From 664bf178e230178befd7b4b6324acd03f07552ff Mon Sep 17 00:00:00 2001
From: Pietro Incardona <incardon@mpi-cbg.de>
Date: Sat, 17 Sep 2016 00:58:38 +0200
Subject: [PATCH] Semi-working vector with complex
---
src/Vector/vector_dist_comm.hpp | 708 +++++++--------------------
src/Vector/vector_dist_unit_test.hpp | 5 +
2 files changed, 173 insertions(+), 540 deletions(-)
diff --git a/src/Vector/vector_dist_comm.hpp b/src/Vector/vector_dist_comm.hpp
index 5b3871f8e..9f45b1c49 100644
--- a/src/Vector/vector_dist_comm.hpp
+++ b/src/Vector/vector_dist_comm.hpp
@@ -30,6 +30,9 @@
template<unsigned int dim, typename St, typename prop, typename Decomposition = CartDecomposition<dim,St>, typename Memory = HeapMemory>
class vector_dist_comm
{
+ //! definition of the send vector for position
+ typedef openfpm::vector<Point<dim, St>, Memory> send_pos_vector;
+
//! VCluster
Vcluster & v_cl;
@@ -40,45 +43,68 @@ class vector_dist_comm
openfpm::vector<size_t> p_map_req;
//! For each near processor, outgoing particle id
- openfpm::vector<openfpm::vector<size_t>> opart;
+ //! \warning opart is assumed to be an ordered list
+ //! first id particle id
+ //! second id shift id
+ //! third id is the processor id
+ openfpm::vector<aggregate<size_t,size_t,size_t>> m_opart;
- //! For each near processor, particle shift vector
- openfpm::vector<openfpm::vector<size_t>> oshift;
+ //! Per processor ordered particles id for ghost_get
+ //! For each processor the internal vector store the id of the
+ //! particles that must be communicated to the other processors
+ openfpm::vector<openfpm::vector<aggregate<size_t,size_t>>> g_opart;
//! For each adjacent processor the size of the ghost sending buffer
openfpm::vector<size_t> ghost_prc_sz;
- //! Sending buffer for the ghost particles properties
- BHeapMemory g_prp_mem;
-
//! Sending buffer for the ghost particles position
- BHeapMemory g_pos_mem;
+ openfpm::vector<send_pos_vector> g_pos_send;
- //! For each adjacent processor it store from which processor come from
- openfpm::vector<size_t> prc_recv;
+ //! It store the list of processor that communicate with us (local processor)
+ //! from the last ghost get
+ openfpm::vector<size_t> prc_recv_get;
- //! the same as prc_recv but for put
+ //! the same as prc_recv_get but for put
openfpm::vector<size_t> prc_recv_put;
- //! Number of received elements
- openfpm::vector<size_t> n_recv_ele;
+ //! the same as prc_recv_get but for map
+ openfpm::vector<size_t> prc_recv_map;
- //! For each adjacent processor it store the size of the receiving message in byte
- openfpm::vector<size_t> recv_sz;
+ //! It store the size of the elements added for each processor that communicate with us (local processor)
+ //! from the last ghost get
+ openfpm::vector<size_t> recv_sz_get;
- //! The same as recv_sz but for put
+ //! The same as recv_sz_get but for put
openfpm::vector<size_t> recv_sz_put;
- //! For each adjacent processor it store the received message for ghost get
- openfpm::vector<BHeapMemory> recv_mem_gg;
-
- //! For each processor it store the received message for global map
- openfpm::vector<BHeapMemory> recv_mem_gm;
+ //! The same as recv_sz_get but for map
+ openfpm::vector<size_t> recv_sz_map;
//! Local ghost marker (across the ghost particles it mark from where we have the)
//! replicated ghost particles that are local
size_t lg_m;
+ /*! \brief Return a valid particle starting from end and tracing back
+ *
+ * \param end actual opart particle pointer
+ * \param actual end particle point
+ *
+ * \return a valid particle
+ *
+ */
+ inline size_t get_end_valid(long int & end, long int & end_id)
+ {
+ end_id--;
+
+ while (end >= 0 && end_id >= 0 && (long int)m_opart.template get<0>(end) == end_id)
+ {
+ end_id--;
+ end--;
+ }
+
+ return end_id;
+ }
+
/*! \brief It store for each processor the position and properties vector of the particles
*
* This structure is used in the map function
@@ -106,9 +132,6 @@ class vector_dist_comm
openfpm::vector<sel_prop, PreAllocHeapMemory<2>, typename memory_traits_lin<sel_prop>::type, memory_traits_lin, openfpm::grow_policy_identity> prp;
};
- //! definition of the send vector for position
- typedef openfpm::vector<Point<dim, St>, ExtPreAlloc<Memory>, typename memory_traits_lin<Point<dim, St>>::type, memory_traits_lin , openfpm::grow_policy_identity> send_pos_vector;
-
//! Flags that indicate that the function createShiftBox() has been called
bool is_shift_box_created = false;
@@ -329,7 +352,7 @@ class vector_dist_comm
* \param prAlloc_pos Memory object for the send buffer
*
*/
- void fill_send_ghost_pos_buf(openfpm::vector<Point<dim, St>> & v_pos,openfpm::vector<send_pos_vector> & g_pos_send, ExtPreAlloc<Memory> * prAlloc_pos)
