Merged in psanan/petsc/psanan/refs-2016-9 (pull request #562)

Man page and reference updates for KSPPIPEFGMRES, KSPPIPEGCR, KSPPIPEFCG, PCTELESCOPE

PCTelescope: add citation

Merge branch 'tisaac/sys-fix-realloc' into tisaac/petscfe-matching-quadrature-order

* tisaac/sys-fix-realloc: (71 commits)
Sys: fix PetscTrReallocDefault() and PetscReallocAlign()
clearify when

Merge branch 'tisaac/sys-fix-realloc' into tisaac/petscfe-matching-quadrature-order

* tisaac/sys-fix-realloc: (71 commits)
Sys: fix PetscTrReallocDefault() and PetscReallocAlign()
clearify when MatMkl_CPardisoSetCntl() can be used in the manual pages
Fixed manual page for -snes_anderson_beta
Update zfftf.c
remove Hermitian information from output since it is only produced in complex case and thus produces different test output
fixes for 64 bit integers in test example, fix uninitialized variable in test example
tests: move runex49 to TESTEXAMPLES_C_NOTSINGLE
add a PCView_SVD to show parameters
-petscpartitioner_type simple was not being picked up by options thus generating test error
missing CHKERRQ(ierr) on PetscPrintf() statements in newly added test example
PetscViewerVTK: Move DM reference increment into the VTK viewer and out of the DM implementation, as suggested by Jed Brown
missing crosslinks between manual pages
Updated 3.7 release notes to clearly indicate how to update usage of KSP/SNES/TS/SetMonitor(xxx,XXXMonitorDefault,NULL,NULL);
Fix for commit b6480e041dd2293a65f96222772d68cdb4ed6306 that broke this example
Example of factorization of a singular matrix may actually work due to round off
removed unused variables
matshell: clean up and add some new MATOPs to Fortran.
Remove unneeded checks for use of the compressed row for diagonal block of matrices in GAMG
ptscotch: update to version 6.0.4
ptscotch: fix buggy pthread detection code on Mac/Linux
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Merge branch 'pr508/psanan/psanan/pc-telescope-nearnullspace/master'

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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PCTelescope: refactor nullspace propagation

PCTelescope: fix memory leak by adding missing MatNullSpaceDestroy() calls

PCTelescope: update nullspace support

Allow for propagation of near nullspaces as well as nullspaces.

Throw an error if the user attempts to propagate remove functions or contexts this way.

Merge branch 'balay/fix-PetscInt-scanf/maint' into knepley/feature-plex-particle-example

This merge is done to be able to use 'PetscInt_FMT' in data_bucket.c

Merge branch 'maint'

Fixed a variety of issues related to iOS builds

Some developers did not properly use relative paths for private include files
file that is not normally compiled had errors due to outdated API in it

Fixed a variety of issues related to iOS builds

Some developers did not properly use relative paths for private include files
file that is not normally compiled had errors due to outdated API in it (why is it compiled with iOS?)
some iOS build scripts had outdated paths for various items
iSO version of makeall implicitly assumed PETSC_DIR had been set (OSX version previously fixed by Satish Balay)

Reported-by: Francisco Schuetze <fjschuetze@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/bddcprivate.c
src/mat/impls/aij/seq/mkl_pardiso/mkl_pardiso.c

Merge branch 'master' into barral/feature-dmplex-adapt

Merge branch 'master' into knepley/feature-parallel-mesh-load

* master: (59 commits)
Increase patchlevel to 3.7.1
Fix manual page for MatGetTransposeNullSpace()
remove unneeded use of PetscCon

