There were some places in the rendering code where floating point
exceptions (FPE) could happen under certain circumstances. Often we do not
care about invalid floating point operation in rendering as they often
occur in degenerate cases that don't contribute anyway. However,
simulations that might include VTK-m might turn on FPE to check their own
operations. In such cases, we don't want errant rendering arithmetic
causing an exception and bringing down the whole code. Thus, we turn on FPE
in some of our test platforms and avoid such operations in general.
`UnknownArrayHandle` allows you to create a new instance of a compatible
array so that when receiving an array of unknown type, a place to put the
output can be created. However, these methods only worked if the number of
components in each value could be determined statically at compile time.
However, there are some special `ArrayHandle`s that can define the number
of components at runtime. In this case, the `ArrayHandle` would throw an
exception if `NewInstanceBasic` or `NewInstanceFloatBasic` was called.
Although rare, this condition could happen when, for example, an array was
extracted from an `UnknownArrayHandle` with `ExtractArrayFromComponents` or
with `CastAndCallWithExtractedArray` and then the resulting array was
passed to a function with arrays passed with `UnknownArrayHandle` such as
`ArrayCopy`.
This is a start of moving the VTK-m User's Guide into the VTK-m source.
This is only the start of the process. There are several goals of this
work.
1. Integrate the documentation into the source code better to better
keep the code up to date.
2. Move the documentation over to Sphinx so that it can be posted online
and be more easily linked.
3. Incoporate Doxygen into the guide to keep the documentation
consistent.
4. Build the user guide examples as part of the VTK-m CI to catch
compatibility changes quickly.
Getting the number of components (or the number of flattened components)
from an `ArrayHandle` is usually trivial. However, if the `ArrayHandle` is
special in that the number of components is specified at runtime, then it
becomes much more difficult to determine.
Getting the number of components is most important when extracting
component arrays (or reconstructions using component arrays) with
`UnknownArrayHandle`. Previously, `UnknownArrayHandle` used a hack to get
the number of components, which mostly worked but broke down when wrapping
a runtime array inside another array such as `ArrayHandleView`.
To prevent this issue, the ability to get the number of components has been
added to `ArrayHandle` proper. All `Storage` objects for `ArrayHandle`s now
need a method named `GetNumberOfComponentsFlat`. The implementation of this
method is usually trivial. The `ArrayHandle` template now also provides a
`GetNumberOfComponentsFlat` method that gets this information from the
`Storage`. This provides an easy access point for the `UnknownArrayHandle`
to pull this information.
We have run into an issue with some Intel compilers where if a `union`
contains a `struct` that has some padding for byte alignment, the value
copy might skip over that padding even when the `union` contains a different
type where those bytes are valid. This breaks the value copy of our
`Variant` class.
This is not a unique problem. We have seen the same thing in other
compilers and already have a workaround for when this happens. The
workaround creates a special struct that has no padding placed at the front
of the `union`. The Intel compiler adds a fun twist in that this
placeholder structure only works if the alignment is at least as high as
the struct that follows it.
To get around this problem, make the alignment of the placeholder `struct`
at large as possible for the size of the `union`.
It was taking too long to compile with a device. Redesign the
placeholder to be simpler and compile faster.
In reflection, the `WarpScalar` filter is surprisingly a superset of the
`WarpVector` features. `WarpScalar` has the ability to displace in the
directions of the mesh normals. In VTK, there is a distinction of normals
to vectors, but in VTK-m it is a matter of selecting the correct one. As
such, it makes little sense to have two separate implementations for the
same operation. The filters have been combined and the interface names have
been generalized for general warping (e.g., "normal" or "vector" becomes
"direction").
In addition to consolidating the implementation, the `Warp` filter
implementation has been updated to use the modern features of VTK-m's
filter base classes. In particular, when the `Warp` filters were originally
implemented, the filter base classes did not support more than one active
scalar field, so filters like `Warp` had to manage multiple fields
themselves. The `FilterField` base class now allows specifying multiple,
indexed active fields, and the updated implementation uses this to manage
the input vectors and scalars.