+ void fill_send_ghost_pos_buf(openfpm::vector<Point<dim, St>> & v_pos,openfpm::vector<send_pos_vector> & g_pos_send)
{
// get the shift vectors
const openfpm::vector<Point<dim, St>> & shifts = dec.getShiftVectors();
@@ -338,20 +361,17 @@ class vector_dist_comm
g_pos_send.resize(ghost_prc_sz.size());
for (size_t i = 0; i < g_pos_send.size(); i++)
{
- // set the preallocated memory to ensure contiguity
- g_pos_send.get(i).setMemory(*prAlloc_pos);
-
// resize the sending vector (No allocation is produced)
g_pos_send.get(i).resize(ghost_prc_sz.get(i));
}
// Fill the send buffer
- for (size_t i = 0; i < opart.size(); i++)
+ for (size_t i = 0; i < g_opart.size(); i++)
{
- for (size_t j = 0; j < opart.get(i).size(); j++)
+ for (size_t j = 0; j < g_opart.get(i).size(); j++)
{
- Point<dim, St> s = v_pos.get(opart.get(i).get(j));
- s -= shifts.get(oshift.get(i).get(j));
+ Point<dim, St> s = v_pos.get(g_opart.get(i).template get<0>(j));
+ s -= shifts.get(g_opart.get(i).template get<1>(j));
g_pos_send.get(i).set(j, s);
}
}
@@ -369,27 +389,24 @@ class vector_dist_comm
* \param g_m ghost marker
*
*/
- template<typename send_vector, typename prp_object, int ... prp> void fill_send_ghost_put_prp_buf(openfpm::vector<prop> & v_prp, openfpm::vector<send_vector> & g_send_prp, ExtPreAlloc<Memory> * prAlloc_prp, size_t & g_m)
+ template<typename send_vector, typename prp_object, int ... prp> void fill_send_ghost_put_prp_buf(openfpm::vector<prop> & v_prp, openfpm::vector<send_vector> & g_send_prp, size_t & g_m)
{
// create a number of send buffers equal to the near processors
// from which we received
- g_send_prp.resize(prc_recv.size());
+ g_send_prp.resize(prc_recv_get.size());
for (size_t i = 0; i < g_send_prp.size(); i++)
{
- // set the preallocated memory to ensure contiguity
- g_send_prp.get(i).setMemory(*prAlloc_prp);
-
// resize the sending vector (No allocation is produced)
- g_send_prp.get(i).resize(n_recv_ele.get(i));
+ g_send_prp.get(i).resize(recv_sz_get.get(i));
}
size_t accum = g_m;
// Fill the send buffer
- for (size_t i = 0; i < prc_recv.size(); i++)
+ for (size_t i = 0; i < prc_recv_get.size(); i++)
{
size_t j2 = 0;
- for (size_t j = accum; j < accum + n_recv_ele.get(i); j++)
+ for (size_t j = accum; j < accum + recv_sz_get.get(i); j++)
{
// source object type
typedef encapc<1, prop, typename openfpm::vector<prop>::layout_type> encap_src;
@@ -402,7 +419,7 @@ class vector_dist_comm
j2++;
}
- accum = accum + n_recv_ele.get(i);
+ accum = accum + recv_sz_get.get(i);
}
}
@@ -417,23 +434,20 @@ class vector_dist_comm
* \param prAlloc_prp Memory object for the send buffer
*
*/
- template<typename send_vector, typename prp_object, int ... prp> void fill_send_ghost_prp_buf(openfpm::vector<prop> & v_prp, openfpm::vector<send_vector> & g_send_prp, ExtPreAlloc<Memory> * prAlloc_prp)
+ template<typename send_vector, typename prp_object, int ... prp> void fill_send_ghost_prp_buf(openfpm::vector<prop> & v_prp, openfpm::vector<send_vector> & g_send_prp)
{
// create a number of send buffers equal to the near processors
g_send_prp.resize(ghost_prc_sz.size());
for (size_t i = 0; i < g_send_prp.size(); i++)
{
- // set the preallocated memory to ensure contiguity
- g_send_prp.get(i).setMemory(*prAlloc_prp);
-
// resize the sending vector (No allocation is produced)
g_send_prp.get(i).resize(ghost_prc_sz.get(i));
}
// Fill the send buffer
- for (size_t i = 0; i < opart.size(); i++)
+ for (size_t i = 0; i < g_opart.size(); i++)
{
- for (size_t j = 0; j < opart.get(i).size(); j++)
+ for (size_t j = 0; j < g_opart.get(i).size(); j++)
{
// source object type
typedef encapc<1, prop, typename openfpm::vector<prop>::layout_type> encap_src;
@@ -441,7 +455,7 @@ class vector_dist_comm
typedef encapc<1, prp_object, typename openfpm::vector<prp_object>::layout_type> encap_dst;
// Copy only the selected properties
- object_si_d<encap_src, encap_dst, OBJ_ENCAP, prp...>(v_prp.get(opart.get(i).get(j)), g_send_prp.get(i).get(j));
+ object_si_d<encap_src, encap_dst, OBJ_ENCAP, prp...>(v_prp.get(g_opart.get(i).template get<0>(j)), g_send_prp.get(i).get(j));
}
}
}
@@ -455,49 +469,51 @@ class vector_dist_comm
* \param pb send buffer
*
*/
- void fill_send_map_buf(openfpm::vector<Point<dim, St>> & v_pos, openfpm::vector<prop> & v_prp,openfpm::vector<size_t> & prc_r, openfpm::vector<size_t> & prc_sz_r, openfpm::vector<pos_prop> & pb)
+ void fill_send_map_buf(openfpm::vector<Point<dim, St>> & v_pos, openfpm::vector<prop> & v_prp, openfpm::vector<size_t> & prc_sz_r, openfpm::vector<openfpm::vector<Point<dim,St>>> & m_pos, openfpm::vector<openfpm::vector<prop>> & m_prp)
{
- pb.resize(prc_r.size());
+ m_prp.resize(prc_sz_r.size());
+ m_pos.resize(prc_sz_r.size());
