From a9c90bb010ea40bccbd07d155ca23ef9a32880a6 Mon Sep 17 00:00:00 2001
From: Pietro Incardona <incardon@mpi-cbg.de>
Date: Sun, 9 Aug 2015 19:29:05 +0200
Subject: [PATCH] Adding refactored files
---
src/Decomposition/ie_ghost.hpp | 244 +++++++++++++++++++++++++++++
src/Decomposition/nn_processor.hpp | 226 ++++++++++++++++++++++++++
2 files changed, 470 insertions(+)
create mode 100644 src/Decomposition/ie_ghost.hpp
create mode 100644 src/Decomposition/nn_processor.hpp
diff --git a/src/Decomposition/ie_ghost.hpp b/src/Decomposition/ie_ghost.hpp
new file mode 100644
index 00000000..76e9eb50
--- /dev/null
+++ b/src/Decomposition/ie_ghost.hpp
@@ -0,0 +1,244 @@
+/*
+ * ie_ghost.hpp
+ *
+ * Created on: Aug 8, 2015
+ * Author: i-bird
+ */
+
+#ifndef SRC_DECOMPOSITION_IE_GHOST_HPP_
+#define SRC_DECOMPOSITION_IE_GHOST_HPP_
+
+#include "common.hpp"
+
+/*! \brief structure that store and compute the internal and external local ghost box
+ *
+ * \tparam dim is the dimensionality of the physical domain we are going to decompose.
+ * \tparam T type of the space we decompose, Real, Integer, Complex ...
+ *
+ * \see CartDecomposition
+ *
+ */
+template<unsigned int dim, typename T>
+class ie_ghost
+{
+ //! for each sub-domain (first vector), contain the list (nested vector) of the neighborhood processors
+ //! and for each processor contain the boxes calculated from the intersection
+ //! of the sub-domains + ghost with the near-by processor sub-domain () and the other way around
+ //! \see calculateGhostBoxes
+ openfpm::vector< openfpm::vector< Box_proc<dim,T> > > box_nn_processor_int;
+
+ //! It store the same information of box_nn_processor_int organized by processor id
+ openfpm::vector< Box_dom<dim,T> > proc_int_box;
+
+ /*! \brief Create the box_nn_processor_int (bx part) structure
+ *
+ * This structure store for each sub-domain of this processors enlarged by the ghost size the boxes that
+ * come from the intersection with the near processors sub-domains (External ghost box)
+ *
+ * \param ghost margins
+ *
+ * \note Are the G8_0 G9_0 G9_1 G5_0 boxes in calculateGhostBoxes
+ * \see calculateGhostBoxes
+ *
+ */
+ void create_box_nn_processor_ext(Ghost<dim,T> & ghost, openfpm::vector<SpaceBox<dim,T>> & sub_domains)
+ {
+/* box_nn_processor_int.resize(sub_domains.size());
+ proc_int_box.resize(getNNProcessors());
+
+ // For each sub-domain
+ for (size_t i = 0 ; i < sub_domains.size() ; i++)
+ {
+ SpaceBox<dim,T> sub_with_ghost = sub_domains.get(i);
+
+ // enlarge the sub-domain with the ghost
+ sub_with_ghost.enlarge(ghost);
+
+ // resize based on the number of adjacent processors
+ box_nn_processor_int.get(i).resize(box_nn_processor.get(i).size());
+
+ // For each processor adjacent to this sub-domain
+ for (size_t j = 0 ; j < box_nn_processor.get(i).size() ; j++)
+ {
+ // Contiguous processor
+ size_t p_id = box_nn_processor.get(i).get(j);
+
+ // store the box in proc_int_box storing from which sub-domain they come from
+ Box_dom & proc_int_box_g = proc_int_box.get(ProctoID(p_id));
+
+ // get the set of sub-domains of the adjacent processor p_id
+ openfpm::vector< ::Box<dim,T> > & nn_processor_subdomains_g = nn_processor_subdomains[p_id].bx;
+
+ // near processor sub-domain intersections
+ openfpm::vector< ::Box<dim,T> > & box_nn_processor_int_gg = box_nn_processor_int.get(i).get(j).bx;
+
+ // for each near processor sub-domain intersect with the enlarged local sub-domain and store it
+ for (size_t b = 0 ; b < nn_processor_subdomains_g.size() ; b++)
+ {
+ ::Box<dim,T> bi;
+
+ bool intersect = sub_with_ghost.Intersect(::Box<dim,T>(nn_processor_subdomains_g.get(b)),bi);
+
+ if (intersect == true)
+ {
+ struct p_box pb;
+
+ pb.box = bi;
+ pb.proc = p_id;
+ pb.lc_proc = ProctoID(p_id);
+
