Several improvements to pinned memory support for VECCUDA.

This commit does the following:

* Moves minimum_bytes_pinned_memory out of the Vec_CUDA structure and makes it a
member of struct _p_Vec;

Several improvements to pinned memory support for VECCUDA.

This commit does the following:

* Moves minimum_bytes_pinned_memory out of the Vec_CUDA structure and makes it a
member of struct _p_Vec; initializes it to 0 at vector creation time.

* Adds a flag inside _p_Vec indicating whether there is a current host (CPU)
allocation that is using pinned memory. This flag is used to determine the
appropriate free() implementation to use for a host allocation.

The above changes make it possible and safe to use at any time the API for
setting the minimum size for the use of pinned memory for host allocations.

VecCUDASetPinnedMemoryMin()/VecCUDAGetPinnedMemoryMin() becomes
VecSetPinnedMemoryMin()/VecGetPinnedMemoryMin() with these changes.
These interfaces now exist for VECVIENNACL as well, but have no effect, as
support for pinned host allocations needs to be added for this case.

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VecCUDA: count bytes using size_t

Modify argument of VecCUDA{Set|Get}PinnedMemoryMin to use size_t.
Document how to set this minimum via options database.

Commit-type: portability-fix
Reported-by:

VecCUDA: count bytes using size_t

Modify argument of VecCUDA{Set|Get}PinnedMemoryMin to use size_t.
Document how to set this minimum via options database.

Commit-type: portability-fix
Reported-by: Richard Tran Mills <rmills@rmills.org>

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Add API to change threshold for using pinned memory

Funded-by:
Project: PETSc for GPU
Time:
Reported-by:
Thanks-to:

Merge branch 'rmills/bindtocpu-not-pintocpu' into 'master'

Changed XXXPinToCPU() to XXXBindToCPU() to prevent confusion.

See merge request petsc/petsc!2477

Changed XXXPinToCPU() to XXXBindToCPU() to prevent confusion.

The reason for this change is that we already use the terminology
"pinned" to refer to memory that is non-pageable, in the context of
Pe

Changed XXXPinToCPU() to XXXBindToCPU() to prevent confusion.

The reason for this change is that we already use the terminology
"pinned" to refer to memory that is non-pageable, in the context of
PetscSF as well as allocating host memory when GPUs are being employed.

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Merge branch 'mark/fix-viewfromoptions' into 'master'

prototype for ViewFromOptions macro-->functions

See merge request petsc/petsc!2083

prototype for ViewFromOptions macro-->functions

Merge remote-tracking branch 'origin/jczhang/feature-sf-on-gpu'

Add GPU-aware VecScatter/PetscSF

See merge request petsc/petsc!1995

Added VecGetArrayInPlace and friends to get array where it is, either on GPU or CPU

Merge branch 'karlrupp/fix-petsccublasgethandle-header' into 'master'

CUDA: Moved PetscCUBLASGetHandle() to separate header petsccublas.h

See merge request petsc/petsc!2074

CUDA: VecCUDAGetArray and friends now always part of the interface.

The availability of these functions no longer depends on CUDA compiled into PETSc.
This simplifies user code built on top: No more

CUDA: VecCUDAGetArray and friends now always part of the interface.

The availability of these functions no longer depends on CUDA compiled into PETSc.
This simplifies user code built on top: No more recompilations required.

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Merge branch 'jczhang/sf-more-opts' [PR #1567]

* jczhang/sf-more-opts:
Add more optimizations in SF and use it as the default for VecScatter.

Delete PetscSFCreateFromZero

PetscSFCreateFromZero is replaced with PetscSFCreate() + PetscSFSetGraphWithPattern(..,PETSC_PATTERN_GATHER)

Merge branch 'dalcinl/fix-visibility' [PR #1851]

* dalcinl/fix-visibility:
Vec: Fix visibility of deprecated VecLock{Push|Pop}()

Merge branch 'maint'

Vec: Tag VecLocked() as deprecated

Vec: Fix visibility of deprecated VecLock{Push|Pop}()

Remove use of _ and __ in front of PETSc include guards. Reason: C99 Reserved Identifiers

Commit-type: portability-fix

Merged in barry/cuda-multigrid-test (pull request #1763)

Various improvements for GPUs (mostly for performance and CUDA)

Various improvements for GPUs (mostly for performance and CUDA)

1) Add VecPinToCPU() for CUDA vector and matrices
2) Move initialization of cuBLAS to PetscInitialize() since it takes 1/2 second and

Various improvements for GPUs (mostly for performance and CUDA)

1) Add VecPinToCPU() for CUDA vector and matrices
2) Move initialization of cuBLAS to PetscInitialize() since it takes 1/2 second and distorts timing with -log_view
3) Add logging for DMCreateMatrix (for large meshes this is very large)
4) Add VecGet/RestoreArrayWrite() to prevent unneeded copies from GPU (only implemented so far for CUDA);
added a small number of usages in the source so that snes tutorials ex19 does not do unneeded communication from the GPU
5) Automatically convert MAIJ matrices to AIJ for CUDA since they are not yet supported natively in PETSc's CUDA matrix implementation
6) Pinned objects should still use the CUDA/ViennaCL versions of Destroy to clean up the GPU stuff

Commit-type: 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

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>

Merge remote-tracking branch 'origin/psanan/docs-remove-manconcepts' [PR #1733]

Man pages: remove Concepts: fields

These fields were previously stripped from the man pages by logic removed in
21a59cba2737d49dc2f0bd12c08db0d2a3f3f209

Remove these fields from all man pages (but

Man pages: remove Concepts: fields

These fields were previously stripped from the man pages by logic removed in
21a59cba2737d49dc2f0bd12c08db0d2a3f3f209

Remove these fields from all man pages (but not from examples).

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 -not -path "*/examples/*" -not -name "*.html" -not -name "*.bib" -exec gsed -i '/Concepts:/ {N; /\n\s*$/d}' {} +
find src -type f -not -path "*/examples/*" -not -name "*.html" -not -name "*.bib" -exec gsed -i '/Concepts:/d' {} +
find include -type f -not -path "*/examples/*" -not -name "*.html" -not -name "*.bib" -exec gsed -i '/Concepts:/ {N; /\n\s*$/d}' {} +
find include -type f -not -path "*/examples/*" -not -name "*.html" -not -name "*.bib" -exec gsed -i '/Concepts:/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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Merge branch 'master' of bitbucket.org:petsc/petsc