+ openfpm::vector<size_t> cnt(prc_sz_r.size());
- for (size_t i = 0; i < prc_r.size(); i++)
+ for (size_t i = 0; i < prc_sz_r.size() ; i++)
{
- // Create the size required to store the particles position and properties to communicate
- size_t s1 = openfpm::vector<Point<dim, St>, HeapMemory, typename memory_traits_lin<Point<dim, St>>::type, memory_traits_lin, openfpm::grow_policy_identity>::calculateMem(prc_sz_r.get(i), 0);
- size_t s2 = openfpm::vector<prop, HeapMemory, typename memory_traits_lin<prop>::type, memory_traits_lin, openfpm::grow_policy_identity>::calculateMem(prc_sz_r.get(i), 0);
-
- // Preallocate the memory
- size_t sz[2] = { s1, s2 };
- PreAllocHeapMemory<2> * mem = new PreAllocHeapMemory<2>(sz);
-
- // Set the memory allocator
- pb.get(i).pos.setMemory(*mem);
- pb.get(i).prp.setMemory(*mem);
-
// set the size and allocate, using mem warant that pos and prp is contiguous
- pb.get(i).pos.resize(prc_sz_r.get(i));
- pb.get(i).prp.resize(prc_sz_r.get(i));
+ m_pos.get(i).resize(prc_sz_r.get(i));
+ m_prp.get(i).resize(prc_sz_r.get(i));
+ cnt.get(i) = 0;
}
- // Run through all the particles and fill the sending buffer
+ // end vector point
+ long int id_end = v_pos.size();
- for (size_t i = 0; i < opart.size(); i++)
+ // end opart point
+ long int end = m_opart.size()-1;
+
+ // Run through all the particles and fill the sending buffer
+ for (size_t i = 0; i < m_opart.size(); i++)
{
- auto it = opart.get(i).getIterator();
- size_t lbl = p_map_req.get(i);
+ size_t lbl = p_map_req.get(m_opart.template get<2>(i));
+ size_t id = m_opart.template get<0>(i);
- while (it.isNext())
- {
- size_t key = it.get();
- size_t id = opart.get(i).get(key);
+ m_pos.get(lbl).set(cnt.get(lbl), v_pos.get(id));
+ m_prp.get(lbl).set(cnt.get(lbl), v_prp.get(id));
+ cnt.get(lbl)++;
- pb.get(lbl).pos.set(key, v_pos.get(id));
- pb.get(lbl).prp.set(key, v_prp.get(id));
+ // swap the particle
+ long int id_valid = get_end_valid(end,id_end);
- ++it;
+ if (id_valid > 0 && (long int)id < id_valid)
+ {
+ v_pos.set(id,v_pos.get(id_valid));
+ v_prp.set(id,v_prp.get(id_valid));
}
}
+
+ v_pos.resize(v_pos.size() - m_opart.size());
+ v_prp.resize(v_prp.size() - m_opart.size());
}
+
/*! \brief allocate and fill the send buffer for the map function
*
* \param v_pos vector of particle positions
@@ -507,54 +523,53 @@ class vector_dist_comm
* \param pb send buffer
*
*/
- template<typename prp_object,int ... prp> void fill_send_map_buf_list(openfpm::vector<Point<dim, St>> & v_pos, openfpm::vector<prop> & v_prp, openfpm::vector<size_t> & prc_r, openfpm::vector<size_t> & prc_sz_r, openfpm::vector<pos_prop_sel<prp_object>> & pb)
+ template<typename prp_object,int ... prp> void fill_send_map_buf_list(openfpm::vector<Point<dim, St>> & v_pos, openfpm::vector<prop> & v_prp, openfpm::vector<size_t> & prc_r, openfpm::vector<size_t> & prc_sz_r, openfpm::vector<openfpm::vector<Point<dim,St>>> & m_pos, openfpm::vector<openfpm::vector<prp_object>> & m_prp)
{
- pb.resize(prc_r.size());
+ m_prp.resize(v_cl.getProcessingUnits());
+ m_pos.resize(v_cl.getProcessingUnits());
+ openfpm::vector<size_t> cnt(v_cl.getProcessingUnits());
for (size_t i = 0; i < prc_r.size(); i++)
{
- // Create the size required to store the particles position and properties to communicate
- size_t s1 = openfpm::vector<Point<dim, St>, HeapMemory, typename memory_traits_lin<Point<dim, St>>::type, memory_traits_lin, openfpm::grow_policy_identity>::calculateMem(prc_sz_r.get(i), 0);
- size_t s2 = openfpm::vector<prp_object, HeapMemory, typename memory_traits_lin<prp_object>::type, memory_traits_lin, openfpm::grow_policy_identity>::calculateMem(prc_sz_r.get(i), 0);
-
- // Preallocate the memory
- size_t sz[2] = { s1, s2 };
- PreAllocHeapMemory<2> * mem = new PreAllocHeapMemory<2>(sz);
-
- // Set the memory allocator
- pb.get(i).pos.setMemory(*mem);
- pb.get(i).prp.setMemory(*mem);
-
// set the size and allocate, using mem warant that pos and prp is contiguous
- pb.get(i).pos.resize(prc_sz_r.get(i));
- pb.get(i).prp.resize(prc_sz_r.get(i));
+ m_pos.get(i).resize(prc_sz_r.get(i));
+ m_prp.get(i).resize(prc_sz_r.get(i));
}
- // Run through all the particles and fill the sending buffer
+ // end vector point
+ long int id_end = v_pos.size();
+
+ // end opart point
+ long int end = m_opart.size()-1;
- for (size_t i = 0; i < opart.size(); i++)
+ // Run through all the particles and fill the sending buffer
+ for (size_t i = 0; i < m_opart.size(); i++)
{
- auto it = opart.get(i).getIterator();
- size_t lbl = p_map_req.get(i);
+ size_t lbl = m_opart.template get<2>(i);
+ size_t id = m_opart.template get<0>(i);
- while (it.isNext())
- {
- size_t key = it.get();
- size_t id = opart.get(i).get(key);
