Kitware Robot authored 5 months ago and Ben Boeckel committed 5 months ago

Also use C++17 syntax rules as the next release expects to use C++17.

- MACOSX_DEPLOYMENT_TARGET>=10 uses dynlib files (as opposed to jnilib
  files).

(cherry picked from commit 6bd65269)

Previously, the conversion from a `vtkm::cont::UnknownArrayHandle` to a
`vtkDataArray` relied on the array being a known `Vec` size. This
restriction has been lifted, and tuples of any size can be converted
from an `ArrayHandleBasic` or an `ArrayHandleSOA` to an
`vtkAOSDataArrayTemplate` or `vtkSOADataArrayTemplate`, respectively.

The code is also more clever about when to copy data to VTK. It avoids
transferring the data if it means copying data from device to host.

VTK-m has added better support for managing arrays of unknown type since
`vtkmDataArray` was created. These changes revamp the implementation to
use these new features and make it more efficient to get values directly
from VTK-m arrays. These should make it easier to add `vtkmDataArray`s
to VTK datasets that could be passed back to VTK-m.

Change the VTK to VTK-m array conversion routines to use
`ArrayHandleRuntimeVec` and `ArrayHandleRecombineVec`. These are new
features of VTK-m that allow you to specify an array with the tuple size
specified at runtime. This change improves three specific things.

* Fixes a bug when importing an array of "odd" tuple size (not 1, 2,
  3, 4, 6, or 9). It was creating arrays of size one less than the
  actual size.
* Avoids using `ArrayHandleGroupVecVariable`, which is supported by
  fewer VTK-m filters.
* The VTK-m `ArrayHandle` now manages a reference back to the VTK
  array, so the `ArrayHandle` will continue to work even if the
  original VTK array is "deleted." This makes the code safer.
* Unifies the implementation of the array conversion among number of
  components to avoid issues with surprise tuple sizes.

-- Instead of initializing kokkos backend for every specific backend,
   move the initialization based on `VTK_USE_KOKKOS` flag using CMAKE compile
   definition

Abhishek Yenpure authored 1 year ago and Lucas Givord committed 1 year ago

(cherry picked from commit 5eb16852)

Abhishek Yenpure authored 1 year ago and Lucas Givord committed 1 year ago

(cherry picked from commit f47258be)

  -- Generalizing the specification of KOKKOS device adapter
  -- Adding an option `VTK_KOKKOS_BACKEND` to specify specific backend
     either `HIP`, `SYCL`, or `CUDA`
  -- Adding warning on VTK_USE_HIP
  -- Adding documentation for flags
  -- Adding updates from review
  -- Adding updates to support Kokkos CUDA backend

* core test does not rely anymore on rendering,
making it more accurate / robust.
* build is optimized as a lot of dependencies are
removed

With this change DataSetConverters convert routine throws an
`vtkm::cont::ErrorBadType` exception if the user tries to convert an
vtkDataSet which is unsupported in VTK-m.

Sujin Philip authored 1 year ago and Vicente Bolea committed 1 year ago

VTK-m's clip no longer copies all of the input points to the output.
Now, only the points that are actually part of the output are copied.
Therfore, the call to clean grid, which was there to remove the unused
points, is no longer required.

Replace 1

cat files.out |  xargs -I %s perl -i~ -0777 -pe 's/\/\*=========================================================================(.|\n)*.*Program:   Visualization Toolkit\n.*Module:.*\n\n  Copyright \(c\) Ken Martin, Will Schroeder, Bill Lorensen\n  All rights reserved.\n  See Copyright.txt or .* for details.\n\n.*\n.*\n.*\n.*\*\//\/\/ SPDX-FileCopyrightText: Copyright \(c\) Ken Martin, Will Schroeder, Bill Lorensen\n\/\/ SPDX-License-Identifier: BSD-3-CLAUSE/g' %s

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cat files.out |  xargs -I %s perl -i~ -0777 -pe 's/\/\*=========================================================================(.|\n)*.*Program:   Visualization Toolkit\n.*Module:.*\n\n  Copyright \(c\) Ken Martin, Will Schroeder, Bill Lorensen\n  All rights reserved.\n  See Copyright.txt or .* for details.\n\n.*\n.*\n.*\n\n.*\*\//\/\/ SPDX-FileCopyrightText: Copyright \(c\) Ken Martin, Will Schroeder, Bill Lorensen\n\/\/ SPDX-License-Identifier: BSD-3-CLAUSE/g' %s

