Merge branch 'barry/2020-09-23/gpu-resource-error' into 'master'

Add specific PETSc error flag for GPU not having resources available

See merge request petsc/petsc!3241

Add specific PETSc error flag for GPU not having resources available

Try three times to initialize CUDA/cuBLAS and cuSPARSE before erroring. This is for GPU tests that sometimes fail since the GPU
i

Add specific PETSc error flag for GPU not having resources available

Try three times to initialize CUDA/cuBLAS and cuSPARSE before erroring. This is for GPU tests that sometimes fail since the GPU
is busy with other tests when a new test is started.

Commit-type: error-checking, testing
/spend 1h

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Merge branch 'balay/fix-gcov' into 'master'

gcov: fixes

See merge request petsc/petsc!3242

gcov: use appropriate maint/master destination branch

'make mergegcov' gets the target branch using check-merge-branch.sh script and passes it to gcov.py

And fix gcov.py [merge] - when diff is empty

Docs: remove old LaTeX-only manual

The manual is now exclusively built with Sphinx, both as part of the
Sphinx HTML docs, and as a standalone PDF built from a subset of the
Sphinx source, using the

Docs: remove old LaTeX-only manual

The manual is now exclusively built with Sphinx, both as part of the
Sphinx HTML docs, and as a standalone PDF built from a subset of the
Sphinx source, using the Sphinx latex builder.

Remove several images and figures which apparently aren't used
anywhere, except for those which are source for images still used
in the manual, which are moved into the Sphinx docs source subtree.

BibTeX files are left in place, as they are used by the Sphinx
docs as well as other scripts (and perhaps even people writing papers).

The TAO LaTeX-only manual is unaffected by these changes.

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Merge branch 'psanan/docs-sphinx-manual-simpler' into 'master'

Docs: simplify Sphinx manual-only build

See merge request petsc/petsc!3232

Docs: Sphinx docs manual build: simplify logic

Use the "latex_documents" option to directly specify a subset of the
documents to use for the latex builder. This allows the removal of
custom logic to

Docs: Sphinx docs manual build: simplify logic

Use the "latex_documents" option to directly specify a subset of the
documents to use for the latex builder. This allows the removal of
custom logic to change the root directory for the manual, remove al of the separate
output directory for the manual, and allows use of the "latexpdf" make mode.

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Build: add Sphinx docs to alldoc

Adds a check on the Python version before building the docs,
to avoid an annoying long-delayed error.

Sphinx Docs: top-level makefile targets build in ${LOC}

Make the Sphinx docs build, as controlled from the top-level
makefile, build in a subdirectory of the usual ${LOC} directory.

Merge branch 'barry/2020-09-13/another-vm-measurement' into 'master'

Another way that gfortran running out of memory on virtual machines is indicate, check for it.

See merge request petsc/petsc!3180

Add another check for not enough memory in VM for gfortran

Commit-type: error-checking
/spend 30m
Reported-by: Yuke Li <yuke.li@weizmann.ac.il>

Merge branch 'barry/2020-08-29/error-gfortran-virtual-memory' into 'master'

Make prints proper very useful error message if VM runs out of memory during calls to gfortran

See merge request petsc/pe

Merge branch 'barry/2020-08-29/error-gfortran-virtual-memory' into 'master'

Make prints proper very useful error message if VM runs out of memory during calls to gfortran

See merge request petsc/petsc!3114

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Make prints proper very useful error message if VM runs out of memory during calls to gfortran

Commit-type: error-checking, portability-fix, configure, usability
/spend 10m
Reported-by: <yohay613@gm

Make prints proper very useful error message if VM runs out of memory during calls to gfortran

Commit-type: error-checking, portability-fix, configure, usability
/spend 10m
Reported-by: <yohay613@gmail.com>

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Merge branch 'knepley/feature-plex-adaptive-interpolation' into 'master'

Knepley/feature plex adaptive interpolation

See merge request petsc/petsc!3018

Configure: Adding BAMG

Merge branch 'barry/2020-06-30/gcov-use-gmake-filelist' into 'master'