+ m_pos.get(lbl).set(cnt.get(lbl), v_pos.get(id));
- pb.get(lbl).pos.set(key, v_pos.get(id));
+ // source object type
+ typedef encapc<1, prop, typename openfpm::vector<prop>::layout_type> encap_src;
+ // destination object type
+ typedef encapc<1, prp_object, typename openfpm::vector<prp_object>::layout_type> encap_dst;
- // source object type
- typedef encapc<1, prop, typename openfpm::vector<prop>::layout_type> encap_src;
- // destination object type
- typedef encapc<1, prp_object, typename openfpm::vector<prp_object>::layout_type> encap_dst;
+ // Copy only the selected properties
+ object_si_d<encap_src, encap_dst, OBJ_ENCAP, prp...>(v_prp.get(id), m_prp.get(lbl).get(cnt.get(lbl)));
- // Copy only the selected properties
- object_si_d<encap_src, encap_dst, OBJ_ENCAP, prp...>(v_prp.get(id), pb.get(lbl).prp.get(key));
+ cnt.get(lbl)++;
+
+ // swap the particle
+ long int id_valid = get_end_valid(end,id_end);
- ++it;
+ if (id_valid > 0 && (long int)id < id_valid)
+ {
+ v_pos.set(id,v_pos.get(id_valid));
+ v_prp.set(id,v_prp.get(id_valid));
}
}
+
}
/*! \brief Label particles for mappings
@@ -565,12 +580,10 @@ class vector_dist_comm
* \param opart id of the particles to send
*
*/
- template<typename obp> void labelParticleProcessor(openfpm::vector<Point<dim, St>> & v_pos,openfpm::vector<openfpm::vector<size_t>> & lbl_p, openfpm::vector<size_t> & prc_sz, openfpm::vector<size_t> & opart)
+ template<typename obp> void labelParticleProcessor(openfpm::vector<Point<dim, St>> & v_pos, openfpm::vector<aggregate<size_t,size_t,size_t>> & lbl_p, openfpm::vector<size_t> & prc_sz)
{
// reset lbl_p
- lbl_p.resize(v_cl.getProcessingUnits());
- for (size_t i = 0; i < lbl_p.size(); i++)
- lbl_p.get(i).clear();
+ lbl_p.clear();
// resize the label buffer
prc_sz.resize(v_cl.getProcessingUnits());
@@ -599,12 +612,9 @@ class vector_dist_comm
if ((long int) p_id != -1)
{
prc_sz.get(p_id)++;
- lbl_p.get(p_id).add(key);
- opart.add(key);
- }
- else
- {
- opart.add(key);
+ lbl_p.add();
+ lbl_p.last().template get<0>() = key;
+ lbl_p.last().template get<2>() = p_id;
}
}
@@ -614,254 +624,6 @@ class vector_dist_comm
}
}
- /*! \brief This function process the received data for the properties and populate the ghost
- *
- * \tparam send_vector type used to send data
- * \tparam prp_object object containing only the properties to send
- * \tparam prp set of properties to send
- *
- * \param v_prp vector of particle properties
- * \param g_m ghost marker
- *
- */
- template<typename send_vector, typename prp_object, int ... prp> void process_received_ghost_prp(openfpm::vector<prop> & v_prp, size_t & g_m)
- {
- n_recv_ele.resize(recv_mem_gg.size());
-
- // Mark the ghost part
- g_m = v_prp.size();
-
- // Process the received data (recv_mem_gg != 0 if you have data)
- for (size_t i = 0; i < dec.getNNProcessors() && recv_mem_gg.size() != 0; i++)
- {
- // calculate the number of received elements
- size_t n_ele = recv_sz.get(i) / sizeof(prp_object);
-
- // add the received particles to the vector
- PtrMemory * ptr1 = new PtrMemory(recv_mem_gg.get(i).getPointer(), recv_sz.get(i));
-
- // create vector representation to a piece of memory already allocated
- openfpm::vector<prp_object, PtrMemory, typename memory_traits_lin<prp_object>::type, memory_traits_lin , openfpm::grow_policy_identity> v2;
-
- v2.setMemory(*ptr1);
-
- // resize with the number of elements and store the number
- // or received elements
- v2.resize(n_ele);
- n_recv_ele.get(i) = n_ele;
-
- // Add the ghost particle
- v_prp.template add_prp<prp_object, PtrMemory, openfpm::grow_policy_identity, prp...>(v2);
- }
- }
-
-
- /*! \brief This function process the received data from ghost put
- *
- * \tparam op operation to do
- * \tparam send_vector type used to send data
- * \tparam prp_object object containing only the properties to send
- * \tparam prp set of properties to send
- *
- * \param v_prp vector of particle properties
- * \param g_m ghost marker
- *
- */
- template<template<typename,typename> class op, typename send_vector, typename prp_object, int ... prp> void process_received_put_ghost_prp(openfpm::vector<prop> & v_prp, size_t g_m)
- {
- // Process the received data (recv_mem_gg != 0 if you have data)
- for (size_t i = 0; i < recv_sz_put.size(); i++)
- {
- // calculate the number of received elements
- size_t n_ele = recv_sz_put.get(i) / sizeof(prp_object);
-
- // add the received particles to the vector
- PtrMemory * ptr1 = new PtrMemory(recv_mem_gg.get(i).getPointer(), recv_sz_put.get(i));
-
- // create vector representation to a piece of memory already allocated
- openfpm::vector<prp_object, PtrMemory, typename memory_traits_lin<prp_object>::type, memory_traits_lin , openfpm::grow_policy_identity> v2;
