetsc.so: undefined reference to `MPI_Type_create_resized'
Vec: Silence compiler warning
Vec: fix typo in comment
Sys: fix C89 compiler warning
VecStash BTS: fix block stash InsertMode accounting
VecStash BTS: fix indexing bug counting sends to rank 0
MatStash BTS: fix memory leak on MAT_SUBSET_OFF_PROC_ENTRIES
VecAssemblyEnd_MPI_BTS: fix donotstash code path
VecAssemblyEnd_MPI_BTS: fix C++ conversion to InsertMode
Sys: fix datatypes test using MPI_Type_create_resized
MatStash BTS: work around lack of offsetof() for non-POD (std::complex)
MatAssembly: move check for InsertMode consistency into MatStashScatter impls
MatStash BTS: fix memory leak on reassembly with MAT_SUBSET_OFF_PROC_ENTRIES
MatStash BTS: small simplification to row ownership calculation
MatStash BTS: add MAT_SUBSET_OFF_PROC_ENTRIES, impl with neighbor-only comm
MatStash: initial BTS (BuildTwoSided) implementation
MatStash: add extension point for new BTS implementation
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Merge branch 'master' into pr352/dmay/pctelescope/master

Merge branch 'master' into pr358/buptphyphy/addmatcreatenormalhermitian/master

Merge branch 'tisaac/dt-fix-geom-punning' into tisaac/plex-feature-tree-fv

Pull in a fix to FE geometry that affects the complex,64bit case

* tisaac/dt-fix-geom-punning: (240 commits)
Plex: fix t

Merge branch 'tisaac/dt-fix-geom-punning' into tisaac/plex-feature-tree-fv

Pull in a fix to FE geometry that affects the complex,64bit case

* tisaac/dt-fix-geom-punning: (240 commits)
Plex: fix type punning problem stuffing (PetscFECellGeom *) in a Vec
PGI compiler cannot handle [restrict] usage therefor disable restrict for PGI compiler Fix ex48.c to use PETSc standard way of marking restrict
PETSC_UNUSED must occur before the typename. With PGI compilers they error if it is after the type name
on solaris in TSAdaptChoose_Basic() negative root for zero could produce -infinity thus causing time step to be decreased even though the error estimate was zero
MatGetSchurComplement: revert test from LUMP back to DIAG and update output
there are no tests for opencl or viennacl so prevent warning message: make[2]: *** No rule to make target `testexamples_OPENCL', needed by `tree'. Stop. make[2]: *** No rule to make target `testexamples_VIENNACL', needed by `tree'. Stop.
incorrect initial conditions function that could produce floating point exception value (and does on windows) due to squareroot of non-negative number
forgot to fix rule for building ex194
move ex193.c to ex194 because someone else created a 193
remove outdate manual page comment
add missing VecRestoreArray()
add missing VecRestoreArray()
missing restore array in example
formating for print statements of test example with __float128 precision
fix example for __float128 precision by using PETSc math macros and casting PetscReal in print statements
remove Tao example custom monitor that produced different results for __float128 precision
all PETSc built in monitors require a valid PetscViewer, NULL is not acceptable
PETSc built in monitors always require viewers to be passed in, no longer support a NULL viewer
use tigher haptol for minres for quad precision because otherwise false positive of indefinite matrix appeared in example
check for PetscMPIInt overflow in ISAllGather()
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Merge branch 'master' into jed/process-options-handler

Merge branch 'tisaac/dmplex-stable-tet-refinement' into tisaac/plex-feature-tree-fv

This feature branch also changed the topology of nonconforming examples:
I am merging so that I can make the regre

Merge branch 'tisaac/dmplex-stable-tet-refinement' into tisaac/plex-feature-tree-fv

This feature branch also changed the topology of nonconforming examples:
I am merging so that I can make the regression output that should be
correct in master and next

* tisaac/dmplex-stable-tet-refinement: (594 commits)
plex: added tet shape regression test
plexrefine: remove replaced code
plex: update test output for new tet refinement order
plex: fix tet refinement for stable element shape
DMPlex: added test of shape quality to ex1
Better to use the proper error handling version of PetscViewerASCIIGetStdout() instead of PETSC_VIEWER_STDOUT_()
Generate a very useful error message if PetscLogView(), PetscLogEventGetPerfInfo() or PetscLogEventGetFlops() is called with a preceeding call to PetscLogBegin() and friends (also -log_summary which triggers a PetscLogBegin())
fix compile warnings
Plex: Fix bug with bcComps initialization
Turn off elemental shared libraries if --with-shared-libraries=0 is used
Bib: Added refs
Bib: Fixed a bunch of errors
add warning/error flag for '-mat_superlu_dist_parsymbfact' when MatInputMode=GLOBAL
makefile: fix format
tests: add back ex6f, runex6f targets - that got removed in 2f1d3d565a6a43067e6df75b043e6343b05fcd1d
accessing option that may never have been set
typo in DMNetworkSetNumVariables() reported by Sean Shahkarami
superlu_dist: update to using latest 4.1 version
fix compile warnings
Generate an error message when trying to overwrite default options of CN and BEULER
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Merge branch 'master' into barry/fix-petscviewer-attempt-2