BRGN: finished tomography test, passed with three test cases: l1dict, l2prox, user (2-norm regularizer ||x||^2)

Both tomography and cs1 examples work with both l2prox and l1dict

algorithm structure changes to combine old L2 reg with new L1 reg, and permit user regularizers

added bounded constraint, non-negative x

Tomography example works: Consolidated A,b, xGT into one file (was three files).

read from binary Mat/Vec, eliminate the array datastructure, works for a small example now!

adding tomography L1 reconstruction example, done for generating data in matlab and convert to petsc binary format, todo read data and test reconstruction

added D matrix for L1 norm

cleared comments of matrix vector dimension, and targeted problem to solve

fixed the initialize x, added template for inserting D matrix

the compressive sensing (sparse regression) test example works with brgn of the smoothed L1 form

debug cs1 with intermediate output

add compressive sensing test example cs1.c

tao-brgn add feature smoothed L1 norm algorithm, after meeting with Todd

brgn modified with approximation of L1 regularizer

Merge branch 'denera/tao-brgn-matlab-segfault-fix' [PR #1184]

* denera/tao-brgn-matlab-segfault-fix:
MATLAB Leastsquares examples segfault fix for BRGN.
Trust region initialization was producing a s

Merge branch 'denera/tao-brgn-matlab-segfault-fix' [PR #1184]

* denera/tao-brgn-matlab-segfault-fix:
MATLAB Leastsquares examples segfault fix for BRGN.
Trust region initialization was producing a segfault on MatMult with the Jacobian.

Evaluating the Jacobian in MATLAB using a SEQAIJ PETSc type, but then converting it to SEQDENSE before using it in Tao operations resolved the problem.

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adding the matlab test to the automated test suite

TaoCreate_XYZ() docstring updates

Change CHKERRQ(ierr) after PetscInitialize() calls in examples to if (ierr) return ierr;

Since the PETSc initialization may not have been completed in the failed PetscInitialize() it is not
propper

Change CHKERRQ(ierr) after PetscInitialize() calls in examples to if (ierr) return ierr;

Since the PETSc initialization may not have been completed in the failed PetscInitialize() it is not
propper to call the PETSc error handling routines

Commit-type: bug-fix, testing-fix, example
Reported-by: jed Brown <jed@jedbrown.org>

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Merge branch 'master' into knepley/feature-multiple-ds

* master: (156 commits)
Added missing CHKERRQ()
KSP ex56: Added alt output file for ex56_2.
Revert "KSP ex56: Updated test output and dom

Merge branch 'master' into knepley/feature-multiple-ds

* master: (156 commits)
Added missing CHKERRQ()
KSP ex56: Added alt output file for ex56_2.
Revert "KSP ex56: Updated test output and domain size for test _2."
DMStag tutorial ex4: fix stencil errors
Hierarchical partitioner: added an alt output file
Add support for DMGetMatrix() with periodic boundary conditions in one dimension for DMDA.
Fixed incorrect 'ntext' argument in PetscOptionsEList call in SNES ex12.c
ISCreateSubIS: Initialize variables owner and lidx to avoid compiler warnings
metis: provide -download-metis-use-doubleprecision option
KSP ex56: Updated test output and domain size for test _2.
Hierarchical partitioner: add a bit documentation
ISCreateSubIS: Added checkers for parameters
Added a test for hierarchical partitioning vertex weights
Plex+Doc: Document options for DMPlexCreateBoxMesh()
Hierarchical partitioner supports vertex weights
Create an API ISCreateSubIS that extracts
Add an alt output file
Plex: Can now give bounds to DMPlexCreateBoxMesh() from options - Use -dm_plex_box_lower and dm_plex_box_upper
PCMG: These methods should be optional
PCMG: Make PCMGGet/SetLevels() proper member functions - Also need to compose them in GAMG
...

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

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Tao ex3: Updated to new interface

DM+DS: Reorganized DS handling completely do that multiple regions can be supported
- A region is labeled portion of the mesh which has the same approximation space for the solution. Note that this i

DM+DS: Reorganized DS handling completely do that multiple regions can be supported
- A region is labeled portion of the mesh which has the same approximation space for the solution. Note that this is NOT the same as the label indicating the support of a field. Regions are the refinement of the field supports into unique approximation space pieces. Right now, we only support a single strategy, namely one space on the regular mesh and one on the hybrid cells, but we only have to change DMCreateDS() to extend the capability.
- Now instead of using PetscDSSetDiscretization() and DMSetDS(), you use DMSetField() and DMCreateDS(). Also, you now must use DMCopyDisc(), instead of DMSetDS(), which copies both the field and DS structure to another DM. These changes have been made in all examples.
- DMGetCellDS() returns the approximation space for that cell
- DMGetDS() return the default space since most people will not use regions. There is still a lot of work left t generalize all methods to multiple DSes, but all old code still functions.
- DMGetRegion/RegionNumDS() gets spaces by label and region number
- DMCreateDS() is the setup method which makes the regions and corresponding DSes. With some work, this could be converted to a lazy initialization.
- Cleaned up access to DS since now we can have more than one
- Projection was improved to extract the DS for the particular cells it is iterating over
- The DS are set from options during Section creation. The idea is that people using DS would also use automatic Section creation, or they would manage things themselves and call SetFromOptions manually.
- I updated the subDM and superDM constructors, but they only work for a single region

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Fix MatSeqAIJFromMatlab() it assumed that the inode structure could change
only if the number of nonzeros changed in the matrix but, in fact, the struture
of the matrix could change while the number

Fix MatSeqAIJFromMatlab() it assumed that the inode structure could change
only if the number of nonzeros changed in the matrix but, in fact, the struture
of the matrix could change while the number of nonzeros remained the same.

Fixed memory leak in example and missing CHKERRQ(ierr);

Commit-type: bug-fix, testing-fix
Reported-by: Alp Dener <adener@anl.gov>

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matlab LS problem residual jacobian API updated to latest

Fixed double-printing of solver header in trust region initialization