The `Warp` filters have also been updated to directly support constant
vectors and scalars, which is common for `WarpScalar` and `WarpVector`,
respectively. Previously, to implement a constant field, you had to add a
field containing an `ArrayHandleConstant`. This is still supported, but an
easier method of just selecting constant vectors or scalars makes this
easier.
Internally, the implementation now uses tricks with extracting array
components to support many different array types (including
`ArrayHandleConstant`. This allows it to simultaneously interact with
coordinates, directions, and scalars without creating too many template
instances.
The `AmrArrays` filter generates some cell fields that specify information
about the hierarchy, which are constant across all cells in a partition.
These were previously stored as an array with the same value throughout.
Now, the field is stored as an `ArrayHandleConstant`, which does not
require any real storage. Recent changes to VTK-m allow code to extract the
array as a component efficiently without knowing the storage type.
Fixes#794
The flying edges algorithm (used when contouring uniform structured cell
sets) was not interpolating cell fields correctly. There was an indexing
issue where a shortcut in the stepping was not incrementing the cell index.
There was a bug in `CleanGrid` when removing degenerate polygons where it
would not detect if the first and last point were the same. This has been
fixed.
There was also an error with function overloading that was causing 0D and
3D cells to enter the wrong computation for degenerate cells. This has also
been fixed.
Fixes#796
Previously, `ArrayHandleConstant` did not really support component
extraction. Instead, it let a fallback operation create a full array on
the CPU.
Component extraction is now quite efficient for `ArrayHandleConstant`. It
creates a basic `ArrayHandle` with one entry and sets a modulo on the
`ArrayHandleStride` to access that value for all indices.
67b7543a3 Adding documentation for flow filter restructure
dbc873efa Changes to address feedback from MR
67716402b Correct export in class declaration
6d1d4f90a Fixing linking issues for flow Analysis class
adcb42455 Removing unnecessary file
78ca3f301 Fixing linking issues for flow Analysis class
0e1ade83a Fixing linking issues for flow Analysis class
12a3bc94e Adding test dependency of filter_flow on tests
...
Acked-by: Kitware Robot <kwrobot@kitware.com>
Merge-request: !3087
Previously, the MIR filter ran a check the dimensionality of the cells in
its input data set to make sure they conformed to the algorithm. The only
real reason this was necessary is because the `MeshQuality` filter can only
check the size of either area or volume, and it has to know which one to
check. However, the `CellMeasures` filter can compute the sizes of all
types of cells simultaneously (as well as more cell types). By using this
filter, the MIR filter can skip the cell type checks and support more mesh
types.
The `GhostCellRemove` filter had some methods inconsistent with the naming
convention elsewhere in VTK-m. The class itself was also in need of some
updated documentation. Both of these issues have been fixed.
Additionally, there were some conditions that could lead to unexpected
behavior. For example, if the filter was asked to remove only ghost cells
and a cell was both a ghost cell and blank, it would not be removed. This
has been updated to be more consistent with expectations.
Previously, `VecFromPortal` could only be set to a standard `Vec`.
However, because this is a `Vec`-like object with a runtime-size, it is
hard to do general arithmetic on it. It is easier to do in place so
there is some place to put the result. To make it easier to operate on
this as the result of other `Vec`-likes, extend the operators like `+=`,
`*=`, etc to support this.
The `ExternalFaces` filter uses hash codes to find duplicate (i.e.
internal) faces. The issue with hash codes is that you have to deal with
unique entries that have identical hashes. The worklet to count how many
unique, unmatched faces were associated with each hash code was correct.
However, the code to then grab the ith unique face in a hash was wrong.
This has been fixed.
Fixes#789
Kokkos 4 switches from their interal library based off of desul to using desul directly.
This removes VTK-m's dependency on the Kokkos internal implementation (Kokkos::Impl) to
using desul directly.
