Fix docs for SNESNCG, add NCG linesearch that was in the code and not connected, call SNESSetFromOptions() on NPC

Commit-type: feature, documentation

Merge branch 'dalcinl/fix-snes_test_jacobian' [PR #1898]

* dalcinl/fix-snes_test_jacobian:
SNES: Fixes to SNESTestJacobian()

Merge branch 'dalcinl/fix-headers' [PR #1897]

* dalcinl/fix-headers:
Minor fixes to headers.

SNES: Fixes to SNESTestJacobian()

* Propagate block sizes to work matrices, otherwise MatAYPX() fails
* Fix MATMPIBAIJ -> MATMPISBAIJ in matrix type list
* Use MatGetType() in favor of `((PetscObjec

SNES: Fixes to SNESTestJacobian()

* Propagate block sizes to work matrices, otherwise MatAYPX() fails
* Fix MATMPIBAIJ -> MATMPISBAIJ in matrix type list
* Use MatGetType() in favor of `((PetscObject)A)->type_name`

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Fix a bunch of PetscValidPointer() -> PetscValidXXXPointer()

Merge branch 'gropp/doc-fixes-1' [PR #1838]

Merge branch 'barry/no-batch-script'

No more batch submission script; this is all due to a very smart idea of Lisandro Dalcin

*) removed or fixed all remaining --know-xx options that required a batch submission script
*) removed all de

No more batch submission script; this is all due to a very smart idea of Lisandro Dalcin

*) removed or fixed all remaining --know-xx options that required a batch submission script
*) removed all details of --known-size-- that are no longer needed
*) cleaned up BAIJMKL source code, made it work with the rest of PETSc and removed is
dependence on a batch submission script, added test case for BAIJMKL
*) update the installation guide on batsch submissions and OpenMP
*) print MKL version, print OpenMP usage with mkl_sparse options

Commit-type: bug-fix, portability-fix, style-fix, feature, documentation, example
Thanks-to: Lisandro Dalcin <dalcinl@gmail.com>

$ ./configure --with-batch
===============================================================================
Configuring PETSc to compile on your system
===============================================================================
=============================================================================== ***** WARNING: Cannot determine if MPI_INT64_T works on your system in batch-mode! Assuming it does work. Run with --known-mpi-int64_t=0 if you know it does not work (very unlikely). Run with --known-mpi-int64_t=1 to remove this warning message. warning message ***** =============================================================================== =============================================================================== ***** WARNING: Cannot determine if MPI_C_DOUBLE_COMPLEX works on your system in batch-mode! Assuming it does work. Run with --known-mpi-c-double-complex=0 if you know it does not work (very unlikely). Run with --known-mpi-c-double-complex=1 to remove this warning message. warning message ***** =============================================================================== =============================================================================== ***** WARNING: Cannot verify that MPI is a shared library - in batch-mode! If MPI is a static library but linked into multiple shared libraries that the application uses, sometimes compiles work - but one might get run-time errors. If you know that the MPI library is shared - run with --known-mpi-shared-libraries=1 option to remove this warning message ***** =============================================================================== =============================================================================== ***** WARNING: Cannot determine if BLAS/LAPACK uses 32 bit or 64 bit integers in batch-mode! Assuming 32 bit integers. Run with --known-64-bit-blas-indices if you know they are 64 bit. Run with --known-64-bit-blas-indices=0 to remove this warning message. warning message ***** ===============================================================================

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Merge from doc-fixes branch

Fixes for doctext update

Merged in barry/optimize-aij-da (pull request #1762)

Non-numeric optimizations focused on AIJ, MatFDColoring, and DMCreateMatrix_DA_*AIJ, looking to improve performance in GPU environments

Non-numeric optimizations focused on AIJ, MatFDColoring, and DMCreateMatrix_DA_*AIJ, looking to improve performance in GPU environments

1) PetscCalloc*() now uses system calloc()
2) Merged some Pets

Non-numeric optimizations focused on AIJ, MatFDColoring, and DMCreateMatrix_DA_*AIJ, looking to improve performance in GPU environments

