From 6b9ab5c7ddd2d5aaf3e92a0dc77276fd9c2e07bf Mon Sep 17 00:00:00 2001
From: tonynsyde <antonio.leo.polito@gmail.com>
Date: Wed, 2 Mar 2016 15:42:07 +0100
Subject: [PATCH] Small fixes in distributed graph and DistParmetisDistribution
---
dist_graph_0_test.vtk | 274 ------------------
dist_graph_1_test.vtk | 274 ------------------
openfpm_data | 2 +-
openfpm_io | 2 +-
src/Decomposition/CartDecomposition.hpp | 60 ++--
.../CartDecomposition_unit_test.hpp | 15 +-
.../DistParMetisDistribution.hpp | 62 +---
src/Decomposition/ParMetisDistribution.hpp | 1 +
src/Graph/CartesianGraphFactory_unit_test.hpp | 2 +-
.../DistCartesianGraphFactory_unit_test.hpp | 5 +-
src/Graph/dist_map_graph.hpp | 79 +++--
src/Graph/dist_map_graph_unit_test.hpp | 148 ++--------
src/main.cpp | 3 +-
src/parmetis_dist_util.hpp | 54 +---
src/parmetis_util.hpp | 96 +-----
15 files changed, 133 insertions(+), 944 deletions(-)
delete mode 100644 dist_graph_0_test.vtk
delete mode 100644 dist_graph_1_test.vtk
diff --git a/dist_graph_0_test.vtk b/dist_graph_0_test.vtk
deleted file mode 100644
index 8e7e4041..00000000
--- a/dist_graph_0_test.vtk
+++ /dev/null
@@ -1,274 +0,0 @@
-# vtk DataFile Version 3.0
-Graph
-ASCII
-DATASET POLYDATA
-POINTS 16 float
-0.500000 0.000000 0.000000
-0.750000 0.000000 0.000000
-0.500000 0.250000 0.000000
-0.750000 0.250000 0.000000
-0.000000 0.000000 0.000000
-0.250000 0.000000 0.000000
-0.000000 0.250000 0.000000
-0.250000 0.250000 0.000000
-0.500000 0.500000 0.000000
-0.750000 0.500000 0.000000
-0.500000 0.750000 0.000000
-0.750000 0.750000 0.000000
-0.000000 0.500000 0.000000
-0.250000 0.500000 0.000000
-0.000000 0.750000 0.000000
-0.250000 0.750000 0.000000
-VERTICES 16 32
-1 0
-1 1
-1 2
-1 3
-1 4
-1 5
-1 6
-1 7
-1 8
-1 9
-1 10
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-1 14
-1 15
-LINES 48 144
-2 0 1
-2 0 5
-2 0 2
-2 1 0
-2 1 3
-2 2 3
-2 2 7
-2 2 8
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-2 3 1
-2 4 5
-2 4 6
-2 5 0
-2 5 4
-2 5 7
-2 6 7
-2 6 12
-2 6 4
-2 7 2
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-2 7 13
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-2 8 10
-2 8 2
-2 9 8
-2 9 11
-2 9 3
-2 10 11
-2 10 15
-2 10 8
-2 11 10
-2 11 9
-2 12 13
-2 12 14
-2 12 6
-2 13 8
-2 13 12
-2 13 15
-2 13 7
-2 14 15
-2 14 12
-2 15 10
-2 15 14
-2 15 13
-POINT_DATA 16
-VECTORS x float
-0.500000 0.000000 0.000000
-0.750000 0.000000 0.000000
-0.500000 0.250000 0.000000
-0.750000 0.250000 0.000000
-0.000000 0.000000 0.000000
-0.250000 0.000000 0.000000
-0.000000 0.250000 0.000000
-0.250000 0.250000 0.000000
-0.500000 0.500000 0.000000
-0.750000 0.500000 0.000000
-0.500000 0.750000 0.000000
-0.750000 0.750000 0.000000
-0.000000 0.500000 0.000000
-0.250000 0.500000 0.000000
-0.000000 0.750000 0.000000
-0.250000 0.750000 0.000000
-SCALARS id unsigned_long
-LOOKUP_TABLE default
-0
-1
-2
-3
-4
-5
-6
-7
-8
-9
-10
-11
-12
-13
-14
-15
-SCALARS global_id unsigned_long
-LOOKUP_TABLE default
-2
-3
-6
-7
-0
-1
-4
-5
-10
-11
-14
-15
-8
-9
-12
-13
-CELL_DATA 64
-SCALARS srcgid unsigned_long
-LOOKUP_TABLE default
-0
-0
-0
-0
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-0
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-14
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-14
-15
-15
-8
-8
-8
-9
-9
-9
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-12
-12
-13
-13
-13
-SCALARS dstgid unsigned_long
-LOOKUP_TABLE default
-0
-0