-
- v2.setMemory(*ptr1);
-
- // resize with the number of elements
- v2.resize(n_ele);
-
- // Add the ghost particle
- v_prp.template merge_prp<op,prp_object, PtrMemory, openfpm::grow_policy_identity, prp...>(v2,opart.get(i));
- }
-
- // process also the local replicated particles
-
- size_t i2 = 0;
-
-#ifdef SE_CLASS1
-
- if (v_prp.size() - lg_m != o_part_loc.size())
- std::cerr << "Error: " << __FILE__ << ":" << __LINE__ << " v_prp.size() - lg_m = " << v_prp.size() - lg_m << " != " << o_part_loc.size() << std::endl;
-
-#endif
-
- for (size_t i = lg_m ; i < v_prp.size() ; i++)
- {
- auto dst = v_prp.get(o_part_loc.template get<0>(i2));
- auto src = v_prp.get(i);
- copy_cpu_encap_encap_op_prp<op,decltype(v_prp.get(0)),decltype(v_prp.get(0)),prp...> cp(src,dst);
-
- boost::mpl::for_each_ref< boost::mpl::range_c<int,0,sizeof...(prp)> >(cp);
-
- i2++;
- }
- }
-
- /*! \brief This function process the received data for the properties and populate the ghost
- *
- * \param v_pos vector of particle positions
- *
- */
- void process_received_ghost_pos(openfpm::vector<Point<dim, St>> & v_pos)
- {
- // Process the received data (recv_mem_gg != 0 if you have data)
- for (size_t i = 0; i < dec.getNNProcessors() && recv_mem_gg.size() != 0; i++)
- {
- // calculate the number of received elements
- size_t n_ele = recv_sz.get(i) / sizeof(Point<dim, St> );
-
- // add the received particles to the vector
- PtrMemory * ptr1 = new PtrMemory(recv_mem_gg.get(i).getPointer(), recv_sz.get(i));
-
- // create vector representation to a piece of memory already allocated
-
- openfpm::vector<Point<dim, St>, PtrMemory, typename memory_traits_lin<Point<dim, St>>::type, memory_traits_lin , openfpm::grow_policy_identity> v2;
-
- v2.setMemory(*ptr1);
-
- // resize with the number of elements
- v2.resize(n_ele);
-
- // Add the ghost particle
- v_pos.template add<PtrMemory, openfpm::grow_policy_identity>(v2);
- }
- }
-
- /*! \brief Process the received particles
- *
- * \param v_pos vector of particle positions
- * \param v_prp vector of particle properties
- * \param out_part list of the out-going particles
- *
- */
- void process_received_map(openfpm::vector<Point<dim, St>> & v_pos, openfpm::vector<prop> & v_prp,openfpm::vector<size_t> & out_part)
- {
- size_t o_p_id = 0;
-
- for (size_t i = 0; i < recv_mem_gm.size(); i++)
- {
- // Get the number of elements
-
- size_t n_ele = recv_mem_gm.get(i).size() / (sizeof(Point<dim, St> ) + sizeof(prop));
-
- // Pointer of the received positions for each near processor
- void * ptr_pos = (unsigned char *) recv_mem_gm.get(i).getPointer();
- // Pointer of the received properties for each near processor
- void * ptr_prp = (unsigned char *) recv_mem_gm.get(i).getPointer() + n_ele * sizeof(Point<dim, St> );
-
- PtrMemory * ptr1 = new PtrMemory(ptr_pos, n_ele * sizeof(Point<dim, St> ));
- PtrMemory * ptr2 = new PtrMemory(ptr_prp, n_ele * sizeof(prop));
-
- // create vector representation to a piece of memory already allocated
-
- openfpm::vector<Point<dim, St>, PtrMemory, typename memory_traits_lin<Point<dim, St>>::type, memory_traits_lin ,openfpm::grow_policy_identity> vpos;
- openfpm::vector<prop, PtrMemory, typename memory_traits_lin<prop>::type, memory_traits_lin ,openfpm::grow_policy_identity> vprp;
-
- vpos.setMemory(*ptr1);
- vprp.setMemory(*ptr2);
-
- vpos.resize(n_ele);
- vprp.resize(n_ele);
-
- // Add the received particles to v_pos and v_prp
-
- size_t j = 0;
- for (; j < vpos.size() && o_p_id < out_part.size(); j++, o_p_id++)
- {
- v_pos.set(out_part.get(o_p_id), vpos.get(j));
- v_prp.set(out_part.get(o_p_id), vprp.get(j));
- }
-
- for (; j < vpos.size(); j++)
- {
- v_pos.add();
- v_pos.set(v_pos.size() - 1, vpos.get(j));
- v_prp.add();
- v_prp.set(v_prp.size() - 1, vprp.get(j));
- }
- }
-
- // remove the (out-going particles) in the vector
-
- v_pos.remove(out_part, o_p_id);
- v_prp.remove(out_part, o_p_id);
- }
-
- /*! \brief Process the received particles
- *
- * \param v_pos vector of particle positions
- * \param v_prp vector of particle properties
- * \param out_part list of the out-going particles
- *
- */
- template<typename prp_object , int ... prp> void process_received_map_list(openfpm::vector<Point<dim, St>> & v_pos, openfpm::vector<prop> & v_prp, openfpm::vector<size_t> & out_part)
- {
- size_t o_p_id = 0;
-
- for (size_t i = 0; i < recv_mem_gm.size(); i++)
- {
- // Get the number of elements
-
- size_t n_ele = recv_mem_gm.get(i).size() / (sizeof(Point<dim, St> ) + sizeof(prp_object));
-
- // Pointer of the received positions for each near processor
- void * ptr_pos = (unsigned char *) recv_mem_gm.get(i).getPointer();
- // Pointer of the received properties for each near processor
