Merge branch 'gropp/doc-fixes-1' [PR #1838]

Remove testing and inserting into petscconf.h items that are not actually used by PETSc

1) PETSC_HAVE_LIBXXXX - which was rarely used
be careful with the package libpng and libjpeg since they hav

Remove testing and inserting into petscconf.h items that are not actually used by PETSc

1) PETSC_HAVE_LIBXXXX - which was rarely used
be careful with the package libpng and libjpeg since they have lib in the name of the package
2) various system include files that are never used or always exist: for example stdlib.h
3) various system functions that are never used or always exist
4) fixes for requires for MUMPS and SuperLU_DIST when dependent packages are installed or not installed (unrelated to the rest of this pull request)
5) packages that always exist such as PETSC_HAVE_BLASLAPACK, or are not used by PETSc such as PETSC_HAVE_NETCFD
6) remove a couple of uses of HAVE_LIB* in the code that were not needed by adjusting the configure code slightly
7) remove all the #if guards for each entry in petscconf.h since petscconf.h already has a guard and
the values are never defined else where the extra guards just make the file cluttered

For a build with about 10 external packages this reduced the size of petscconf.h from 1236 lines to 828/4 around 220 entries.

Commit-type: style-fix, cleanup

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

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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

Merge from doc-fixes branch

fix incorrect PetscInt usage.

This example breaks with arch-linux-cxx-cmplx-pkgs-64idx on fedora30

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

Fixes for doctext update

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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Merge branch 'barry/cleanup-oldfortran-rules' [PR #1808]

* barry/cleanup-oldfortran-rules:
Remove no longer needed buildmod rules for building Fortran libraries from various directories

Merged in haplav/feature-matload-dense-hdf5 (pull request #1795)

MatLoad_Dense_HDF5

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

Merge remote-tracking branch 'origin/barry/add-petscarrayxxx-ops' [PR #1771]

PetscViewerHDF5Load added _Private suffix and made PETSC_EXTERN.

Needs to PETSC_EXTERN as it is now used in Mat.

Remove no longer needed buildmod rules for building Fortran libraries from various directories

Commit-type: cleanup
Reported-by: Jose E. Roman <jroman@dsic.upv.es>

Merged in barry/with-package-fc-moab-fix (pull request #1788)

Add -with-{hdf5,moab}-fc={true,false} add HDF5 test to make test, fix MOAB handling of zlib

Merged in barry/rm-cmake-legacy (pull request #1714)

Remove legacy and cmake compile systems

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

Remove dead Matlab code, fix typo, fix caste needed for const free

Commit-type: portability-fix
Reported-by: Satish Balay <balay@mcs.anl.gov>

fix -Wunused-value and -Wunused-but-set-variable warnings

PetscViewerHDF5ReadSizes_Private & PetscViewerHDF5ReadSelectHyperslab_Private clearer & more general

Remove unneeded casts from vsectionis.c that broke PetscArrayzero(), add missing output file

Commit-type: bug-fix, testing-fix