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patchkernel: add support for parallel surface skd-tree searches #78

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merged 8 commits into from
Aug 3, 2020
Merged

patchkernel: add support for parallel surface skd-tree searches #78

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cadd24e
patchkernel: add SkdBox class to PatchSkdTree
edoardolombardi May 25, 2020
7353c06
patchkernel: fix skd tree for empty patches
edoardolombardi Jul 8, 2020
78e2cd4
patchkernel: use the flag interior-only instead of include-ghost in s…
andrea-iob Jul 24, 2020
a42e9e1
patchkernel: allow to consider only interior cells when building surf…
edoardolombardi Jun 17, 2020
9bd6bdc
patchkernel: allow to consider only interior cells in skd-tree searches
andrea-iob Jul 24, 2020
814437e
patchkernel: add functions to perform surface skd-tree searches on mu…
andrea-iob Jul 23, 2020
2b5aaff
patchkernel: add support for parallel surface skd-tree searches
edoardolombardi Jul 24, 2020
8a6698e
test/surfunstructured: add a test for the parallell skd-tree
edoardolombardi Jun 17, 2020
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519 changes: 415 additions & 104 deletions src/patchkernel/patch_skd_tree.cpp
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96 changes: 79 additions & 17 deletions src/patchkernel/patch_skd_tree.hpp
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Original file line number Diff line number Diff line change
Expand Up @@ -64,10 +64,30 @@ friend class PatchSkdTree;

};

class SkdNode {
class SkdBox {

public:
SkdBox();
SkdBox(const std::array<double,3> &boxMin, const std::array<double,3> &boxMax);

const std::array<double, 3> & getBoxMin() const;
const std::array<double, 3> & getBoxMax() const;

double evalPointMinDistance(const std::array<double, 3> &point) const;
double evalPointMaxDistance(const std::array<double, 3> &point) const;

bool boxContainsPoint(const std::array<double,3> &point, double offset) const;
bool boxIntersectsSphere(const std::array<double,3> &center, double radius) const;

protected:
std::array<double, 3> m_boxMin;
std::array<double, 3> m_boxMax;

};

class SkdNode : public SkdBox {

friend class PatchSkdTree;
friend class SkdNodeAllocator;

public:
static const std::size_t NULL_ID;
Expand All @@ -85,23 +105,18 @@ friend class SkdNodeAllocator;
std::vector<long> getCells() const;
long getCell(std::size_t n) const;

const std::array<double, 3> & getBoxMin() const;
const std::array<double, 3> & getBoxMax() const ;
const SkdBox & getBoundingBox() const;

std::array<double,3> evalBoxWeightedMean() const;

bool isLeaf() const;
bool hasChild(ChildLocation child) const;
std::size_t getChildId(ChildLocation child) const;

bool boxContainsPoint(const std::array<double,3> &point, double offset) const;
bool boxIntersectsSphere(const std::array<double,3> &center, double radius) const;

double evalPointMinDistance(const std::array<double, 3> &point) const;
double evalPointMaxDistance(const std::array<double, 3> &point) const;
double evalPointDistance(const std::array<double, 3> &point) const;
double evalPointDistance(const std::array<double, 3> &point, bool ignoreGhosts) const;

void findPointClosestCell(const std::array<double, 3> &point, long *id, double *distance) const;
void updatePointClosestCell(const std::array<double, 3> &point, long *id, double *distance) const;
void findPointClosestCell(const std::array<double, 3> &point, bool ignoreGhosts, long *id, double *distance) const;
void updatePointClosestCell(const std::array<double, 3> &point, bool ignoreGhosts, long *id, double *distance) const;

protected:
struct Allocator : std::allocator<SkdNode>
Expand All @@ -125,9 +140,6 @@ friend class SkdNodeAllocator;
std::size_t m_cellRangeBegin;
std::size_t m_cellRangeEnd;

std::array<double,3> m_boxMin;
std::array<double,3> m_boxMax;

std::array<std::size_t, MAX_CHILDREN> m_children;

void initializeBoundingBox();
Expand All @@ -138,6 +150,34 @@ friend class SkdNodeAllocator;

};

#if BITPIT_ENABLE_MPI
struct SkdGlobalCellDistance {

public:
static MPI_Datatype getMPIDatatype();
static MPI_Op getMPIMinOperation();
static void executeMPIMinOperation(SkdGlobalCellDistance *in, SkdGlobalCellDistance *inout, int *len, MPI_Datatype *datatype);

int & getRank();
long & getId();
double & getDistance();

void exportData(int *rank, long *id, double *distance) const;

private:
static bool m_MPIDatatypeInitialized;
static MPI_Datatype m_MPIDatatype;

static bool m_MPIMinOperationInitialized;
static MPI_Op m_MPIMinOperation;

double m_distance;
long m_id;
int m_rank;

};
#endif

class PatchSkdTree {

public:
Expand All @@ -158,6 +198,10 @@ class PatchSkdTree {

std::size_t evalMaxDepth(std::size_t rootId = 0) const;

#if BITPIT_ENABLE_MPI
const SkdBox & getPartitionBox(int rank) const;
#endif

protected:
SkdPatchInfo m_patchInfo;
std::vector<std::size_t> m_cellRawIds;
Expand All @@ -168,16 +212,34 @@ class PatchSkdTree {

std::vector<SkdNode, SkdNode::Allocator> m_nodes;

bool m_includeGhosts;
bool m_interiorOnly;

#if BITPIT_ENABLE_MPI
int m_rank;
int m_nProcessors;
MPI_Comm m_communicator;
std::vector<SkdBox> m_partitionBoxes;
#endif

PatchSkdTree(const PatchKernel *patch, bool includeGhosts = true);
PatchSkdTree(const PatchKernel *patch, bool interiorOnly = false);

SkdNode & _getNode(std::size_t nodeId);

#if BITPIT_ENABLE_MPI
bool isCommunicatorSet() const;
const MPI_Comm & getCommunicator() const;
void setCommunicator(MPI_Comm communicator);
void freeCommunicator();
#endif

private:
void createChildren(std::size_t parentId, std::size_t leaftThreshold);
void createLeaf(std::size_t nodeId);

#if BITPIT_ENABLE_MPI
void buildPartitionBoxes();
#endif

};

}
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