+ //
+ // Updating
+ //
+ // vb_ext
+ // box_nn_processor_int
+ // proc_int_box
+ //
+ // They all store the same information but organized in different ways
+ // read the description of each for more information
+ //
+ vb_ext.add(pb);
+ box_nn_processor_int_gg.add(bi);
+ proc_int_box_g.ebx.add();
+ proc_int_box_g.ebx.last() = bi;
+ proc_int_box_g.ebx.last().sub = i;
+
+ // Search for the correct id
+ size_t k = 0;
+ size_t p_idp = ProctoID(p_id);
+ for (k = 0 ; k < proc_adj_box.get(p_idp).size() ; k++)
+ {
+ if (proc_adj_box.get(p_idp).get(k) == i)
+ break;
+ }
+ if (k == proc_adj_box.get(p_idp).size())
+ std::cerr << "Error: " << __FILE__ << ":" << __LINE__ << " sub-domain not found\n";
+
+ proc_int_box_g.ebx.last().id = (k * nn_processor_subdomains_g.size() + b) * v_cl.getProcessingUnits() + p_id;
+ }
+ }
+ }
+ }*/
+ }
+
+ /*! \brief Create the box_nn_processor_int (nbx part) structure, the geo_cell list and proc_int_box
+ *
+ * This structure store for each sub-domain of this processors the boxes that come from the intersection
+ * of the near processors sub-domains enlarged by the ghost size (Internal ghost box). These boxes
+ * fill a geometrical cell list. The proc_int_box store the same information ordered by near processors
+ *
+ * \param ghost margins
+ *
+ * \note Are the B8_0 B9_0 B9_1 B5_0 boxes in calculateGhostBoxes
+ * \see calculateGhostBoxes
+ *
+ */
+ void create_box_nn_processor_int(Ghost<dim,T> & ghost, openfpm::vector<SpaceBox<dim,T>> & sub_domains, const openfpm::vector<openfpm::vector<long unsigned int> > & box_nn_processors, const nn_prcs<dim,T> & nn_p )
+ {
+ box_nn_processor_int.resize(sub_domains.size());
+ proc_int_box.resize(nn_p.getNNProcessors());
+
+ // For each sub-domain
+ for (size_t i = 0 ; i < sub_domains.size() ; i++)
+ {
+ // For each processor contiguous to this sub-domain
+ for (size_t j = 0 ; j < box_nn_processor.get(i).size() ; j++)
+ {
+ // Contiguous processor
+ size_t p_id = box_nn_processor.get(i).get(j);
+
+ // get the set of sub-domains of the contiguous processor p_id
+ openfpm::vector< ::Box<dim,T> > & nn_p_box = nn_p.get nn_processor_subdomains[p_id].bx;
+
+ // get the local processor id
+ size_t lc_proc = nn_processor_subdomains[p_id].id;
+
+ // For each near processor sub-domains enlarge and intersect with the local sub-domain and store the result
+ for (size_t k = 0 ; k < nn_p_box.size() ; k++)
+ {
+
+ // enlarge the near-processor sub-domain
+ ::Box<dim,T> n_sub = nn_p_box.get(k);
+
+ // local sub-domain
+ ::SpaceBox<dim,T> l_sub = sub_domains.get(i);
+
+ // Create a margin of ghost size around the near processor sub-domain
+ n_sub.enlarge(ghost);
+
+ // Intersect with the local sub-domain
+ p_box b_int;
+ bool intersect = n_sub.Intersect(l_sub,b_int.box);
+
+ // store if it intersect
+ if (intersect == true)
+ {
+ // the box fill with the processor id
+ b_int.proc = p_id;
+
+ // fill the local processor id
+ b_int.lc_proc = lc_proc;
+
+ //
+ // Updating
+ //
+ // vb_int
+ // box_nn_processor_int
+ // proc_int_box
+ //
+ // They all store the same information but organized in different ways
+ // read the description of each for more information
+ //
+
+ // add the box to the near processor sub-domain intersections
+ openfpm::vector< ::Box<dim,T> > & p_box_int = box_nn_processor_int.get(i).get(j).nbx;
+ p_box_int.add(b_int.box);
+ vb_int.add(b_int);
+
+ // store the box in proc_int_box storing from which sub-domain they come from
+ Box_dom & pr_box_int = proc_int_box.get(ProctoID(p_id));
+ Box_sub<dim,T> sb;
+ sb = b_int.box;
+ sb.sub = i;
+
+ // Search for the correct id
+ size_t s = 0;
+ size_t p_idp = ProctoID(p_id);
+ for (s = 0 ; s < proc_adj_box.get(p_idp).size() ; s++)
+ {
+ if (proc_adj_box.get(p_idp).get(s) == i)
