MatLoad_Dense_HDF5 impl.

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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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>

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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Binary I/O: Various fixes and enhancements

* Change PetscBinary[Synchronized]Read() to allow for reading
items up to EOF without erroring
* Fix PetscViewerBinaryRead() to properly return the numbe

Binary I/O: Various fixes and enhancements

* Change PetscBinary[Synchronized]Read() to allow for reading
items up to EOF without erroring
* Fix PetscViewerBinaryRead() to properly return the number of items read
* Fix PetscViewerRead() to prevent infinite loops at EOF
* Various fixes for PetscDataType PETSC_COMPLEX

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Merged in stefano_zampini/fix-matcomputeexplicitop (pull request #1570)

Allow specifying an operator type when computing operators explicitly

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

Merged in stefano_zampini/fix-matcomputeexplicitop (pull request #1570)

Allow specifying an operator type when computing operators explicitly

Approved-by: BarryFSmith <bsmith@mcs.anl.gov>
Approved-by: Patrick Sanan <patrick.sanan@gmail.com>

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Add optimized form of MatGetColumnVector()

Commit-type: feature
Reported-by: Piyoosh Jaysaval <Piyoosh.Jaysaval@pnnl.gov>

MatSetOption_MPIDense: skip MAT_IGNORE_ZERO_ENTRIES

Revert the function name where it is referenced

fix uninitialized warning

/sandbox/petsc/petsc.next-3/src/mat/impls/dense/mpi/mpidense.c: In function ‘MatMatTransposeMultNumeric_MPIDense_MPIDense’:
/sandbox/petsc/petsc.next-3/include/petsclog

fix uninitialized warning

/sandbox/petsc/petsc.next-3/src/mat/impls/dense/mpi/mpidense.c: In function ‘MatMatTransposeMultNumeric_MPIDense_MPIDense’:
/sandbox/petsc/petsc.next-3/include/petsclog.h:356:96: warning: ‘recvbuf’ may be used uninitialized in this function [-Wmaybe-uninitialized]
((petsc_isend_ct++,0) || PetscMPITypeSize(&(petsc_isend_len),(count),(datatype)) || MPI_Isend((buf),(count),(datatype),(dest),(tag),(comm),(request)))
^
/sandbox/petsc/petsc.next-3/src/mat/impls/dense/mpi/mpidense.c:2058:29: note: ‘recvbuf’ was declared here
PetscScalar *sendbuf, *recvbuf, *carray;
^

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MatMatTranposeMult: add allgatherv algorithm for MPIDense, document

MATMPIDENSE: added MatMatTransposeMult_MPIDense_MPIDense()