- void * ptr_prp = (unsigned char *) recv_mem_gm.get(i).getPointer() + n_ele * sizeof(Point<dim, St> );
-
- PtrMemory * ptr1 = new PtrMemory(ptr_pos, n_ele * sizeof(Point<dim, St> ));
- PtrMemory * ptr2 = new PtrMemory(ptr_prp, n_ele * sizeof(prp_object));
-
- // create vector representation to a piece of memory already allocated
-
- openfpm::vector<Point<dim, St>, PtrMemory, typename memory_traits_lin<Point<dim, St>>::type, memory_traits_lin ,openfpm::grow_policy_identity> vpos;
- openfpm::vector<prp_object, PtrMemory, typename memory_traits_lin<prp_object>::type, memory_traits_lin ,openfpm::grow_policy_identity> vprp;
-
- vpos.setMemory(*ptr1);
- vprp.setMemory(*ptr2);
-
- vpos.resize(n_ele);
- vprp.resize(n_ele);
-
- // Add the received particles to v_pos and v_prp
-
- size_t j = 0;
- for (; j < vpos.size() && o_p_id < out_part.size(); j++, o_p_id++)
- {
- v_pos.set(out_part.get(o_p_id), vpos.get(j));
- v_prp.template set_o<decltype(vprp.get(j)), prp... >(out_part.get(o_p_id), vprp.get(j));
- }
-
- for (; j < vpos.size(); j++)
- {
- v_pos.add();
- v_pos.set(v_pos.size() - 1, vpos.get(j));
- v_prp.template set_o<decltype(vprp.get(j)), prp... >(v_prp.size() - 1, vprp.get(j));
- }
- }
-
- // remove the (out-going particles) in the vector
-
- v_pos.remove(out_part, o_p_id);
- v_prp.remove(out_part, o_p_id);
- }
-
/*! \brief Calculate send buffers total size and allocation
*
* \tparam prp_object object containing only the properties to send
@@ -898,9 +660,9 @@ class vector_dist_comm
template<typename prp_object> void calc_send_ghost_put_buf(openfpm::vector<Point<dim, St>> & v_pos, openfpm::vector<prop> & v_prp, size_t & size_byte_prp, size_t & size_byte_pos)
{
// Calculate the total size required for the sending buffer
- for (size_t i = 0; i < recv_sz.size(); i++)
+ for (size_t i = 0; i < recv_sz_get.size(); i++)
{
- size_t alloc_ele = openfpm::vector<prp_object, HeapMemory, typename memory_traits_lin<prp_object>::type, memory_traits_lin , openfpm::grow_policy_identity>::calculateMem(n_recv_ele.get(i), 0);
+ size_t alloc_ele = openfpm::vector<prp_object, HeapMemory, typename memory_traits_lin<prp_object>::type, memory_traits_lin , openfpm::grow_policy_identity>::calculateMem(recv_sz_get.get(i), 0);
size_byte_prp += alloc_ele;
}
}
@@ -923,12 +685,8 @@ class vector_dist_comm
ghost_prc_sz.resize(dec.getNNProcessors());
// Buffer that contain for each processor the id of the particle to send
- opart.clear();
- opart.resize(dec.getNNProcessors());
-
- // Buffer that contain for each processor the id of the shift vector
- oshift.clear();
- oshift.resize(dec.getNNProcessors());
+ g_opart.clear();
+ g_opart.resize(dec.getNNProcessors());
// Iterate over all particles
auto it = v_pos.getIteratorTo(g_m);
@@ -947,78 +705,15 @@ class vector_dist_comm
// add particle to communicate
ghost_prc_sz.get(p_id)++;
- opart.get(p_id).add(key);
- oshift.get(p_id).add(vp_id.get(i).second);
+ g_opart.get(p_id).add();
+ g_opart.get(p_id).last().template get<0>() = key;
+ g_opart.get(p_id).last().template get<1>() = vp_id.get(i).second;
}
++it;
}
}
- /*! \brief Call-back to allocate buffer to receive incoming elements (particles)
- *
- * \param msg_i message size required to receive from i
- * \param total_msg message size to receive from all the processors
- * \param total_p 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 void pointer parameter for additional data to pass to the call-back
- *
- */
- static void * msg_alloc_ghost_put(size_t msg_i, size_t total_msg, size_t total_p, size_t i, size_t ri, void * ptr)
- {
- vector_dist_comm<dim, St, prop, Decomposition, Memory> * v = static_cast<vector_dist_comm<dim, St, prop, Decomposition, Memory> *>(ptr);
-
- v->recv_sz_put.resize(v->dec.getNNProcessors());
- v->recv_mem_gg.resize(v->dec.getNNProcessors());
- v->prc_recv_put.resize(v->dec.getNNProcessors());
-
- // Get the local processor id
- size_t lc_id = v->dec.ProctoID(i);
-
- // resize the receive buffer
- v->recv_mem_gg.get(lc_id).resize(msg_i);
- v->recv_sz_put.get(lc_id) = msg_i;
-
- // save the processor id
- v->prc_recv_put.get(lc_id) = i;
-
- return v->recv_mem_gg.get(lc_id).getPointer();
- }
-
- /*! \brief Call-back to allocate buffer to receive incoming elements (particles)
- *
- * \param msg_i message size required to receive from i
- * \param total_msg message size to receive from all the processors
- * \param total_p 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 void pointer parameter for additional data to pass to the call-back
- *
- */
- static void * msg_alloc_ghost_get(size_t msg_i, size_t total_msg, size_t total_p, size_t i, size_t ri, void * ptr)
- {