+ break;
+ }
+ if (s == proc_adj_box.get(p_idp).size())
+ std::cerr << "Error: " << __FILE__ << ":" << __LINE__ << " sub-domain not found\n";
+
+ sb.id = (k * proc_adj_box.get(p_idp).size() + s) * v_cl.getProcessingUnits() + v_cl.getProcessUnitID();
+
+ pr_box_int.ibx.add(sb);
+
+ // update the geo_cell list
+
+ // get the cells this box span
+ const grid_key_dx<dim> p1 = geo_cell.getCellGrid(b_int.box.getP1());
+ const grid_key_dx<dim> p2 = geo_cell.getCellGrid(b_int.box.getP2());
+
+ // Get the grid and the sub-iterator
+ auto & gi = geo_cell.getGrid();
+ grid_key_dx_iterator_sub<dim> g_sub(gi,p1,p2);
+
+ // add the box-id to the cell list
+ while (g_sub.isNext())
+ {
+ auto key = g_sub.get();
+ geo_cell.addCell(gi.LinId(key),vb_int.size()-1);
+ ++g_sub;
+ }
+ }
+ }
+ }
+ }
+ }
+};
+
+
+#endif /* SRC_DECOMPOSITION_IE_GHOST_HPP_ */
diff --git a/src/Decomposition/nn_processor.hpp b/src/Decomposition/nn_processor.hpp
new file mode 100644
index 00000000..b4328817
--- /dev/null
+++ b/src/Decomposition/nn_processor.hpp
@@ -0,0 +1,226 @@
+/*
+ * nn_processor.hpp
+ *
+ * Created on: Aug 9, 2015
+ * Author: i-bird
+ */
+
+#ifndef SRC_DECOMPOSITION_NN_PROCESSOR_HPP_
+#define SRC_DECOMPOSITION_NN_PROCESSOR_HPP_
+
+#include "common.hpp"
+
+/*! \brief This class store the adjacent processors and the adjacent sub_domains
+ *
+ * \tparam dim is the dimensionality of the physical domain we are going to decompose.
+ * \tparam T type of the space we decompose, Real, Integer, Complex ...
+ *
+ * \see CartDecomposition
+ *
+ */
+template<unsigned int dim, typename T>
+class nn_prcs
+{
+ //! Virtual cluster
+ Vcluster & v_cl;
+
+ //! List of adjacent processors
+ openfpm::vector<size_t> nn_processors;
+
+ // for each near-processor store the sub-domain of the near processor
+ std::unordered_map<size_t, N_box<dim,T>> nn_processor_subdomains;
+
+ // for each processor store the set of the sub-domains sent to the adjacent processors
+ openfpm::vector<openfpm::vector<size_t>> proc_adj_box;
+
+ //! contain the internal adjacent sub-domains sent to the other processors
+ openfpm::vector< openfpm::vector< ::SpaceBox<dim,T>> > boxes;
+
+ // Receive counter
+ size_t recv_cnt;
+
+ /*! \brief Message allocation
+ *
+ * \param message size required to receive from i
+ * \param total message size to receive from all the processors
+ * \param the total number of processor want to communicate with you
+ * \param i processor id
+ * \param ri request id (it is an id that goes from 0 to total_p, and is unique
+ * every time message_alloc is called)
+ * \param ptr a pointer to the vector_dist structure
+ *
+ * \return the pointer where to store the message
+ *
+ */
+ static void * message_alloc(size_t msg_i ,size_t total_msg, size_t total_p, size_t i, size_t ri, void * ptr)
+ {
+ // cast the pointer
+ nn_prcs<dim,T> * cd = static_cast< nn_prcs<dim,T> *>(ptr);
+
+ // Resize the memory
+ cd->nn_processor_subdomains[i].bx.resize(msg_i / sizeof(::Box<dim,T>) );
+
+ // Return the receive pointer
+ return cd->nn_processor_subdomains[i].bx.getPointer();
+ }
+
+public:
+
+ nn_prcs(Vcluster & v_cl)
+ :v_cl(v_cl){}
+
+ /*! \brief Create the list of adjacent processors and the list of adjacent sub-domains
+ *
+ * \param box_nn_processors
+ *
+ */
+ void create(const openfpm::vector<openfpm::vector<long unsigned int> > & box_nn_processor, const openfpm::vector<SpaceBox<dim,T>> & sub_domains)
+ {
+ // produce the list of the contiguous processor (nn_processors) and link nn_processor_subdomains to the
+ // processor list
+ for (size_t i = 0 ; i < box_nn_processor.size() ; i++)
+ {
+ for (size_t j = 0 ; j < box_nn_processor.get(i).size() ; j++)
+ {
+ nn_processors.add(box_nn_processor.get(i).get(j));
+ }
+ }
+