Replace 3

cat files.out |  xargs -I %s perl -i~ -0777 -pe 's/\/\*=========================================================================\n.*Program:.*Visualization Toolkit\n.*Copyright \(c\) Ken Martin, Will Schroeder, Bill Lorensen\n.*All rights reserved.\n.*See Copyright.txt or .* for details.\n.*\n.*\n.*\n.*\*\//\/\/ SPDX-FileCopyrightText: Copyright \(c\) Ken Martin, Will Schroeder, Bill Lorensen\n\/\/ SPDX-License-Identifier: BSD-3-CLAUSE/g' %s

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cat files.out |  xargs -I %s perl -i~ -0777 -pe 's/\/\*=========================================================================\n\n.*Program:.*Visualization Toolkit\n\n.*Copyright \(c\) Ken Martin, Will Schroeder, Bill Lorensen\n.*All rights reserved.\n.*See Copyright.txt or .* for details.\n\n.*\n.*\n.*\n\n=========================================================================\*\//\/\/ SPDX-FileCopyrightText: Copyright \(c\) Ken Martin, Will Schroeder, Bill Lorensen\n\/\/ SPDX-License-Identifier: BSD-3-CLAUSE/g' %s

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cat files.out |  xargs -I %s perl -i~ -0777 -pe 's/\/\*=========================================================================\n\n.*Program:.*Visualization Toolkit\n.*Module:.*\n\n.*Copyright \(c\) Ken Martin, Will Schroeder, Bill Lorensen\n.*All rights reserved.\n.*See Copyright.txt or .* for details.\n\n.*\n.*\n.*\n\n=========================================================================\*\//\/\/ SPDX-FileCopyrightText: Copyright \(c\) Ken Martin, Will Schroeder, Bill Lorensen\n\/\/ SPDX-License-Identifier: BSD-3-CLAUSE/g' %s

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cat files.out |  xargs -I %s perl -i~ -0777 -pe 's/\/\*=========================================================================\n\n.*Program:.*Visualization Toolkit\n.*Module:.*\n\n.*Copyright \(c\) Ken Martin, Will Schroeder, Bill Lorensen\n.*All rights reserved.\n.*See Copyright.txt or .* for details.\n\n.*\n.*\n.*\n\n.*=========================================================================\*\//\/\/ SPDX-FileCopyrightText: Copyright \(c\) Ken Martin, Will Schroeder, Bill Lorensen\n\/\/ SPDX-License-Identifier: BSD-3-CLAUSE/g' %s

Replace 7

cat files.out |  xargs -I %s perl -i~ -0777 -pe 's/\/\*=========================================================================\n\n.*Program:.*Visualization Toolkit\n.*Module:.*\n\n.*Copyright \(c\) Ken Martin, Will Schroeder, Bill Lorensen\n.*All rights reserved.\n\n.*See Copyright.txt or .* for details.\n\n.*\n.*\n.*\n\n=========================================================================\*\//\/\/ SPDX-FileCopyrightText: Copyright \(c\) Ken Martin, Will Schroeder, Bill Lorensen\n\/\/ SPDX-License-Identifier: BSD-3-CLAUSE/g' %s

Replace 8

cat files.out |  xargs -I %s perl -i~ -0777 -pe 's/\/\*==================================================================\n\n.*Program:.*Visualization Toolkit\n.*Module:.*\n\n.*Copyright \(c\) Ken Martin, Will Schroeder, Bill Lorensen\n.*All rights reserved.\n.*See Copyright.txt or .* for details.\n\n.*\n.*\n.*\n\n===================================================================\*\//\/\/ SPDX-FileCopyrightText: Copyright \(c\) Ken Martin, Will Schroeder, Bill Lorensen\n\/\/ SPDX-License-Identifier: BSD-3-CLAUSE/g' %s

