Merge branch 'jczhang/fix-valid-gpu-array' into maint

Rename: v->valid_GPU_array/matrix==> v->offloadmask and PetscOffloadFlag==>PetscOffloadMask

See merge request petsc/petsc!2141

Rename valid_GPU_array/matrix to offloadmask

Merge branch 'stefanozampini/gpu-bddc' into 'master'

Improvements towards BDDC on GPUs

See merge request petsc/petsc!2067

Fix compilation error for nvcc in optimized code with AVX-512 (march=native on my GPU workstation)

for some reason, the host compiler fails with this error message
/home/zampins/Devel/petsc/include/

Fix compilation error for nvcc in optimized code with AVX-512 (march=native on my GPU workstation)

for some reason, the host compiler fails with this error message
/home/zampins/Devel/petsc/include/../src/mat/impls/aij/seq/aij.h(535): error: identifier "_mm512_reduce_add_pd" is undefined

This optimized C kernel is not used in the GPU classes, so it is safe to skip its declaration

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MATSEQAIJVIENNACL: implement MatSeqAIJGetArray

Merge branch 'stefano_zampini/GPU-matdensecuda' [PR #1911]

* stefano_zampini/GPU-matdensecuda:
GPU: Initial implementation for SeqDense class on GPUs.

MATSEQAIJVIENNACL: minor changes

MatSEQAIJ{CUSPARSE|VIENNACL}: do not copy to the GPU if not at the final stage of assembly

Merge branch 'hannah/gpu-computation-logging' [PR #1843]

* hannah/gpu-computation-logging:
Adding GPU flop rate and GPU time.

PetscLogGpuTimeStart -> Begin

Adding Gpu flop rate and GPU time

Merged in hannah/gpu-communication-logging (pull request #1814)

Hannah/gpu communication logging

Approved-by: BarryFSmith <bsmith@mcs.anl.gov>
Approved-by: Richard Mills <rtm@eecs.utk.edu>

Adding vector logging, started matrix logging

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

Various improvements for GPUs (mostly for performance and CUDA)

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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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 branch 'master' of bitbucket.org:petsc/petsc

Merge branch 'barry/feature-pintocpu' [PR #1641]

* barry/feature-pintocpu:
Adding a MatPinToCPU() and VecPinToGPU() capability
For matrices this will prevent copies to the GPU when they will never b

Merge branch 'barry/feature-pintocpu' [PR #1641]

* barry/feature-pintocpu:
Adding a MatPinToCPU() and VecPinToGPU() capability
For matrices this will prevent copies to the GPU when they will never be used there.
For vectors this will prevent vectors from boucing back and forth between the CPU.

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Based on discussion with Oana I am adding a MatPinToCPU() and VecPinToGPU() capability. For matrices this
will prevent copies to the GPU when they will never be used there. For vectors this will
prev

Based on discussion with Oana I am adding a MatPinToCPU() and VecPinToGPU() capability. For matrices this
will prevent copies to the GPU when they will never be used there. For vectors this will
prevent vectors from boucing back and forth between the CPU and GPU when most of the work is in the CPU. An
example of the place that needs to avoid bouncing is in MatFDColoringApply_XXXX()

Commit-type: feature, documentation, example
Thanks-to: Oana Marin <oanam@mcs.anl.gov>

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Merge branch 'master' into jpusztay/feature-swarm-symplectic-example

Merge branch 'master' into jpustay/feature-swarm-example

Merged petsc/petsc into master