Merge branch 'pr421/alex/feature-veccuda'

* pr421/alex/feature-veccuda
The rationale of this pull request is to have GPU-enabled vectors purely based on CUDA,
and with the possibility of placing a u

Merge branch 'pr421/alex/feature-veccuda'

* pr421/alex/feature-veccuda
The rationale of this pull request is to have GPU-enabled vectors purely based on CUDA,
and with the possibility of placing a user-provided array on the GPU side.

Conflicts:
src/vec/vec/impls/seq/seqcusp/cuspvecimpl.h
src/vec/vec/impls/seq/seqviennacl/viennaclvecimpl.h

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Add missing code for the case PETSC_HAVE_VECCUDA

MPI-Uni builds should not warn about unused mpiio options because MPI-IO
is irrelevent on one process. This removes unneeded nightly build warnings

Reported-by: nightly tests

Removed driver_types.h (included with cuda_runtime.h)

Add include cuda_runtime.h for cudaGetDeviceCount etc.

Mem: Move memory check before unloading dynamic libraries
- Ignore dynamic library allocations

Merge branch 'hzhang/fix-pcredundant'

Vec: added new type VECCUDA based on VECCUSP

add PetscSubcommSetOptionsPrefix()

add PetscOptionsBegin/End to PetscSubcommSetFromOptions()

Merge branch 'master' into tisaac/dmforest

* master: (136 commits)
Make error message specific to exactly what matrix is supported
Prevent fblaslapack or f2cblaslapack from being compiled with t

Merge branch 'master' into tisaac/dmforest

* master: (136 commits)
Make error message specific to exactly what matrix is supported
Prevent fblaslapack or f2cblaslapack from being compiled with the -no-prec-dev Intel compiler option since it can produce incorrect results
Fix for PCReset_HYPRE to make it reentrant.
replace default superlu_dist '-mat_superlu_dist_colperm METIS_AT_PLUS_A' with MMD_ATA to avoid different random numbers for nightly tests
fixes for merge from maint patch
Added PCReset_HYPRE() so it may be used with SNESVI solvers
remove Microsoft compiler message for paste macros used for handling Blas/Lapack macro name mangling for example
Increase the number of PetscViewerPushFormat() possible to 25 and use a macro PETSCVIEWERFORMATPUSHESMAX for the value
Configure: Remove redundant logging
Bib: Added ref
nightlybuids: fix permissions of script
MatRegisterDestroy() does not exist but it is listed in manual pages
externalpackages-git: save local changes if any - in git stash - before 'git checkout -f' Useful incase --with-package-commit=HEAD option was msissing [perhaps due to a typo]
nightlybuilds: add xsdk builds
Add architectures for testing xsdk package downloads (Trilinos, Hypre, SuperLU)
create another version of TurnForward() for adaptive time stepping specifically
Configure: Give proper default if HOME is missing from the environment
fix abbreviation
allow zeropivot for MatSOR_SeqAIJ_Inode, node size=1
add test case using adpative time stepping for checkpointing type 'NONE'
...

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Merge branch 'barry/fix-log-summary-format'

Variable declared within lines of C code, violates C89 standard

Reported-by: Nightly-tests

fix --with-cuda and --with-cusp to compile with --with-64-bit-indices
Do not know if cuda and cusp will work with --64-bit-indices since my test box cuda/cusp does not work

Reported-by: Rajeev Das <

fix --with-cuda and --with-cusp to compile with --with-64-bit-indices
Do not know if cuda and cusp will work with --64-bit-indices since my test box cuda/cusp does not work

Reported-by: Rajeev Das <rajeev.das@cnl.ca>

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if someone puts PetscViewerSetFormat(PETSC_VIEWER_STDOUT_WORLD,PETSC_VIEWER_ASCII_INDEX);
in their code and forgets to reset the format before PetscFinalize, then
-log_summary will not print.

Also a

if someone puts PetscViewerSetFormat(PETSC_VIEWER_STDOUT_WORLD,PETSC_VIEWER_ASCII_INDEX);
in their code and forgets to reset the format before PetscFinalize, then
-log_summary will not print.

Also added to the documentation that -log_summary is deprecated for -log_view

Reported-by: Jed Brown <jed@jedbrown.org>

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fixed up formatting of references in manualpages to consistent style

References:
+ 1. - ref1
. 2. - ref2
- 3. - ref3

previously the formatting was varied and ugly

Update PetscOptionsGetString() fortran documentation to include new PetscOptions argument

Reported-by: Hammond, Glenn E <gehammo@sandia.gov>

Merge remote-tracking branch 'origin/knepley/feature-plex-add-time' into tisaac/dmforest

Both branches changeds DM projection behavior, so I wanted to sort it
out before merging

* origin/knepley/fe

Merge remote-tracking branch 'origin/knepley/feature-plex-add-time' into tisaac/dmforest

Both branches changeds DM projection behavior, so I wanted to sort it
out before merging

* origin/knepley/feature-plex-add-time: (59 commits)
SNES ex69: Updated to new function API, fixed test output
SNES ex75: Fixed for new function API
add fortran stub for TSMonitorLGSetTransform() and fix TSMonitorLG for multiple fields but no names provided for fields
add -binary_write_double so __float128 precision can save as double to binary files
TSClone() did not clone Fortran function pointers hence some TS methods would fail if functions provided in Fortan
petsc4py: update to snapshot with 'barry/petscoptions-object' changes
fix bad merge that introduced 2 copies of the MPI_Comm_free()
update example to use MAT_INPLACE_MATRIX, not REUSE
incorrect addition of float to PetscInt
update for new PetscOptions API
TS ex18: Fixed function API and test output
Function now takes PetscOptions as first argument, this was missed during the first round of updates
bugfix for MatSetOption_Elemental()
fix test example no change output that was missing a line
fixes for new PetscOptions.. API that are needed based on problems with nightly build
Plex ex3: Use new function API
SNES ex62: Use new function API
SNES ex12: Use new function API
Plex: Fixed unused options in examples
Plex+DMDA: Add time to signatures
...

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PetscFinalize(): Destroy the log after finalizing packages.

Finalizing a package could generate log/info data, in which case we
need to have the log data structures around.