This filter takes a `DataSet` and returns a point cloud representation that
has a vertex cell associated with each point in it. This is useful for
filling in a `CellSet` for data that has points but no cells. It is also
useful for operations in which you want to throw away the cell geometry and
operate on the data as a collection of disparate points.
Although the contour filter was recently divided into 2 filters, flying
edges and marching cubes, the marching cubes version still had many
conditions and was the file that took the longest to compile on Frontier.
To help speed up parallel compiles and prevent a single run of a
compiler from being overwhelmed, the compilation of all the marching
cubes conditions has been split up using instantiations.
There are occasions when you need a worklet to opeate on 2D or 3D
indices. Most worklets operate on 1D indices, which requires recomputing
the 3D index in each worklet instance. A workaround is to use a worklet
that does a 3D scheduling and pull the working index from that.
The problem was that there was no easy way to get this 3D index. To
provide this option, a feature was added to the `BoundaryState` class
that can be provided by `WorkletPointNeighborhood`.
Thus, to get a 3D index in a worklet, use the
`WorkletPointNeighborhood`, add `Boundary` as an argument to the
`ExecutionSignature`, and then call `GetCenterIndex` on the
`BoundaryState` object passed to the worklet operator.
The file `ArrayRangeCompute.cxx` was taking a long time to compile with
some device compilers. This is because it precompiles the range computation
for many types of array structures. It thus compiled the same operation
many times over.
The new implementation compiles just as many cases. However, the
compilation is split into many different translation units using the
instantiations feature of VTK-m's configuration. Although this rarely
reduces the overall CPU time spent during compiling, it prevents parallel
compiles from waiting for this one build to complete. It also avoids
potential issues with compilers running out of resources as it tries to
build a monolithic file.
Previously, the `ComputeMoments` filter only operated on a finite set of
array types as its input field. This included a prescribed list of `Vec`
sizes for the input. The filter has been updated to use more generic
interfaces to the field's array (and float fallback) to enable the
computation of moments on any type of scalar field.
The internal array copy has an optimization to use the device the array
exists on to do the copy. However, if that device is disabled the copy
would fail. This problem has been fixed.
The `FilterField` class provides convenience functions for subclasses to
determine the `ArrayHandle` type for scalar and vector fields. However, you
needed to know the specific size of vectors. For filters that support an
input field of any type, a new form, `CastAndCallVariableVecField` has been
added. This calls the underlying functor with an `ArrayHandleRecombineVec`
of the appropriate component type.
The `CastAndaCallVariableVecField` method also reduces the number of
instances created by having a float fallback for any component type that
does not satisfy the field types.
The legacy VTK file reader previously only supported a specific set of Vec
lengths (i.e., 1, 2, 3, 4, 6, and 9). This is because a basic array
handle has to have the vec length compiled in. However, the new
`ArrayHandleRuntimeVec` feature is capable of reading in any vec-length
and can be leveraged to read in arbitrarily sized vectors in field
arrays.
There was an error in `operator-=` for `IteratorFromArrayPortal` that went
by unnoticed. The operator is fixed and regression tests for the operators
has been added.
`UnknownArrayHandle` is supposed to treat `ArrayHandleRuntimeVec` the
same as `ArrayHandleBasic`. However, the `NewInstance` methods were
failing because they need custom handling of the vec size.
In addition to using uniform coordinates, the ContourFlyingEdges filter can now process any type of coordinate system, making the filter use Flying Edges in more cases
In order to compile the contour filter more efficiently, we split the contour filter into two separate translation units, corresponding to the new filters ContourFlyingEdges and ContourMarchingCells. The API for Contour filter is left totally unchanged, and tries to use flying edges if the dataset is structured and uniform.
All three contour filters inherit from the `AbstractContour` class, providing utility methods used in the implementations.
Previously, tetrahedralize/triangulate would blindly convert all the cells to tetrahedra/triangles, even when they were already. Now, the dataset is directly returned if the CellSet is a CellSetSingleType of tetras/triangles, and no further processing is done in the worklets for CellSetExplicit when all shapes are tetras or triangles.