-0
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diff --git a/dist_graph_1_test.vtk b/dist_graph_1_test.vtk
deleted file mode 100644
index a28bfade..00000000
--- a/dist_graph_1_test.vtk
+++ /dev/null
@@ -1,274 +0,0 @@
-# vtk DataFile Version 3.0
-Graph
-ASCII
-DATASET POLYDATA
-POINTS 16 float
-0.500000 0.000000 0.000000
-0.750000 0.000000 0.000000
-0.500000 0.250000 0.000000
-0.750000 0.250000 0.000000
-0.500000 0.500000 0.000000
-0.750000 0.500000 0.000000
-0.000000 0.750000 0.000000
-0.000000 0.500000 0.000000
-0.000000 0.000000 0.000000
-0.250000 0.000000 0.000000
-0.000000 0.250000 0.000000
-0.250000 0.250000 0.000000
-0.500000 0.750000 0.000000
-0.750000 0.750000 0.000000
-0.250000 0.500000 0.000000
-0.250000 0.750000 0.000000
-VERTICES 16 32
-1 0
-1 1
-1 2
-1 3
-1 4
-1 5
-1 6
-1 7
-1 8
-1 9
-1 10
-1 11
-1 12
-1 13
-1 14
-1 15
-LINES 48 144
-2 0 1
-2 0 9
-2 0 2
-2 1 0
-2 1 3
-2 2 3
-2 2 11
-2 2 4
-2 2 0
-2 3 2
-2 3 5
-2 3 1
-2 4 5
-2 4 14
-2 4 12
-2 4 2
-2 5 4
-2 5 13
-2 5 3
-2 6 15
-2 6 7
-2 7 14
-2 7 6
-2 7 10
-2 8 9
-2 8 10
-2 9 0
-2 9 8
-2 9 11
-2 10 11
-2 10 7
-2 10 8
-2 11 2
-2 11 10
-2 11 14
-2 11 9
-2 12 13
-2 12 15
-2 12 4
-2 13 12
-2 13 5
-2 14 4
-2 14 7
-2 14 15
-2 14 11
-2 15 12
-2 15 6
-2 15 14
-POINT_DATA 16
-VECTORS x float
-0.500000 0.000000 0.000000
-0.750000 0.000000 0.000000
-0.500000 0.250000 0.000000
-0.750000 0.250000 0.000000
-0.500000 0.500000 0.000000
-0.750000 0.500000 0.000000
-0.000000 0.750000 0.000000
-0.000000 0.500000 0.000000
-0.000000 0.000000 0.000000
-0.250000 0.000000 0.000000
-0.000000 0.250000 0.000000
-0.250000 0.250000 0.000000
-0.500000 0.750000 0.000000
-0.750000 0.750000 0.000000
-0.250000 0.500000 0.000000
-0.250000 0.750000 0.000000
-SCALARS id unsigned_long
-LOOKUP_TABLE default
-0
-1
-2
-3
-5
-6
-7
-4
-8
-9
-10
-11
-12
-13
-14
-15
-SCALARS global_id unsigned_long
-LOOKUP_TABLE default
-2
-3
-6
-7
-10
-11
-12
-8
-0
-1
-4
-5
-14
-15
-9
-13
-CELL_DATA 64
-SCALARS srcgid unsigned_long
-LOOKUP_TABLE default
-0
-0
-0
-0
-0
-0
-0
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-0
-0
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-5
-5
-14
-14
-14
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-15
-9
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-9
-9
-13
-13
-13
-SCALARS dstgid unsigned_long
-LOOKUP_TABLE default
-0
-0
-0
-0
-0
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diff --git a/openfpm_data b/openfpm_data
index 7e41886a..524a87a9 160000
--- a/openfpm_data
+++ b/openfpm_data
@@ -1 +1 @@
-Subproject commit 7e41886aadce576e0e46c8f0eb60ba11473b64ca
+Subproject commit 524a87a925b8230b019264ca957293f686974f88
diff --git a/openfpm_io b/openfpm_io
index dbc37eff..136310cb 160000
--- a/openfpm_io
+++ b/openfpm_io
@@ -1 +1 @@
-Subproject commit dbc37efff49ac7622db19f3944422e496fc5cdc6
+Subproject commit 136310cb5b8b776eb405f58d5721c879a8d013b5
diff --git a/src/Decomposition/CartDecomposition.hpp b/src/Decomposition/CartDecomposition.hpp
index 621c64ba..28245e25 100755
--- a/src/Decomposition/CartDecomposition.hpp
+++ b/src/Decomposition/CartDecomposition.hpp
@@ -137,6 +137,18 @@ private:
//! Cell-list that store the geometrical information of the local internal ghost boxes
CellList<dim, T, FAST> lgeo_cell;
+ // Heap memory receiver
+ HeapMemory hp_recv;
+
+ // vector v_proc
+ openfpm::vector<size_t> v_proc;
+
+ // Receive counter
+ size_t recv_cnt;
+