Replace sandia 1

 cat files.out | xargs -I %s perl -i~ -0777 -pe 's/\/\*=========================================================================\n\n.*Program:.*Visualization Toolkit\n.*Module:.*\n\n-------------------------------------------------------------------------\n.*Copyright 2008 Sandia Corporation.\n.*Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation,\n.*the U.S. Government retains certain rights in this software.\n-------------------------------------------------------------------------\n\n.*Copyright \(c\) Ken Martin, Will Schroeder, Bill Lorensen\n.*All rights reserved.\n.*See Copyright.txt or .* for details.\n\n.*\n.*\n.*\n\n=========================================================================\*\//\/\/ SPDX-FileCopyrightText: Copyright \(c\) Ken Martin, Will Schroeder, Bill Lorensen\n\/\/ SPDX-FileCopyrightText: Copyright 2008 Sandia Corporation\n\/\/ SPDX-License-Identifier: LicenseRef-BSD-3-CLAUSE-Sandia-USGov/g' %s

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cat files.out | xargs -I %s perl -i~ -0777 -pe 's/\/\*=========================================================================\n\n.*Program:.*Visualization Toolkit\n.*Module:.*\n.*Language:.*\n\n.*Copyright \(c\) .* Ken Martin, Will Schroeder, Bill Lorensen\n.*All rights reserved.\n.*See Copyright.txt or .* for details.\n\n.*\n.*\n.*\n\n=========================================================================\*\//\/\/ SPDX-FileCopyrightText: Copyright \(c\) Ken Martin, Will Schroeder, Bill Lorensen\n\/\/ SPDX-License-Identifier: BSD-3-CLAUSE/g' %s

Manual 1

Replace 10

cat files.out | xargs -I %s perl -i~ -0777 -pe 's/\/\*=========================================================================\n\n.*Program:.*\n.*Module:.*\n\n.*Copyright \(c\) Ken Martin, Will Schroeder, Bill Lorensen\n.*All rights reserved.\n.*See Copyright.txt or .* for details.\n\n.*\n.*\n.*\n\n=========================================================================\*\//\/\/ SPDX-FileCopyrightText: Copyright \(c\) Ken Martin, Will Schroeder, Bill Lorensen\n\/\/ SPDX-License-Identifier: BSD-3-CLAUSE/g' %s

Replace 11

cat files.out | xargs -I %s perl -i~ -0777 -pe 's/\/\*=========================================================================\n.*Program:.*\n.*Module:.*\n.*Copyright \(c\) Ken Martin, Will Schroeder, Bill Lorensen\n.*All rights reserved.\n.*See Copyright.txt or .* for details.\n.*\n.*\n.*\n=========================================================================\*\//\/\/ SPDX-FileCopyrightText: Copyright \(c\) Ken Martin, Will Schroeder, Bill Lorensen\n\/\/ SPDX-License-Identifier: BSD-3-CLAUSE/g' %s

Replace Valve 1

cat files.out | xargs -I %s perl -i~ -0777 -pe 's/\/\*=========================================================================\n\n.*Program:.*\n.*Module:.*\n\n.*Copyright \(c\) Ken Martin, Will Schroeder, Bill Lorensen\n.*All rights reserved.\n.*See Copyright.txt or .* for details.\n\n.*\n.*\n.*\n\nParts Copyright Valve Corporation from.*\nunder their BSD license found here:\n.*\n\n=========================================================================\*\//\/\/ SPDX-FileCopyrightText: Copyright \(c\) Ken Martin, Will Schroeder, Bill Lorensen\n\/\/ SPDX-FileCopyrightText: Copyright (c) 2015, Valve Corporation\n\/\/ SPDX-License-Identifier: BSD-3-CLAUSE/g' %s

Manual 2

Manual 3

manual 4

manual sandia 1

manual 5

Replace ParaView 1

cat files.out | xargs -I %s perl -i~ -0777 -pe 's/\/\*=========================================================================\n\n.*Program:.*\n.*Module:.*\n\n.*Copyright \(c\) Sandia Corporation, Kitware Inc.\n.*All rights reserved.\n.*See Copyright.txt or .* for details.\n\n.*\n.*\n.*\n\n=========================================================================\*\//\/\/ SPDX-FileCopyrightText: Copyright \(c\) Ken Martin, Will Schroeder, Bill Lorensen\n\/\/ SPDX-FileCopyrightText: Copyright (c) Sandia Corporation, Kitware Inc\n\/\/ SPDX-License-Identifier: BSD-3-CLAUSE/g' %s

