Merge branch 'barry/2022-05-03/cleanup-makefiles' into 'main'

remove unneeded stuff from makefiles

See merge request petsc/petsc!5211

Add -include */petscdir.mk to makefile that lacked it

for i in `git ls-files | grep makefile | xargs grep -L petscdir.mk`; do
echo $i ;
str=`echo $i |sed -e 's?[-a-zA-Z0-9]*/?../?g' -e 's?makef

Add -include */petscdir.mk to makefile that lacked it

for i in `git ls-files | grep makefile | xargs grep -L petscdir.mk`; do
echo $i ;
str=`echo $i |sed -e 's?[-a-zA-Z0-9]*/?../?g' -e 's?makefile?petsckdir.mk?g'` ;
cp $i tmp
echo "-include $str" > $i
cat tmp >> $i
done

Commit-type: makefile, housekeeping
/spend 15m

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remove garbage from makefiles

Including
* unused FLAGS variables
* All: lib that did not work
* stray blank lines etc

Commit-type: housekeeping
/spend 1h

Merge branch 'jacobf/2021-09-04/petscdevice-cupminitialization' into 'main'

Replace current CUPM initialization with unified PetscDevice version

See merge request petsc/petsc!4310

- Replace the current CUPM initialization infrastructure with PetscDevice.
- Remove -petsc_use_default_null_stream and -[cuda|hip]_synchronize options
- Remove PetscCUDASynchronize and PetscHIPSynchr

- Replace the current CUPM initialization infrastructure with PetscDevice.
- Remove -petsc_use_default_null_stream and -[cuda|hip]_synchronize options
- Remove PetscCUDASynchronize and PetscHIPSynchronize
- Remove PetscCUDAInitialize(), PetscCUDAInitializeCheck(), PetscHIPInitialize(), and
PetscHIPInitializeCheck()
- Remove PetscCUBLASInitializeHandle(), PetscCUSOLVERDnInitializeHandle(),
PetscHIPBLASInitializeHandle(), and PetscHIPSOLVERInitializeHandle().
- Remove petsc_gputimer_begin and petsc_gputimer_begin
- Add -device_enable, -device_select and -device_view options
- Replace -[cuda|hip]_device with split options -device_enable_[cuda|hip] and -device_select_[cuda|hip]
- Replace -[cuda|hip]_view with -device_view_[cuda|hip]
- Add PetscDeviceInitType
- Add PetscDeviceInitialize() and PetscDeviceInitialized()
- Add PetscDeviceView()

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Merge branch 'jed/rm-distutils' into 'main'

config: remove distutils from build

See merge request petsc/petsc!4253

config: remove distutils from build

distutils is deprecated and will be removed in Python-3.12:

https://www.python.org/dev/peps/pep-0632/

Most features carry over readily with sysconfig (part of

config: remove distutils from build

distutils is deprecated and will be removed in Python-3.12:

https://www.python.org/dev/peps/pep-0632/

Most features carry over readily with sysconfig (part of minimal python,
unlike distutils, which is often an optional package). One exception is
distutils.sysconfig.parse_makefile, which is more full-featured than
sysconfig._parse_makefile (a private method that exists in python 2.7
and all tested python 3 versions). Specifically, _parse_makefile()
cannot handled lines continued with trailing backslash (\) and thus we
must forbid continuations for DIRS and SOURCE* lines -- just use a line
as long as it needs to be. This system will hopefully be renovated anyway.

Commit-type: portability

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Merge branch 'jacobf/2021-05-18/petscdevice-context' into 'main'

Feature: PetscDeviceContext

See merge request petsc/petsc!3994

Added PetscDevice to manage interaction and configuration of available devices.

Added PetscDeviceContext class to manage stream interactions for CUDA and HIP device
backends. The new class is design

Added PetscDevice to manage interaction and configuration of available devices.

Added PetscDeviceContext class to manage stream interactions for CUDA and HIP device
backends. The new class is designed to facilitate a fork-join parallelization model for
asynchronous compute.

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Merge branch 'dalcinl/vendor-libyaml' into 'master'

Vendor LibYAML

See merge request petsc/petsc!3652

YAML: Move YAML options implementation sources closer to related sources

Merge branch 'haplav/feature-petschavepackage' into 'master'

add PetscHasExternalPackage() parsing PETSC_HAVE_PACKAGES

See merge request petsc/petsc!3470

add PetscHasExternalPackage() parsing PETSC_HAVE_PACKAGES

Merge branch 'scott/hip-sys-vec' into 'master'

Implementation of HIP for sys and vec packages

See merge request petsc/petsc!3056

Implementation of HIP for sys and vec packages

This implements the vec functionality including tests.
In the sys level, we handle the initialization issues, but it is tested
at the vec level.

Works

Implementation of HIP for sys and vec packages

This implements the vec functionality including tests.
In the sys level, we handle the initialization issues, but it is tested
at the vec level.

Works with ROCm 3.9.

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Merge branch 'jczhang/fix-cupminit-manpage' into 'master'

Add manpages for PetscCUDAInitialize/PetscHIPInitialize

See merge request petsc/petsc!3115

Add manpages for PetscCUDAInitialize/PetscHIPInitialize

Merge branch 'jczhang/add-kokkos-init' into 'master'

Add Kokkos initialization

See merge request petsc/petsc!3048

Add Kokkos initialization

Merge remote-tracking branch 'origin/maint'

Merge branch 'jolivet/fix-elemental-deadlock' into 'maint'

MATELEMENTAL deadlock when first Mat is on a subcommunicator

See merge request petsc/petsc!2862

Fix a deadlock with MATELEMENTAL

Merge branch 'maint'

Merge branch 'jose/cuda-visibility/maint' into 'maint'

Fix visibility issues with CUDA

See merge request petsc/petsc!2282

Fix visibility issues with CUDA

- VecSet_SeqCUDA() called from densecuda.cu
- PetscCUBLASInitializedHandle() should be declared PETSC_EXTERN