+ // make the list sorted and unique
+ std::sort(nn_processors.begin(), nn_processors.end());
+ auto last = std::unique(nn_processors.begin(), nn_processors.end());
+ nn_processors.erase(last, nn_processors.end());
+
+ // create a buffer with the sub-domains of this processor, the informations ( the boxes )
+ // of the sub-domains contiguous to the processor A are sent to the processor A and
+ // the information of the contiguous sub-domains in the near processors are received
+ //
+ proc_adj_box.resize(getNNProcessors());
+ boxes.resize(nn_processors.size());
+
+ for (size_t b = 0 ; b < box_nn_processor.size() ; b++)
+ {
+ for (size_t p = 0 ; p < box_nn_processor.get(b).size() ; p++)
+ {
+ size_t prc = box_nn_processor.get(b).get(p);
+
+ // id of the processor in the processor list
+ // [value between 0 and the number of the near processors]
+ size_t id = nn_processor_subdomains[prc].id;
+
+ boxes.get(id).add(sub_domains.get(b));
+ proc_adj_box.get(id).add(b);
+ }
+ }
+
+ // Intersect all the local sub-domains with the sub-domains of the contiguous processors
+
+ // Get the sub-domains of the near processors
+ v_cl.sendrecvMultipleMessagesNBX(nn_processors,boxes,nn_prcs<dim,T>::message_alloc, this ,NEED_ALL_SIZE);
+
+
+ }
+
+ /*! \brief Get the number of Near processors
+ *
+ * \return the number of near processors
+ *
+ */
+ inline size_t getNNProcessors() const
+ {
+ return nn_processors.size();
+ }
+
+ /*! \brief Return the processor id of the near processor list at place id
+ *
+ * \param id
+ *
+ * \return return the processor rank
+ *
+ */
+ inline size_t IDtoProc(size_t id)
+ {
+ return nn_processors.get(id);
+ }
+
+ /*! \brief Get the sub-domain pf an adjacent processor
+ *
+ * \param p_id adjacent processor (id from 0 to getNNProcessors())
+ *
+ * \return the sub-domains
+ *
+ */
+ inline const openfpm::vector< ::Box<dim,T> > & getAdjacentSubdomain(size_t p_id)
+ {
+ return nn_processor_subdomains[p_id].bx;
+ }
+
+ /*! \brief Get the adjacent processor id
+ *
+ * \param p_id adjacent processor (id from 0 to getNNProcessors())
+ *
+ * \return the processor rank
+ *
+ */
+ inline size_t getAdjacentProcessor(size_t p_id)
+ {
+ return nn_processor_subdomains[p_id].id;
+ }
+
+
+ /*! \brief Get the local sub-domains adjacent to a processor p_id
+ *
+ * \param p_id adjacent processor (id from 0 to getNNProcessors())
+ *
+ * \return the sub-domains
+ *
+ */
+ inline const openfpm::vector<size_t> & getInternalAdjSubdomain(size_t p_id)
+ {
+ return proc_adj_box.get(p_id);
+ }
+
+ /*! \brief Convert the processor rank to the id in the list
+ *
+ * \param p processor rank
+ *
+ * \return the id
+ *
+ */
+ inline size_t ProctoID(size_t p)
+ {
+ return nn_processor_subdomains[p].id;
+ }
+
+ /*! \brief Write the decomposition as VTK file
+ *
+ * The function generate several files
+ *
+ * 1) subdomains_adjacent_X.vtk sub-domains adjacent to the local processor (X)
+ *
+ * where X is the local processor rank
+ *
+ * \param output directory where to write the files
+ * \param p_id id of the local processor
+ *
+ */
+ bool write(std::string output) const
+ {
+ //! subdomains_adjacent_X.vtk sub-domains adjacent to the local processor (X)
+ VTKWriter<openfpm::vector<::Box<dim,T>>,VECTOR_BOX> vtk_box2;
+ for (size_t p = 0 ; p < nn_processors.size() ; p++)
+ {
+ size_t prc = nn_processors.get(p);
+ auto it = nn_processor_subdomains.find(prc);
+ if (it != nn_processor_subdomains.end())
+ vtk_box2.add(nn_processor_subdomains.at(prc).bx);
+ }
+ vtk_box2.write(output + std::string("subdomains_adjacent_") + std::to_string(v_cl.getProcessUnitID()) + std::string(".vtk"));
+
+ return true;
+ }
+
+};
+
+
+#endif /* SRC_DECOMPOSITION_NN_PROCESSOR_HPP_ */
--
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