Manual Sandia 2

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cat files.out | xargs -I %s perl -i~ -0777 -pe 's/\/\*=========================================================================\n\n.*Program:.*\n\n.*Copyright \(c\) Ken Martin, Will Schroeder, Bill Lorensen\n.*All rights reserved.\n.*See Copyright.txt or .* for details.\n\n.*\n.*\n.*\n\n.*=========================================================================\*\//\/\/ SPDX-FileCopyrightText: Copyright \(c\) Ken Martin, Will Schroeder, Bill Lorensen\n\/\/ SPDX-License-Identifier: BSD-3-CLAUSE/g' %s

Manual sandia 3

replace 14

cat files.out | xargs -I %s perl -i~ -0777 -pe 's/\/\*=========================================================================\n\n.*Program:.*\n.*Module:.*\n.*Copyright \(c\) Ken Martin, Will Schroeder, Bill Lorensen\n.*All rights reserved.\n.*See Copyright.txt or .* for details.\n\n.*\n.*\n.*\n\n.*=========================================================================\*\//\/\/ SPDX-FileCopyrightText: Copyright \(c\) Ken Martin, Will Schroeder, Bill Lorensen\n\/\/ SPDX-License-Identifier: BSD-3-CLAUSE/g' %s

Manual sandia 4

Manual 6

manual 7

manual sandia 5

Manual Kitware SAS 1

manual 7

Manual 10

manual 11

manual 12

manual 15

Fix wrong spdx name

Remove useless cmake copyright

Remove useless copyrights

Remove useless copyright and license statement in python files

Removal glsl

cat files.out | xargs -I %s perl -i~ -0777 -pe "s/.*=========================================================================\n.*\n.*Program:.*\n.*Module:.*\n.*\n.*Copyright \(c\) Ken Martin, Will Schroeder, Bill Lorensen\n.*All rights reserved.\n.*See Copyright.txt or .*for details.\n.*\n.*\n.*\n.*\n.*\n.*=========================================================================\n//g" %s

Replace sandia accel

cat files.out | xargs -I %s perl -i~ -0777 -pe 's/\/\/=============================================================================\n.*\n.*Copyright \(c\) Kitware, Inc.\n.*All rights reserved.\n.*See LICENSE.txt for details.\n.*\n.*This.*\n.*the.*\n.*PURPOSE.*\n.*\n.*Copyright 2012 Sandia Corporation.\n.*Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation,\n.*the U.S. Government retains certain rights in this software.\n.*\n.*=============================================================================/\/\/ SPDX-FileCopyrightText: Copyright \(c\) Ken Martin, Will Schroeder, Bill Lorensen\n\/\/ SPDX-FileCopyrightText: Copyright (c) Kitware, Inc.\n\/\/ SPDX-FileCopyrightText: Copyright 2012 Sandia Corporation.\n\/\/ SPDX-License-Identifier: LicenseRef-BSD-3-Clause-Sandia-USGov/g' %s

Manual sandia accel

manual Kitware inc

Manual fixups

Manual 14

Replace 15

cat files.out | xargs -I %s perl -i~ -0777 -pe 's/\/\*=========================================================================\n\n.*Program:.*\n.*Module:.*\n\n.*Copyright \(c\) Kitware, Inc.\n.*All rights reserved.\n.*See LICENSE file for details.\n\n.*\n.*\n.*\n\n=========================================================================\*\//\/\/ SPDX-FileCopyrightText: Copyright \(c\) Ken Martin, Will Schroeder, Bill Lorensen\n\/\/ SPDX-License-Identifier: BSD-3-CLAUSE/g' %s

