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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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.

To refactor the comments to follow petsc style.

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

Conflicts:
include/petsc/finclude/petscmat.h
src/mat/examples/tests/makefile

To refactor the comments to follow petsc style.

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

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

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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 'pr361/master/Fande-Kong/pcgasm-increaseoverlap'

Conflicts:
src/contrib/nightlysummary/runhtml.py
src/mat/examples/tests/makefile

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 'master' into mark/eigen-rand

Error in MatGetSubMatrix_MPIAIJ() MatGetOwnershipRangeColumn() final argument is one plus last location not the length

Reported-by: Danqing Wu <wuda@mcs.anl.gov>

Merge branch 'master' into tisaac/plex-feature-tree-fv

Merge in Barry's fix to synchonized print out of plex objects into
updated output files.

* master: (31 commits)
fix %nd for plex printf that

Merge branch 'master' into tisaac/plex-feature-tree-fv

Merge in Barry's fix to synchonized print out of plex objects into
updated output files.

* master: (31 commits)
fix %nd for plex printf that should be %nD
PGI compiler requires cast to char* of this array for some reason
Incorrect use of %d for %D in viewing of PetscSection
update output for suitesparse examples with new KSP view data
changed boomeramg advanced smoother output files to use short format so there are less differences with different systems
fix some issues with PetscViewerFlush() and PetscViewerASCIIPushSynchronized() within the plex object viewing
incorrectly used stride value instead of local size in check that ISSTRIDE has same layout as columns of matrix
try using int(w) for Fortran case to integer instead of int(w,integer) since the latter failed on most systems claiming integer was not a constant. Very unclear to me what that second argument is suppose to be
SNES function evaluations were not counted for certain Jacobian computations
nightlybuilds: fix vec/ex7,ex7f link issue by using the correct LIBS option
nightlybuilds: move location of petsc.clone(s) on bb44 from nfs to /sandbox
nightlybuilds: arch-linux-complex-gcov -> arch-linux-cmplx-gcov to be consistant with other config tests
add __float128 data file neeed by test example 10 otherwise test example crashes with --with-precision=__float128 builds
cast fortran integer that may be 64bit with int() to prevent compiler warning about Warning: Possible change of value in conversion from INTEGER(8) to INTEGER(4) at (1)
removed unneeded definition of Sqr in example since PetscSqr should be used, and was in other parts of the same example!
nightlybuilds: run 'git gc' in the build clones
opensolaris: use 'FFLAGS=-ftrap=%none' this way fortran examples on solaris do not crash in lapack during 'div by zero' Also use the updated path to mpich
when I swapped the role of coulping and rest in fieldsplit I missed a place
cannot use PetscMalloc2() on arrays that will be freed as two seperate arrays
C++ cannot handle [PETSC_RESTRICT]
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Merge branch 'master' into mark/eigen-rand

incorrectly used stride value instead of local size in check that ISSTRIDE has same layout as columns of matrix

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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check for PetscMPIInt overflow in ISAllGather()

Though this routine is not scalable it is used in multiple places in PETSc and maybe used
on problems large enough to produce overflow of PetscMPIInt(

check for PetscMPIInt overflow in ISAllGather()

Though this routine is not scalable it is used in multiple places in PETSc and maybe used
on problems large enough to produce overflow of PetscMPIInt() when running with 64 bit PETSc integers.

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made MatGetSubMatrix_MPIAIJ scalable if one is requesting certain rows and ALL columns
This is useful for some fieldsplit preconditioners, for example in Xolotl

Merge branch 'master' into barry/fix-petscviewer-attempt-2

Merge branch 'knepley/remove-pbgl'

* knepley/remove-pbgl:
Mat: Removed PBGL

Merge branch 'barry/fix-matshift/maint'

Merging with Barry's refactor of PetscViewerGetSubComm

Merge branch 'barry/fix-petscviewer-attempt-2' into dmay/pcsemiredundant

Merge branch 'barry/fix-nonew-notcollective/maint' into jed/mat-assembly-perf

Jed this fucking 6+ month running thing in next that is not in master is a royal fucking pain in the ass and
an abuse of

Merge branch 'barry/fix-nonew-notcollective/maint' into jed/mat-assembly-perf

Jed this fucking 6+ month running thing in next that is not in master is a royal fucking pain in the ass and
an abuse of git. I think it is not justified to ever have anything in next for more than a few weeks at most.
Either take it out of next if it is broken or put it in master if it is not broken. Hanging around in next but
not master for ever is not a good policy.

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