Barry/2020 06 30/gcov use gmake filelist

See merge request petsc/petsc!2939

Fixes and improvements to gcov mechamism

* do not use --coverage on external files, just wastes time
* Use list of files generated by gmakegentest.py for gcov files instead of walking the directory

Fixes and improvements to gcov mechamism

* do not use --coverage on external files, just wastes time
* Use list of files generated by gmakegentest.py for gcov files instead of walking the directory
* Have gcov.py generate unique directories so different builds or phases of builds won't overwrite each other
* fix failure with old version of make
* fix more UnicodeDecodeError: 'utf-8' codec can't decode byte 0x88 in position 7892: invalid start byte errors

* Uses new approach for tracking tested lines and lines of source code (much more accurate than old code)
* now works for ifdef lines that appear in only some builds
* makes table and html files for source file changes since master branch
* makes seperate table for C source and C fortran stub source
* fix up pipeline-analyze job to generate and upload appropriate artifacts

Commit-type: feature
/spend 20h

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Merge branch 'haplav/buildsystem-obey-with-make-dir' into 'master'

configure: Obey --with-make-dir, improve make-related output.

See merge request petsc/petsc!2978

configure: Obey --with-make-dir, improve make-related output.

* Print full path to make in the final configure overview.
* Print full path to make in the configure's "make hint" if make was download

configure: Obey --with-make-dir, improve make-related output.

* Print full path to make in the final configure overview.
* Print full path to make in the configure's "make hint" if make was downloaded/explicitly specified, and is not in PATH.
* Print full path to make in the "make all" output.
* Print the make hint even if configure is otherwise skipped (state has not changed).
* Check downloaded make as well.
* Minor error handling/messaging improvements.

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Merge branch 'jed/doc-snes' into 'master'

doc: SNES: use list-table and update some references

See merge request petsc/petsc!3010

doc: editor recommendations, including clangd and vscode

Merge branch 'barry/2020-07-16/kokkos' into 'master'

Barry/2020 07 16/kokkos Installe Kokkos, example using Kokkos, testing infrastructure for Kokkos

See merge request petsc/petsc!2984

Add Kokkos test example, testing infrastructure and to CI

Move updates to gmake system for double suffix from adams/feature-dmplex-snes-landau-kokkos-barry

Commit-type: feature
Funded-by: ECP
/spen

Add Kokkos test example, testing infrastructure and to CI

Move updates to gmake system for double suffix from adams/feature-dmplex-snes-landau-kokkos-barry

Commit-type: feature
Funded-by: ECP
/spend 15h30m

Thanks-to: Junchao Zhang <junchao.zhang@gmail.com>

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Merge branch 'psanan/sphinx-docs-make-target' into 'master'

Add target to top-level Makefile to build Sphinx docs in a virtual env.

See merge request petsc/petsc!3014

Add target to top-level Makefile to build Sphinx docs in a virtual env.

As a convenience, add a target to the top-level makefile which creates
a virtual environment using Python 3.3 or later (so tha

Add target to top-level Makefile to build Sphinx docs in a virtual env.

As a convenience, add a target to the top-level makefile which creates
a virtual environment using Python 3.3 or later (so that the venv module
exists by default).

Also add a target to clean these docs, cleaning up using the Sphinx
makefile, and also removing the virtual environment created.

For many developers, it would be more natural to make sure that the
requirements in src/sphinx_docs/requirements.txt are satisfied with
their local Python, and use work in src/sphinx_docs, using the Makefile
there.

Note: the Sphinx build itself will still configure its own minimal build of
the "classic" PETSc docs (to have an index of man pages available),
using a dedicated PETSC_ARCH (currently arch-sphinx-minimal).
This is redundant and confusing in some ways, but has the
advantage of having the Sphinx build be fairly self-contained, which is
very handy for building it e.g. on ReadTheDocs, or indeed in an
unconfigured local build of PETSc.

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