- vector_dist_comm<dim, St, prop, Decomposition, Memory> * v = static_cast<vector_dist_comm<dim, St, prop, Decomposition, Memory> *>(ptr);
-
- v->recv_sz.resize(v->dec.getNNProcessors());
- v->recv_mem_gg.resize(v->dec.getNNProcessors());
- v->prc_recv.resize(v->dec.getNNProcessors());
-
- // Get the local processor id
- size_t lc_id = v->dec.ProctoID(i);
-
- // resize the receive buffer
- v->recv_mem_gg.get(lc_id).resize(msg_i);
- v->recv_sz.get(lc_id) = msg_i;
-
- // save the processor id
- v->prc_recv.get(lc_id) = i;
-
- return v->recv_mem_gg.get(lc_id).getPointer();
- }
-
/*! \brief Call-back to allocate buffer to receive incoming elements (particles)
*
* \param msg_i size required to receive the message from i
@@ -1126,14 +821,14 @@ public:
template<int ... prp> inline void ghost_get_(openfpm::vector<Point<dim, St>> & v_pos, openfpm::vector<prop> & v_prp, size_t & g_m, size_t opt = WITH_POSITION)
{
// Unload receive buffer
- for (size_t i = 0 ; i < recv_sz.size() ; i++)
- recv_sz.get(i) = 0;
+ for (size_t i = 0 ; i < recv_sz_get.size() ; i++)
+ recv_sz_get.get(i) = 0;
// Sending property object
typedef object<typename object_creator<typename prop::type, prp...>::type> prp_object;
// send vector for each processor
- typedef openfpm::vector<prp_object, ExtPreAlloc<Memory>, typename memory_traits_lin<prp_object>::type, memory_traits_lin, openfpm::grow_policy_identity> send_vector;
+ typedef openfpm::vector<prp_object> send_vector;
// reset the ghost part
v_pos.resize(g_m);
@@ -1151,43 +846,28 @@ public:
calc_send_ghost_buf<prp_object>(v_pos,v_prp,size_byte_prp, size_byte_pos);
- // Create memory for the send buffer
-
- g_prp_mem.resize(size_byte_prp);
- if (opt != NO_POSITION)
- g_pos_mem.resize(size_byte_pos);
-
- // Create and fill send buffer for particle properties
-
- ExtPreAlloc<Memory> * prAlloc_prp = new ExtPreAlloc<Memory>(size_byte_prp, g_prp_mem);
-
+ // Send and receive ghost particle information
openfpm::vector<send_vector> g_send_prp;
- fill_send_ghost_prp_buf<send_vector, prp_object, prp...>(v_prp,g_send_prp, prAlloc_prp);
+ fill_send_ghost_prp_buf<send_vector, prp_object, prp...>(v_prp,g_send_prp);
// Create and fill the send buffer for the particle position
-
- ExtPreAlloc<Memory> * prAlloc_pos;
- openfpm::vector<send_pos_vector> g_pos_send;
if (opt != NO_POSITION)
- {
- prAlloc_pos = new ExtPreAlloc<Memory>(size_byte_pos, g_pos_mem);
- fill_send_ghost_pos_buf(v_pos,g_pos_send, prAlloc_pos);
- }
+ fill_send_ghost_pos_buf(v_pos,g_pos_send);
// Create processor list
openfpm::vector<size_t> prc;
- for (size_t i = 0; i < opart.size(); i++)
+ for (size_t i = 0; i < g_opart.size(); i++)
prc.add(dec.IDtoProc(i));
- // Send/receive the particle properties information
- v_cl.sendrecvMultipleMessagesNBX(prc, g_send_prp, msg_alloc_ghost_get, this);
- process_received_ghost_prp<send_vector, prp_object, prp...>(v_prp,g_m);
+ prc_recv_get.clear();
+ recv_sz_get.clear();
+ v_cl.SSendRecvP<send_vector,decltype(v_prp),prp...>(g_send_prp,v_prp,prc,prc_recv_get,recv_sz_get);
if (opt != NO_POSITION)
{
- // Send/receive the particle properties information
- v_cl.sendrecvMultipleMessagesNBX(prc, g_pos_send, msg_alloc_ghost_get, this);
- process_received_ghost_pos(v_pos);
+ prc_recv_get.clear();
+ recv_sz_get.clear();
+ v_cl.SSendRecv(g_pos_send,v_pos,prc,prc_recv_get,recv_sz_get);
}
add_loc_particles_bc(v_pos,v_prp,g_m,opt);
@@ -1213,9 +893,6 @@ public:
{
typedef KillParticle obp;
- // outgoing particles-id
- openfpm::vector<size_t> out_part;
-
// Processor communication size
openfpm::vector<size_t> prc_sz(v_cl.getProcessingUnits());
@@ -1227,7 +904,7 @@ public:
v_prp.resize(g_m);
// Contain the processor id of each particle (basically where they have to go)
- labelParticleProcessor<obp>(v_pos,opart, prc_sz, out_part);
+ labelParticleProcessor<obp>(v_pos,m_opart, prc_sz);
// Calculate the sending buffer size for each processor, put this information in
// a contiguous buffer
@@ -1248,34 +925,15 @@ public:
// Sending property object
typedef object<typename object_creator<typename prop::type, prp...>::type> prp_object;
- // Allocate the send buffers
-
- openfpm::vector<pos_prop_sel<prp_object>> pb;
-
- // fill the send buffers
- fill_send_map_buf_list<prp_object,prp...>(v_pos,v_prp,prc_r, prc_sz_r, pb);
-
- // Create the set of pointers
- openfpm::vector<void *> ptr(prc_r.size());
- for (size_t i = 0; i < prc_r.size(); i++)
- {
- ptr.get(i) = pb.get(i).pos.getPointer();
- }
-
- // convert the particle number to buffer size
- for (size_t i = 0; i < prc_sz_r.size(); i++)
- {
- prc_sz_r.get(i) = prc_sz_r.get(i) * (sizeof(prp_object) + sizeof(Point<dim, St> ));
- }
-
- // Send and receive the particles
-
- recv_mem_gm.clear();