I've been seeing errors in a nightly build that compiles for CUDA Pascal
using GCC5. The issue is that one of the `ArrayHandleMultiplexer` tests
is failing to copy an implicit array correctly. I think the problem is
that in this test the first and second type of the `Variant` are the same
size, but the first type has some padding in the middle whereas the
second type does not. When using this second type, the values in the
same position of the padding of the first type don't seem to be
initialized properly in the kernel invocation.
My nonexhaustive experiment shows that things work OK as long as the
first type is large enough and has no fillers. Enforce this by adding an
internal entry to the union that is completely full.
This new filtered designed for bi-variate analysis builds the continuous scatterplot of a 3D tetrahedralized mesh for two given scalar point fields. The continuous scatterplot is an extension of the discrete scatterplot for continuous bi-variate analysis.
The clip filter used to copy the input points and point fields as is,
regardless of if they were actually part of the output. With this change,
we track which input points are actually part of the output and copy
only those values.
Address: #112
ac889b500 Implement VecTraits class for all types
Acked-by: Kitware Robot <kwrobot@kitware.com>
Acked-by: Li-Ta Lo <ollie@lanl.gov>
Merge-request: !3018
f545feba8 Add changelog for documenting data license
a24358a1a Document source of WarpX files
60559ce9b Document the source of venn250.vtk
796ec9638 Document data that comes from VisIt tutorial
06391c4e6 Clarify license for ECL data
Acked-by: Kitware Robot <kwrobot@kitware.com>
Acked-by: Vicente Bolea <vicente.bolea@kitware.com>
Merge-request: !3016
The `VecTraits` class allows templated functions, methods, and classes to
treat type arguments uniformly as `Vec` types or to otherwise differentiate
between scalar and vector types. This only works for types that `VecTraits`
is defined for.
The `VecTraits` templated class now has a default implementation that will
be used for any type that does not have a `VecTraits` specialization. This
removes many surprise compiler errors when using a template that, unknown
to you, has `VecTraits` in its implementation.
One potential issue is that if `VecTraits` gets defined for a new type, the
behavior of `VecTraits` could change for that type in backward-incompatible
ways. If `VecTraits` is used in a purely generic way, this should not be an
issue. However, if assumptions were made about the components and length,
this could cause problems.
Fixes#589
The precompiled `ArrayRangeCompute` function was not following proper fast
paths for special arrays. For example, when computing the range of an
`ArrayHandleUniformPointCoordinates`, the ranges should be taken from the
origin and spacing of the special array. However, the precompiled version
was calling the generic range computation, which was doing an unnecessary
reduction over the entire array. These fast paths have been fixed.
These mistakes in the code were caused by quirks in how templated method
overloading works. To prevent this mistake from happening again in the
precompiled `ArrayRangeCompute` function and elsewhere, all templated forms
of `ArrayRangeCompute` have been deprecated. Most will call
`ArrayRangeCompute` with no issues. For those that need the templated
version, `ArrayRangeComputeTemplate` replaces the old templated
`ArrayRangeCompute`. There is exactly one templated declaration of
`ArrayRangeComputeTemplate` that uses a class, `ArrayRangeComputeImpl`,
with partial specialization to ensure the correct form is used.
`vtkm::cont::DataSet` is a dynamic object that can hold cell sets and
fields of many different types, none of which are known until runtime. This
causes a problem with serialization, which has to know what type to compile
the serialization for, particularly when unserializing the type at the
receiving end. The original implementation "solved" the problem by creating
a secondary wrapper object that was templated on types of field arrays and
cell sets that might be serialized. This is not a great solution as it
punts the problem to algorithm developers.
This problem has been completely solved for fields, as it is possible to
serialize most types of arrays without knowing their type now. You still
need to iterate over every possible `CellSet` type, but there are not that
many `CellSet`s that are practically encountered. Thus, there is now a
direct implementation of `Serialization` for `DataSet` that covers all the
data types you are likely to encounter.
