Variable topology fields
Changes to fetching in topology maps that lets you properly deal with cases where you do not know how many values are being fetched at compile time. For example, explicit cell sets can have any number of cell shapes that have different numbers of nodes.
This change should resolve issue #26.
See merge request !128
Workaround thrust 1.8 inclusive scan issue.
Starting in thrust 1.8 the implementation of scan inclusive inside
thrust became highly optimized by using parallel task groups. This
new implementation has a bug that only exists when using custom
binary operators, large size arrays, release mode, and no
debugger or mem-checker attached.
While I have submitted the issue to thrust, we need to be able
to work around the existing issue. The solution I have chosen is
to mark all vtkm::exec::cuda::interal::WrappedBinaryOperators
as being commutative as far as thrust is concerened. To make
sure we don't get any unexpected behavior I have also had
to create WrappedBinaryPredicate so that we don't mark any
predicate as commutative.
See merge request !129
Starting in thrust 1.8 the implementation of scan inclusive inside
thrust became highly optimized by using parallel task groups. This
new implementation has a bug that only exists when using custom
binary operators, large size arrays, release mode, and no
debugger or mem-checker attached.
While I have submitted the issue to thrust, we need to be able
to work around the existing issue. The solution I have chosen is
to mark all vtkm::exec::cuda::interal::WrappedBinaryOperators
as being commutative as far as thrust is concerened. To make
sure we don't get any unexpected behavior I have also had
to create WrappedBinaryPredicate so that we don't mark any
predicate as commutative.
The PGI compiler appearently saw the condition (var != var) and optimized
it to always be false. However, in this particular case var was holding
a NaN value that we were testing to make sure it does not equal itself.
Get around the problem by comparing the variable to the result of a
function call.
My version of the PGI compiler was having problems with using
IteratorFromArrayPortal with STL algorithms. I traced the problem to
iterator_facade checking to see if the reference type we gave it was
a real reference (e.g. T&). It is not, iterator_facade downgraded the
iterator trait to a simple input iterator tag even though I declared
it with a random access traversal. I don't know what the reference type
has to do with random access, but in any case the value object is
designed to behave like a reference in that when you assign to it
the value gets propagated to the array. To tell boost this is the case,
I made a specialization of boost::is_reference that declares the
value type as a reference.
I'm not sure why it failed for me but not elsewhere. It might be that
this version of the PGI compiler is using "old-style" iterator traits
whereas other were using newer style that matches better the boost
iterator traits that iterator_facade is actually using.
BOOST_MPL_ASSERT is causing warnings in the PGI compiler. Apparently,
when BOOST_MPL_ASSERT succeeds it declares a static object with a unqiue
name scoped to the file. The problem is that the PGI compiler is pretty
picky about things being declared without being used, so it was emitting
useless warnings about successful BOOST_MPL_ASSERTs. However,
BOOST_STATIC_ASSERT does not seem to have this problem, so for the benefit
of PGI change the compile-time assert method.
The PGI compiler is fussy about finding declared variables and methods
that have limited scope and are never used. Thus, it is complaining about
some internal test classes that are properly implementing the ArrayPortal
interface even though not all of it is being accessed.
To get around the problem, put them in a non-anonymous namespace with a
name unlikely to conflict with anything. The compiler will recognize that
it is possible to access these classes outside the scope of the file and
shut up about items not being used.
This class was used to store a group of from field data in a topology
map. However, the fetching has been changed to use a customized class
for each type of fetch that can be optimized for the fetch type and does
not require to know the number of items in the fetch at compile time.
Thus, this class is no longer needed, so it is being removed.
This change removes the requirement to specify some maximum cell length
in each of the worklets, which is basically impossible. It also makes
some of the loading more lazy, which might help reduce the number of
registers required in a worklet.
Previously when you fetched the indices from an explicit cell set, you
would get back a Vec of a fixed length an expected to use a subset of
it. Now you get back a Vec-like object that reports the exact length.
This Vec-like is implemented with VecFromPortal, so that the data does
not need to be copied to the stack. Rather, it is pulled from memory as
requested.
This class holds a Vec and exposes some number of components. The class
is used when you need a Vec of a size that is not known at compile time
but that a maximum length of reasonable size is known.
We want to be able to get topological connections where it is difficult
to know how many values you get each time. In this change, the type of
the vector holding the from indices is determined from the connectivity
object, and the worklet does not know the type (it must be templated).
Although you do not need to specify the max number for this value set
(you still currently do for field values), we still need to change the
type for explicit sets that uses something that does not rely on the Vec
class. The cell-to-point method also needs a Vec wrapper that allows it
to shorten the vector dynamically.
Some changes to the Vec class and VecTraits in anticipation of creating
Vec-like objects. The following changes are made:
* Add GetNumberOfComponents to Vec, which returns NUM_COMPONENTS.