Manual 16

Removing non-standard file header

cat files.out | xargs -I %s perl -i~ -0777 -pe 's/\/\/ \-\*\- c\+\+.*\n\n//g' %s

Manual removal non standard header

Adding custom sandia and lanl licenses

Fix missing header common core

Manual missing headers

Add missing sandia

cat files.out  | xargs -I %s perl -i~ -0777 -pe 's/\A\/\/ SPDX-FileCopyrightText.*\n\/\/ SPDX-License-Identifier.*\n\n\/\*\n.*Copyright 2004 Sandia Corporation.\n.*Under.*\n.*license.*\n.*U.*\n.*or.*\n.*statement.*\n \*\//\/\/ SPDX-FileCopyrightText: Copyright \(c\) Ken Martin, Will Schroeder, Bill Lorensen\n\/\/ SPDX-FileCopyrightText: Copyright 2004 Sandia Corporation\n\/\/ SPDX-License-Identifier: LicenseRef-BSD-3-Clause-Sandia-USGov/g' %s

Adding missing sandia licenses

Adding sandia licenses

Adding missing sandia licenses

Replace sandia

Adding sandia module changes

Use new custom license system

Replace sandia

cat files.out  | xargs -I %s perl -i~ -0777 -pe 's/\A\/\/ SPDX-FileCopyrightText.*\n\/\/ SPDX-License-Identifier.*\n\/\*-------------------------------------------------------------------------\n.*Copyright 2009 Sandia Corporation.\n.*Under the terms of Contract DE-AC04-94AL85000.*\n.*the.*\n-------------------------------------------------------------------------\*\//\/\/ SPDX-FileCopyrightText: Copyright \(c\) Ken Martin, Will Schroeder, Bill Lorensen\n\/\/ SPDX-FileCopyrightText: Copyright 2009 Sandia Corporation\n\/\/ SPDX-License-Identifier: LicenseRef-BSD-3-Clause-Sandia-USGov/g' %s

Adding missing sandia licenses

Sandia final fixup license

Adding missing sandia license

Fix remaining sandia license

Manual LANL license

Replace sandia BSD

cat files.out  | xargs -I %s perl -i~ -0777 -pe 's/\A\/\/ SPDX-FileCopyrightText.*\n\/\/ SPDX-License-Identifier.*\n\/\*----------------------------------------------------------------------------\n.*Copyright \(c\) Sandia Corporation\n.*See Copyright.txt.*\n.*----------------------------------------------------------------------------\*\//\/\/ SPDX-FileCopyrightText: Copyright \(c\) Ken Martin, Will Schroeder, Bill Lorensen\n\/\/ SPDX-FileCopyrightText: Copyright \(c\) Sandia Corporation\n\/\/ SPDX-License-Identifier: BSD-3-Clause/g' %s

Replace Kitware, Inc.

 cat files.out  | xargs -I %s perl -i~ -0777 -pe 's/\A\/\*=========================================================================\n\n.*Program.*\n.*Module.*\n\n.*Copyright \(c\) Kitware, Inc.\n.*All rights reserved.\n.*See Copyright.txt.*\n\n.*This.*\n.*the.*\n.*PURPOSE.*\n\n=========================================================================\*\//\/\/ SPDX-FileCopyrightText: Copyright \(c\) Ken Martin, Will Schroeder, Bill Lorensen\n\/\/ SPDX-FileCopyrightText: Copyright \(c\) Kitware, Inc.\n\/\/ SPDX-License-Identifier: BSD-3-Clause/g' %s

Manual ParaView license

Remove useless license statement in cmake files

Manual licenses

Replace lanl

 cat files.out  | xargs -I %s perl -i~ -0777 -pe 's/\A\/\/ SPDX-FileCopyrightText.*\n\/\/ SPDX-License-Identifier.*\n\n\/\*.*\n.*\n.*Copyright \(c\) 2000.*2009.*Lawrence Livermore National Security, LLC\n.*Produced at the Lawrence.*\n.*LLNL-CODE-400124\n.*All rights reserved.\n.*\n.*This.*\n.*see.*\n.*file.*\n.*http.*\n.*\n.*\//\/\/ SPDX-FileCopyrightText: Copyright \(c\) Ken Martin, Will Schroeder, Bill Lorensen\n\/\/ SPDX-FileCopyrightText: Copyright \(c\) 2000 - 2009, Lawrence Livermore National Security, LLC\n\/\/ SPDX-License-Identifier: BSD-3-Clause/g' %s

