MatSetValuesDevice: Cleanup and simplify code, including example

User reported crash of example code. Kernel was passed an ierr that lived in CPU memory

MatSetValuesDevice: do not include private h

MatSetValuesDevice: Cleanup and simplify code, including example

User reported crash of example code. Kernel was passed an ierr that lived in CPU memory

MatSetValuesDevice: do not include private headers from public headers

Feature: MatSetValuesDevice determines automatically from the context (where it is included from) if it is being used from C, CUDA, or Kokkos, PETSC_DEVICE_FUNC_DEC no longer needs to be set before including petscaijdevice.h

Feature: MatSetValuesDevice() now ignores all values outside the global column range.

PetscSplitCSRDataStructure is now a pointer, not a struct, like most PETSc objects, please leave it that way.

Fix all uses of CTABLE that were related to the original MatSetValuesDevice()

Have atomicAdd use Kokkos atomic-add with CPU build when building with Kokkos.

Cuda should now work with --download-openmpi, this is done by updating updateCompilers() to rerun portions of packages/cuda.py after the compilers are reset to use MPI wrappers. This is needed because the resetting of the compilers removes all the compiler flags and packages/cuda.py sets certain values into these flags that was previously lost.

Add MPICXX_INCLUDES, MPICXX_LIBS to fix compile targets for Kokkos examples

'make check' now runs properly for Kokkos test of src/snes/ex3k, fixed bug in the makefile wrt MPI_IS_MPIUNI check

Testing makefile rules: add ex*cu binaries to clean rule

Reported-by: Sam Fagbemi <samkorede24@gmail.com>
Thanks-to: Stefano Zampini <stefano.zampini@gmail.com>
Thanks-to: Mark Adams <mfadams@lbl.gov>

/spend 16h

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Merge branch 'barry/2021-05-14/add-doctext-wargdesc' into 'main'

Add sowing doctext -Wargdesc argument to error on missing argument descriptions

See merge request petsc/petsc!3979

Add sowing doctext -Wargdesc argument to error on missing argument descriptions

Save sowing doctext output to file so it can be checked after all manualpages
are built

Update sowing URl to retreive

Add sowing doctext -Wargdesc argument to error on missing argument descriptions

Save sowing doctext output to file so it can be checked after all manualpages
are built

Update sowing URl to retreive Sowing with additional error checking

Still to do is compare the name of the manual page with the name of the function

Commit-type: error-checking, docs
/spend 35m

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Merge remote-tracking branch 'origin/release'

Merge branch 'psanan-release-patch-93660' into 'release'

Docs: remove docsetdate from alldoc12 target

See merge request petsc/petsc!4023

Docs: remove docsetdate from alldoc12 target

This does not work as used within the Sphinx docs build.

Merge remote-tracking branch 'origin/release'

Merge branch 'psanan/docs-tao-manual-migrate' into 'release'

Docs: Migrate TAO manual to Sphinx to create unified PETSc/TAO Users Manual

See merge request petsc/petsc!3966

Docs: Migrate TAO manual to Sphinx to create unified PETSc/TAO Users Manual

* Move the entire TAO manual to a chapter in the PETSc manual (not including commented-out material and unused resources)

Docs: Migrate TAO manual to Sphinx to create unified PETSc/TAO Users Manual

* Move the entire TAO manual to a chapter in the PETSc manual (not including commented-out material and unused resources)
* Rename the manual to "PETSc/TAO Users Manual"
* Update authors list

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Merge branch 'barry/2021-04-12/support-for-nvhpc' into 'main'

These are fixes needed for clean builds with NVIDIA's HPC software toolkit

See merge request petsc/petsc!3882

Various fixes for NVIDIA's nvhpc toolkit

The nvhpc systems separates the CUDA math libaries and includes from the regular CUDA material
thus cuda.py has to detect and manage this separation automati

Various fixes for NVIDIA's nvhpc toolkit

The nvhpc systems separates the CUDA math libaries and includes from the regular CUDA material
thus cuda.py has to detect and manage this separation automatically.

Note also the nvhpc includes the MPI compilers in another directory which should be used with MPI.

Do not use outer C++ compiler as Kokkos compiler as that may not match the compiler used by nvcc, instead use the C++ compiler that nvcc uses. This is tricky because this compiler has to have access to the MPI headers since it sees all of the PETSc headers.

/spend 14h

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Merge remote-tracking branch 'origin/release'

Merge branch 'psanan/docs/readd-docsetdate' into 'release'

Docs: Add missing docsetdate to alldoc12 target

See merge request petsc/petsc!3991

Docs: Add missing docsetdate to alldoc12 target

This target is used by the Sphinx docs to build the "classic" docs.

Merge remote-tracking branch 'origin/release'

Merge branch 'psanan/docs-move-to-toplevel-doc' into 'release'

Docs: move src/docs/sphinx_docs/ to doc/

See merge request petsc/petsc!3866

Docs: move src/docs/sphinx_docs to doc/, without updating paths in the doc source

Merge remote-tracking branch 'origin/release'

Merge branch 'psanan/docs-extra-html' into 'release'

Build some "classic" docs with Sphinx docs

See merge request petsc/petsc!3684

Merge remote-tracking branch 'origin/release'

Merge branch 'balay/fix-website-main-docs' into 'main'

docs: update website main docs from correct tarball

See merge request petsc/petsc!3828

Merge branch 'balay/fix-check-kokkos-kernels' into 'release'

fix 'make check' for kokkos-kernels

See merge request petsc/petsc!3820

fix 'make check' for kokkos-kernels

Co-Authored-by: Junchao Zhang <jczhang@mcs.anl.gov>

docs: update website main docs from correct tarball

Docs: Build some "classic" docs with Sphinx docs

* Move the minimal configure of PETSc to its own script
* Add logic in the Sphinx conf.py to run this script to
* configure PETSc if needbe and bui

Docs: Build some "classic" docs with Sphinx docs

* Move the minimal configure of PETSc to its own script
* Add logic in the Sphinx conf.py to run this script to
* configure PETSc if needbe and build some docs
* move them into a location to be included with html_extra_path

This allows pages generated with the "classic" logic to be used
consistently with Sphinx builds.

This removes the ability to steal htmlmap from an existing
docs build, because the required html sources are in the src/ and
include/ tree and we hope to easily copy them.

To avoid having to wait around too much, the "classic" build won't auto-update with changes
(you are instructed with a message what to delete to do this).

Includes some custom logic to try to detect if being build on
GitLab CI, to set base URLs for man page links correctly.

Includes some placeholder logic for ReadTheDocs, to be removed.

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