* Likewise, all VecTraits have a GetNumberOfComponents method.
* The ToVec method in VecTraits is changed to CopyInto so that it can be
used when the length of the Vec-like is not known. CopyInto is also
added to Vec.
* VecTraits has a typedef named IsSizeStatic which is set to
VecTraitsTagSizeStatic when the number of components is known at compile
time and VecTraitsTagSizeVariable when the number of components is not
known until runtime.
Rename pragma guard
rename boost pre/post header guards to be thirdparty pre/post header guards to make it clear you can use them around thrust and tbb.
See merge request !125
Add in-place (in-out) arrays to worklets.
Previously, all arrays passed to worklets were designated as either
input or output. No in-place operation was permitted. This change adds
the FieldInOut tag for ControlSignature in both WorkletMapField and
WorkletMapTopology that allows you to read and write from the same
array.
See merge request !124
Previously, all arrays passed to worklets were designated as either
input or output. No in-place operation was permitted. This change adds
the FieldInOut tag for ControlSignature in both WorkletMapField and
WorkletMapTopology that allows you to read and write from the same
array.
The use of is_sorted in Benchmarker.h was ambiguous
Benchmarker provides its own implementation of is_sorted since this
method was not introduced until C++11 and not all compilers necessarily
support it. However, for those that did, the system is_sorted conflicted
with the provided is_sorted. To get around the problem, specify the full
namespace of the is_sorted being used (which is standard practice in
VTK-m anyway).
See merge request !122
Benchmarker provides its own implementation of is_sorted since this
method was not introduced until C++11 and not all compilers necessarily
support it. However, for those that did, the system is_sorted conflicted
with the provided is_sorted. To get around the problem, specify the full
namespace of the is_sorted being used (which is standard practice in
VTK-m anyway).
Clean up CellSet
Underneath the CellSet implementation is a set of supporting classes that manage the actual structure in both the control and execution environments. However, the implementation of these classes was a bit confusing and inconsistent. The following changes are made:
* Most significantly, there is no longer any Connectivity classes in the control environment. This functionality has been wrapped up into the CellSet classes, which is more consistent and easier to understand. (There was a definite distinction between CellSet and Connectivity, but it was subtle and difficult to understand.) This also means that edits to CellSets happen to CellSets directly.
* The set of classes for structured and explicit cell sets match. There is different functionality within, but the class naming and meaning are consistent.
* Make the class names more consistent with the rest of VTK-m class names. Specifically classes like ExplicitConnectivity become ConnectivityExplicit. Also, the words regular and structured were being used interchangeably. Now, always use structured except when dealing specifically with grids of regular spacing.
* The connectivity classes were using the nomenclature "From" and "To" to specify topological elements of links. The same concept in worklet classes were using the nomenclature "Src" and "Dest." For consistency, all references are changed to "From" and "To".
* Unlike explicit cell sets, structured cell sets have functionality shared between control and execution environments. Rather than duplicate it or create unique exposed classes, have a shared internal implementation in vtkm::internal.
See merge request !117
The storage used will now be aligned to `VTKM_CACHE_LINE_SIZE bytes,
resulting in slightly better cache usage and load/store performance.
This define is set in `StorageBasic.h We also now detect if Posix is
available in Configure.h and will define VTKM_POSIX with _POSIX_VERSION
if it's available.
The AlignedAllocator used by StorageBasic is also STL compatible
and can be used in STL containers so user's can use it in their
std::vector and pass aligned user memory to the storage.
(Re-) Add a helper structure that holds the connectivity information for
a particular topology connection (e.g. from points to cells) to make it
easier to manage connections in multiple different directions in
CellSetExplicit.
Unlike the previous version of connectivity, this structure is
considered "internal" and not exposed through the API so that
CellSetExplicit can better manage the data. Also, many of the helper
methods remain in CellSetExplicit since they were specific for point-to-
Also, CellSetExplicit has a mechanism to take an arbitrary pair of
TopologyElementTags and get the appropriate connectivity. This should
simplify adding connections in the future.
1ea6f732 Add our own version of is_sorted to check the assert
311b5dcc Remove C++11 feature is_sorted and increase time alloted to run bench
Acked-by: Kitware Robot <kwrobot@kitware.com>
Merge-request: !115
Don't use patched version of TBB on newer versions.
We have a patched version of TBB's parallel_for.h in our files that
fixes a problem with using std::swap. This issue has since been fixed in
TBB, so for newer versions we should revert back to TBB's
implementation.
See merge request !118
Robert Maynard tells me that the TBB backend has been tried on versions
of TBB back to 4.0. Since the patch appears to work across them, allow
those versions too.
We have a patched version of TBB's parallel_for.h in our files that
fixes a problem with using std::swap. This issue has since been fixed in
TBB, so for newer versions we should revert back to TBB's
implementation.