- v_cl.sendrecvMultipleMessagesNBX(prc_sz_r.size(), (size_t *) prc_sz_r.getPointer(), (size_t *) prc_r.getPointer(), (void **) ptr.getPointer(), vector_dist_comm::message_alloc_map, this, NEED_ALL_SIZE);
+ //! position vector
+ openfpm::vector<openfpm::vector<Point<dim, St>>> m_pos;
+ //! properties vector
+ openfpm::vector<openfpm::vector<prp_object>> m_prp;
- // Process the incoming particles
+ fill_send_map_buf_list<prp_object,prp...>(v_pos,v_prp,prc_r, prc_sz_r, m_pos, m_prp);
- process_received_map_list<prp_object, prp...>(v_pos,v_prp,out_part);
+ v_cl.SSendRecv(m_pos,v_pos,prc_r,prc_recv_map,recv_sz_map);
+ v_cl.SSendRecvP<openfpm::vector<prp_object>,decltype(v_prp),prp...>(m_prp,v_prp,prc_r,prc_recv_map,recv_sz_map);
// mark the ghost part
@@ -1297,9 +955,6 @@ public:
*/
template<typename obp = KillParticle> void map_(openfpm::vector<Point<dim, St>> & v_pos, openfpm::vector<prop> & v_prp, size_t & g_m)
{
- // outgoing particles-id
- openfpm::vector<size_t> out_part;
-
// Processor communication size
openfpm::vector<size_t> prc_sz(v_cl.getProcessingUnits());
@@ -1311,7 +966,7 @@ public:
v_prp.resize(g_m);
// Contain the processor id of each particle (basically where they have to go)
- labelParticleProcessor<obp>(v_pos,opart, prc_sz, out_part);
+ labelParticleProcessor<obp>(v_pos,m_opart, prc_sz);
// Calculate the sending buffer size for each processor, put this information in
// a contiguous buffer
@@ -1329,34 +984,15 @@ public:
}
}
- // Allocate the send buffers
-
- openfpm::vector<pos_prop> pb;
-
- // fill the send buffers
- fill_send_map_buf(v_pos,v_prp,prc_r, prc_sz_r, pb);
-
- // Create the set of pointers
- openfpm::vector<void *> ptr(prc_r.size());
- for (size_t i = 0; i < prc_r.size(); i++)
- {
- ptr.get(i) = pb.get(i).pos.getPointer();
- }
-
- // convert the particle number to buffer size
- for (size_t i = 0; i < prc_sz_r.size(); i++)
- {
- prc_sz_r.get(i) = prc_sz_r.get(i) * (sizeof(prop) + sizeof(Point<dim, St> ));
- }
-
- // Send and receive the particles
-
- recv_mem_gm.clear();
- v_cl.sendrecvMultipleMessagesNBX(prc_sz_r.size(), (size_t *) prc_sz_r.getPointer(), (size_t *) prc_r.getPointer(), (void **) ptr.getPointer(), vector_dist_comm::message_alloc_map, this, NEED_ALL_SIZE);
+ //! position vector
+ openfpm::vector<openfpm::vector<Point<dim, St>>> m_pos;
+ //! properties vector
+ openfpm::vector<openfpm::vector<prop>> m_prp;
- // Process the incoming particles
+ fill_send_map_buf(v_pos,v_prp, prc_sz_r, m_pos, m_prp);
- process_received_map(v_pos,v_prp,out_part);
+ v_cl.SSendRecv(m_pos,v_pos,prc_r,prc_recv_map,recv_sz_map);
+ v_cl.SSendRecv(m_prp,v_prp,prc_r,prc_recv_map,recv_sz_map);
// mark the ghost part
@@ -1417,7 +1053,7 @@ public:
typedef object<typename object_creator<typename prop::type, prp...>::type> prp_object;
// send vector for each processor
- typedef openfpm::vector<prp_object, ExtPreAlloc<Memory>, typename memory_traits_lin<prp_object>::type, memory_traits_lin, openfpm::grow_policy_identity> send_vector;
+ typedef openfpm::vector<prp_object> send_vector;
// Calculate memory and allocation for the send buffers
@@ -1427,20 +1063,12 @@ public:
calc_send_ghost_put_buf<prp_object>(v_pos,v_prp,size_byte_prp, size_byte_pos);
- // Create memory for the send buffer
-
- g_prp_mem.resize(size_byte_prp);
-
- // Create and fill send buffer for particle properties
-
- ExtPreAlloc<Memory> * prAlloc_prp = new ExtPreAlloc<Memory>(size_byte_prp, g_prp_mem);
-
openfpm::vector<send_vector> g_send_prp;
- fill_send_ghost_put_prp_buf<send_vector, prp_object, prp...>(v_prp,g_send_prp, prAlloc_prp,g_m);
+ fill_send_ghost_put_prp_buf<send_vector, prp_object, prp...>(v_prp,g_send_prp,g_m);
- // Send/receive the particle properties information
- v_cl.sendrecvMultipleMessagesNBX(prc_recv, g_send_prp, msg_alloc_ghost_put, this);
- process_received_put_ghost_prp<op,send_vector, prp_object, prp...>(v_prp,g_m);
+ // Send and receive ghost particle information
+ op_ssend_recv_merge<op> opm(g_opart);
+ v_cl.SSendRecvP_op<op_ssend_recv_merge<op>,send_vector,decltype(v_prp),prp...>(g_send_prp,v_prp,prc_recv_get,opm,prc_recv_put,recv_sz_put);
}
};
diff --git a/src/Vector/vector_dist_unit_test.hpp b/src/Vector/vector_dist_unit_test.hpp
index 47ee46c08..413bf7aac 100644
--- a/src/Vector/vector_dist_unit_test.hpp
+++ b/src/Vector/vector_dist_unit_test.hpp
@@ -180,9 +180,14 @@ void Test2D_ghost(Box<2,float> & box)
//! [Redistribute the particles and sync the ghost properties]
+ vd.write("debug_before");
+
// redistribute the particles according to the decomposition
vd.map();
+ vd.write("debug_after");
+ vd.getDecomposition().write("debug_decomposition");
+
auto v_it2 = vd.getIterator();
while (v_it2.isNext())
--
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