The old `SerializableDataSet` has been deprecated. In the unlikely event an
algorithm needs to transfer a non-standard type of `CellSet` (such as a
permuted cell set), it can use the replacement `DataSetWithCellSetTypes`,
which just specifies the cell set types.
The `UnknownArrayHandle` has been updated to allow
`ArrayHandleRuntimeVec` to work interchangeably with basic
`ArrayHandle`. If an `ArrayHandleRuntimeVec` is put into an
`UnknownArrayHandle`, it can be later retrieved as an `ArrayHandleBasic`
as long as the base component type matches and it has the correct amount
of components. This means that an array can be created as an
`ArrayHandleRuntimeVec` and be used with any filters or most other
features designed to operate on basic `ArrayHandle`s. Likewise, an array
added as a basic `ArrayHandle` can be retrieved in an
`ArrayHandleRuntimeVec`. This makes it easier to pull arrays from VTK-m
and place them in external structures (such as `vtkDataArray`).
The new `ArrayHandleRuntimeVec` is a fancy `ArrayHandle` allows you to
specify a basic array of `Vec`s where the number of components of the `Vec`
are not known until runtime. (It can also optionally specify scalars.) The
behavior is much like that of `ArrayHandleGroupVecVariable` except that its
representation is much more constrained. This constrained representation
allows it to be automatically converted to an `ArrayHandleBasic` with the
proper `Vec` value type. This allows one part of code (such as a file
reader) to create an array with any `Vec` size, and then that array can be
fed to an algorithm that expects an `ArrayHandleBasic` of a certain value
type.
While updating the user's guide, I noticed a couple of minor problems
with how filters map fields. First, if a filter was using
`CreateResultCoordinateSystem`, it did not respect the
`PassCoordinateSystems` flag. Second, if both an `initializer_list` and
a mode was given to `SetFieldsToPass`, the mode was captured
incorrectly. Both problems are corrected.
The `GetNumberOfComponents` and `GetNumberOfComponentsFlat` methods in
`UnknownArrayHandle` have been updated to correctly report the number of
components in special `ArrayHandle`s where the `Vec` sizes of the values
are not selected until runtime.
Previously, these methods always reported 0 because the value type could
not report the size of the `Vec`. The lookup has been modified to query the
`ArrayHandle`'s `Storage` for the number of components where supported.
Note that this only works on `Storage` that provides a method to get the
runtime `Vec` size. If that is not provided, as will be the case if the
number of components can vary from one value to the next, it will still
report 0.
This feature is implemented by looking for a method named
`GetNumberOfComponents` is the `Storage` class for the `ArrayHandle`. If
this method is found, it is used to query the size at runtime.
Previously, `VectorMagnitude` only worked with `Vec`s of size 2, 3, or
4. It now works with `Vec`s of any size. It also avoids a memory copy of
non-float types (although it does add a little arithmetic in the
computation).
Previously, the probe filter only worked on certain `Vec` sizes and
converted many types to floating point.
This change uses the extract component feature to pull data from any
array at its natural component type.
The bad part of this change is that it has to call the worklet
separately for each component in the field. That adds overhead and
probably lowers the cache efficiency. It was implemented this way
because the cell interpolation function does not work with the
recombined vecs returned from extract array.
The previous version of the `PointAverage` filter used a float fallback
to handle most array types. The problem with this approach other than
converting field types perhaps unexpectantly is that it does not work
with every `Vec` size. This change uses the extract by component feature
of `UnknownArrayHandle` to handle every array type.
To implement this change the `PointAverage` worklet had to be changed to
handle recombined vecs. This change resulted in a feature degridation
where it can no longer be compiled for inputs of incompatible `Vec`
sizes. This feature dates back to when worklets like this were exposed
in the interface. This worklet class is now hidden away from the exposed
interface, so this degredation should not affect end users. There are
some unit tests that use this worklet to test other features, and these
had to be updated.