1) PetscCalloc*() now uses system calloc()
2) Merged some PetscMalloc*()
3) Eliminated unneeded PetscCalloc*()
4) Removed some memory allocations and copies in MatFDColoringSetUp(), added local variables for better compiler optimization
5) Added MatSetValues_SeqAIJ_SortedFull(), added MatSetOption(MAT_SORTED_FULL)
6) Optimized DMCreateMatrix_DA_*AIJ for nonperiodic case to automatically have sorted columns (faster MatSetValues() times)
7) Eliminated call to PetscMemzero() in PetscFree()

Commit-type: style-fix, feature

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Merge remote-tracking branch 'origin/barry/add-petscarrayxxx-ops' [PR #1771]

Remove dead Matlab code, fix typo, fix caste needed for const free

Commit-type: portability-fix
Reported-by: Satish Balay <balay@mcs.anl.gov>

Add PetscArraycmp(), PetscArraycpy(), PetscArrayzero(), PetscArraymove(), update code to use new forms

Replace a couple multi-mallocs with a single malloc
Replace backwards loops in MatSetValues_*()

Add PetscArraycmp(), PetscArraycpy(), PetscArrayzero(), PetscArraymove(), update code to use new forms

Replace a couple multi-mallocs with a single malloc
Replace backwards loops in MatSetValues_*() with PetscArraymove()

Commit-type: style-fix, feature

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Merged in barry/update-collective-on (pull request #1744)

Update the use of Collective on in the manual pages to reflect the new style

Merged in knepley/feature-dualspace-bdm (pull request #1699)

Knepley/feature dualspace bdm

Update the use of Collective on in the manual pages to reflect the new style

Commit-type: style-fix, documentation
Thanks-to: Patrick Sanan <patrick.sanan@gmail.com>

Merged in knepley/fix-snes-test (pull request #1734)

SNES: Allow SNESTestJacobian() to function without calling SNESSolve()

Approved-by: BarryFSmith <bsmith@mcs.anl.gov>

SNES: Allow SNESTestJacobian() to function without calling SNESSolve()

Merged in psanan/man-pages-remove-keywords (pull request #1717)

Man pages: Remove .keywords fields

Approved-by: BarryFSmith <bsmith@mcs.anl.gov>

Man pages: remove .keywords: fields

This field is recognized by doctext from Sowing (http://wgropp.cs.illinois.edu/projects/software/sowing/doctext/node20.htm#Node20),
but it doesn't seem to be unif

Man pages: remove .keywords: fields

This field is recognized by doctext from Sowing (http://wgropp.cs.illinois.edu/projects/software/sowing/doctext/node20.htm#Node20),
but it doesn't seem to be uniformly used or maintained.

Thus, remove all .keywords: fields, and a following blank line, if present.

This is accomplished with GNU sed (gsed on OS X), with the following commands.
*Warning* that this type of command can corrupt a .git directory,
so be cautious in reusing or modifying these commands. They first look
for and delete matching lines with a following line consisting of only whitespace,
and then delete any remaining matching lines.

find src/ -type f -exec gsed -i '/keywords:/ {N; /\n\s*$/d}' {} +
find src/ -type f -exec gsed -i '/keywords:/d' {} +
find include/ -type f -exec gsed -i '/keywords:/ {N; /\n\s*$/d}' {} +
find include/ -type f -exec gsed -i '/keywords:/d' {} +

Hints on the sed command obtained from: https://unix.stackexchange.com/questions/100754/how-to-delete-a-specific-line-and-the-following-blank-line-using-gnu-sed

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SNES: Initialize memory

Merged in barry/log-memory (pull request #1677)

Introduce logging of memory usage to the PETSc event logging infrastructure.

Introduce logging of memory usage to the PETSc event logging infrastructure.

The logging can be turned on and viewed with the options -log_view -log_view_memory

The logging requires the use of the

Introduce logging of memory usage to the PETSc event logging infrastructure.

The logging can be turned on and viewed with the options -log_view -log_view_memory

The logging requires the use of the PETSc malloc so may slow the runs slightly but since it is not
doing error checking of the memory it should not slow down the computations significently.

Four pieces of information about memory are logged and display in four additional columns in the table.
They are documented in the output above the table. Each column provides a particular "view" of the
memory usage in the event and they complement each other.

This should make it much easier for developers focusing on memory usage in their implementations
to understand the usage in the code, where the memory is being utilized, how it scales with problem size and number of processes etc.

Commit-type: feature

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