Manual LANL

NVIDIA license impact

Manual Indiana

Manual copyrights

More manual licenses

More manual licenses

Replace Atamai

 cat a.out  | xargs -I %s perl -i~ -0777 -pe 's/\A\/\/ SPDX-FileCopyrightText.*\n\/\/ SPDX-License-Identifier.*\n\/\*.*\n\n.*Copyright \(c\) 2006 Atamai, Inc.\n\nUse.*\nbinary.*\nconditions.*\n\n1.*\n   form.*\n   the.*\n   license.*\n\n2.*\n   notice.*\n   in.*\n   distribution.*\n\n3.*\n   and.*\n\nTHE.*\nWITHOUT.*\nTHE.*\nPURPOSE.*\nMODIFY.*\nBE.*\n.*\nOR.*\nTHE.*\nPOSSIBILITY.*\n\n.*\*\//\/\/ SPDX-FileCopyrightText: Copyright \(c\) Ken Martin, Will Schroeder, Bill Lorensen\n\/\/ SPDX-FileCopyrightText: Copyright \(c\) 2006 Atamai, Inc.\n\/\/ SPDX-License-Identifier: BSD-3-Clause/g' %s

Manual MIT

Manual licenses

Xdmf2 License

PLY license

Manual VRML licenses

replace Netcdf license

Manual OpenXR license

Manual Licenses

Example Licenses manual

Manual Copyrights and licenses

Manual licensing

Removing empty lines

Manual licenses

Manual final pass

Manual Dicom

Replace all cxx without copyright info

find .  -name "*.cxx" -exec grep -L "SPDX" {} \; | grep -v ThirdParty | grep -v Utilities > files.out

cat files.out |  xargs -I %s perl -i~ -0777 -pe 's/\A(.*)\n/\/\/ SPDX-FileCopyrightText: Copyright \(c\) Ken Martin, Will Schroeder, Bill Lorensen\n\/\/ SPDX-License-Identifier: BSD-3-Clause\n$1\n/g' %s

Replace all header missing license

find .  -name "*\.h" -exec grep -L "SPDX" {} \; | grep -v ThirdParty | grep -v Utilities > files.out

cat files.out |  xargs -I %s perl -i~ -0777 -pe 's/\A(.*)\n/\/\/ SPDX-FileCopyrightText: Copyright \(c\) Ken Martin, Will Schroeder, Bill Lorensen\n\/\/ SPDX-License-Identifier: BSD-3-Clause\n$1\n/g' %s

Manual from build

Add missing license

Replace copyright.txt

Remove license files

Manual fixes found by building

Fix header testing

Add license in vtkEncodeString

Manual new filters

Review JF

Run the threshold filter on the output to discard based on ghost and
blank cells and points.

Using the abort features of VTK and VTK-m, enable abort support for the
vtkmContour filter and test it.

There was a bug, where the worklet `ReorderHex` was being explicitly marked as
device only (not using VTKM_EXEC) when CUDA was enabled. However, in
`BuildSingleTypeVoxelCellSetVisitor` where the worklet is invoked, the
Cuda device was explicitly being disabled. This results in undefined
behaviour. This path is only trigered when converting an unstructured
grid containing all Voxels to vtkm DataSet.

A recent change in VTK-m starts treating coordinate points as fields.
This requires special handling when we don't want to process
coordinates.

Addresses: #18855

This path was previously disabled because there was a bug in VTK-m's flying
edges implementation that caused crashes. The issue has since been resolved.

Addresses: #18856

1. Simplify the `ArrayHandleWrapper` classes into a single
   `ArrayHandleHelper` class.
2. Add ComputeRange functions that use VTK-m to compute the ranges.
3. Refactor the code to access the array only when setting/getting
   values. This way we can avoid unnecessary memory transfers.

Previously, this was disabled due to an issue with vtk-m's contour
filter which has now been resolved.

vtkmContour was treating `ComputeScalars` as a flag to turn on/off the
interpolation and generation of all of the fields in the output.
As per its superclass `vtkContourFilter`, it should only affect the generation
of the scalar field.

For modules in Accelerators, Charts, Web, Domains, Geovis, Parallel

This will allow the wheels to use the VTK test suite to validate
themselves.