Test MPI gpu awareness and use default -use_gpu_aware_mpi 1

Added functionality to selectively filter PetscInfo() output based on calling class to
mimic some OS system logs. New functionality includes:
- Filter for a set of classes
- Filter out a set of class

Added functionality to selectively filter PetscInfo() output based on calling class to
mimic some OS system logs. New functionality includes:
- Filter for a set of classes
- Filter out a set of classes
- Filter for MPI/PETSC_COMM_SELF
- Filter for anything not on MPI/PETSC_COMM_SELF
- Writing PetscInfo() output to new file
- Appending output to existing PetscInfo() file
- Any combination of the above

Credit to Vaclav Hapla for raising the initial issue, helping design the eventual API, and
substantially assisting in debugging.

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Merge branch 'rmills/remove-hostdataregisteredaspagelocked' into 'master'

Remove occurrences of veccuda->hostDataRegisteredAsPageLocked.

See merge request petsc/petsc!2624

Remove a test of -sf_window_flavor dynamic

Use a 3d submatrix to describle indices in packing

Init some vars

Change PetscMemcpyWithMemType to PetscSFLinkMemcpy and make it asynchronous

With that, all cuda calls in SF are asynchronous and work on link->stream. The reason is we want to avoid sudden 'join poi

Change PetscMemcpyWithMemType to PetscSFLinkMemcpy and make it asynchronous

With that, all cuda calls in SF are asynchronous and work on link->stream. The reason is we want to avoid sudden 'join points' caused by synchronous cuda calls.

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Add option -sf_use_stream_aware_mpi

No need to get mtypes in PetscSFXxxEnd(). The cuda call is not cheap.

Remove ex2 since the graph is not a true SF

Update alt output

Refactor SF packing

1) Separate out local communication from remote communication
2) Directly pass root/leafdata to MPI when suitable

Remove occurrences of veccuda->hostDataRegisteredAsPageLocked.

This flag appears to have been introduced long ago, and is no longer
used. Removing it to prevent confusion.

Fix incorrect one-line 'if' statement in VecDestroy_SeqViennaCL_Private().

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

Fix memory leak in VecGetLocalVector_SeqCUDA().

Jose E. Roman <jroman@dsic.upv.es> identified this bug via SLEPc tests
and provided the patch to fix it.

Thanks-to: Jose E. Roman <jroman@dsic.upv.es>

Fix bug: pinned_memory flag was not being propagated in Vec{Get|Restore}LocalVector_SeqCUDA().

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

Promote examples/{tests,tutorials}/ to {tests,tutorials}/

This shortens paths and improves consistency between test target names
and paths to the source and output files. Most of the work was
compl

Promote examples/{tests,tutorials}/ to {tests,tutorials}/

This shortens paths and improves consistency between test target names
and paths to the source and output files. Most of the work was
completed by this script, followed by mild cleanup of nonconforming
cases.

for makefile in `git ls-files 'src/*makefile'`; do
if rg -q 'DIRS.*\bexamples\b' $makefile; then
base=$(dirname $makefile)
dirs=$(cd $base/examples && ls -d tests tutorials 2>/dev/null | xargs echo)
perl -pi -e "s#^(DIRS.*)\bexamples\b#\1${dirs}#" $makefile
git rm $base/examples/makefile
for t in $dirs; do
git mv $base/examples/$t $base/
perl -pi -e "s#^(LOCDIR[[:space:]]*=).*#\1 $base/$t/#" $base/$t
done
fi
done

git grep -l -E -z 'examples/(tutorials|tests)' | xargs -0 perl -pi -e 's#examples/(tutorials|tests)#\1#g'
git checkout @ \
src/docs/website/documentation/changes/ \
src/benchmarks/results/

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