Merge branch 'master' into knepley/feature-parallel-mesh-load

* master: (59 commits)
Increase patchlevel to 3.7.1
Fix manual page for MatGetTransposeNullSpace()
remove unneeded use of PetscContainer to hold iscoloring in SNESComputeNGSDefaultSecant()
added SNESView for ngs, added options database to ngs manual page, removed dead routine
gcov: enable in mpiuni test
incorrect capitalization of an even name
force same number of iterations for output of ml example
changed output for ml example to not be machine dependent
DMP4est: access data after setup
SNESLineSearch_Apply was labeled with PETSC_EXTERN in one place but when declared this was not visible hence library build failed under Microsoft.
Example had print statements of complex numbers
Fix more errors in agmres for 64 bit integers
builds: fix nampespase conflict with 'analyzer-buid' and checkBuilds.py
gcov: add more packages to test
add a couple of KSP that were not represented in testing
gcov: enable more externalpackages for this test
fixes for agmres for 64 bit indices, fix for findvisibleprivatefunctions to be portable for Mac and Linux
get GAMG to get null space (more)
fix c++ compile errors
Add test example for kacmarz preconditioner since gcov indicated there was NONE
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Merge branch 'master' of bitbucket.org:petsc/petsc into mark/gamg-nullspacefix

Merge branch 'maint'

Merge branch 'dmay/telescope-nullspace-fix' into maint

PCTelescope:
* Corrected bug fix and should hopefully also make the static analyser happy

PCTelescope:
* Bug fixes for nullspace

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

Merge branch 'pr426/dmay/dmay/pctelescope-mods/master'

PCTelescope - fix for static analysis warnings:
* I think that this commit will remove the last warning about indexing a null pointer

PCTelescope - Fixes reported by static analysis:
* Initialize variables which are otherwise set inside if (isActiveRank(sred->psubcomm)){} statements

Merge branch 'tisaac/sf-fix-multi-sf-leaves' into tisaac/dmp4est-feature-injection

* tisaac/sf-fix-multi-sf-leaves: (174 commits)
PetscSF: fix PetscSFGetMultiSF() for sparse leaves
PetscSF: make

Merge branch 'tisaac/sf-fix-multi-sf-leaves' into tisaac/dmp4est-feature-injection

* tisaac/sf-fix-multi-sf-leaves: (174 commits)
PetscSF: fix PetscSFGetMultiSF() for sparse leaves
PetscSF: make regression test that fails
few more clang static analyzer fixes
many issues detected by clang static analyzer
Update hypre to its release version
Updates for xSDKTrilinos builds
Added --download-xsdktrilinos
Communicator passed to VecCreateSeq should be PETSC_COMM_SELF
PCMG man page: fix typo in options name
Bib: Added refs
DMLabel: Removed unused variable
Metis tries to use backtrace which requires -lexecinfo on some systems such as freebsd Remove -lexecinfo from freebsd configure files since it is only needed by metis
add alternative output that occurs on some systems due to use of random number generator in partitioner
Plex: When creating cohesive submeshes, fix memory leak
Plex ex11: Updated output for new distribution algorithm
Plex: When explicitly distributing the depth label, we must recreate empty strata
Plex: When partitioning, the cell numbering should include hybrid points
Plex: Allow cell and vertex numberings to include hybrid points
need to show diffs of ex22 if it fails
Support two different output for test example, since due to roundoff this example can produce slightly different convergence history
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Merge branch 'master' into sanderarens/fix-plex-neumann-bc

* master: (28 commits)
few more clang static analyzer fixes
many issues detected by clang static analyzer
Update hypre to its release

Merge branch 'master' into sanderarens/fix-plex-neumann-bc

* master: (28 commits)
few more clang static analyzer fixes
many issues detected by clang static analyzer
Update hypre to its release version
Updates for xSDKTrilinos builds
Added --download-xsdktrilinos
DMLabel: Removed unused variable
Plex: When creating cohesive submeshes, fix memory leak
Plex ex11: Updated output for new distribution algorithm
Plex: When explicitly distributing the depth label, we must recreate empty strata
Plex: When partitioning, the cell numbering should include hybrid points
Plex: Allow cell and vertex numberings to include hybrid points
Plex ex1: Fixed output for empty strata
DMLabel: Added DMLabelHasStratum()
Minor changes and fix to bugs introduced in 82f73ecaa
Modified makefile to fix aijcusparse tests
Add missing code for the case PETSC_HAVE_VECCUDA
Fix bugs introduced in 82f73ecaa
Use VECCUDA with MATAIJCUSPARSE
CUDA: Fixed visibility and disabled Fortran bindings for VecScatters on GPU.
Replace kernels with thrust
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