+ // reference counter of the object in case is shared between object
+ long int ref_cnt;
+
/*! \brief Constructor, it decompose and distribute the sub-domains across the processors
*
* \param v_cl Virtual cluster, used internally for communications
@@ -356,18 +368,6 @@ private:
}
}
- // Heap memory receiver
- HeapMemory hp_recv;
-
- // vector v_proc
- openfpm::vector<size_t> v_proc;
-
- // Receive counter
- size_t recv_cnt;
-
- // reference counter of the object in case is shared between object
- long int ref_cnt;
-
public:
/*! \brief Cart decomposition constructor
@@ -478,8 +478,8 @@ public:
| | | | | |
| | | | | |
+--------------+---+---------------------------+----+ |
- | |
- +-----------------------------------+
+ | |
+ +-----------------------------------+
\endverbatim
@@ -510,8 +510,8 @@ public:
| | | | | |
| | | | | |
+--------------+------------------------------------+ | |
- | | | |
- +----------------------------------------+----+------------------------------+
+ | | | |
+ +----------------------------------------+----+------------------------------+
\endverbatim
@@ -523,18 +523,18 @@ public:
*
*
\verbatim
- ^ p2[1]
- |
- |
- +----+----+
- | |
- | |
- p1[0]<-----+ +----> p2[0]
- | |
- | |
- +----+----+
- |
- v p1[1]
+ ^ p2[1]
+ |
+ |
+ +----+----+
+ | |
+ | |
+ p1[0]<-----+ +----> p2[0]
+ | |
+ | |
+ +----+----+
+ |
+ v p1[1]
\endverbatim
@@ -655,7 +655,7 @@ public:
dist.decompose();
- createSubdomains(v_cl);
+ //createSubdomains(v_cl);
}
/*! \brief Refine the decomposition, available only for ParMetis distribution, for Metis it is a null call
@@ -681,7 +681,7 @@ public:
dlb.setUnbalance(unbalance);
if (v_cl.getProcessUnitID() == 0)
{
- //std::cout << std::setprecision(3) << unbalance << "\n";
+ std::cout << std::setprecision(3) << unbalance << "\n";
}
}
diff --git a/src/Decomposition/CartDecomposition_unit_test.hpp b/src/Decomposition/CartDecomposition_unit_test.hpp
index b762530d..115a094e 100755
--- a/src/Decomposition/CartDecomposition_unit_test.hpp
+++ b/src/Decomposition/CartDecomposition_unit_test.hpp
@@ -144,8 +144,8 @@ BOOST_AUTO_TEST_CASE( CartDecomposition_test_2D )
dec.rebalance(dlb);
dec.printCurrentDecomposition(i+1);
- }
+ }
// create a ghost border
dec.calculateGhostBoxes();
@@ -271,17 +271,6 @@ BOOST_AUTO_TEST_CASE( CartDecomposition_test_2D_sar)
dec.printCurrentDecomposition(i);
}
- //print statistics
- /*
- if(vcl.getProcessUnitID() == 0)
- {
- float avg = dec.getTotalMovedV()/((etime-stime)/tstep);
-
- std::cout << "Moved vertices average: " << avg << "\n";
- std::cout << "Max number of moved vertices: " << dec.getMaxMovedV() << "\n";
- }
- */
-
// create a ghost border
dec.calculateGhostBoxes();
@@ -379,7 +368,7 @@ BOOST_AUTO_TEST_CASE( CartDecomposition_test_3D)
float stime = 0.0, etime = 10.0, tstep = 0.1;
- for(float t = stime, i = 1, t_sim = 1; t < etime; t = t + tstep, i++)
+ for(float t = stime, i = 1; t < etime; t = t + tstep, i++)
{
if(t < etime/2)
diff --git a/src/Decomposition/DistParMetisDistribution.hpp b/src/Decomposition/DistParMetisDistribution.hpp
index b97b1e2a..49e136fc 100644
--- a/src/Decomposition/DistParMetisDistribution.hpp
+++ b/src/Decomposition/DistParMetisDistribution.hpp
@@ -91,10 +91,12 @@ public:
//! Create sub graph
DistGraphFactory<dim, DistGraph_CSR<nm_v, nm_e>> dist_g_factory;
- sub_g = dist_g_factory.template construct<NO_EDGE, nm_v::id, nm_v::global_id, nm_e::srcgid, nm_e::dstgid, T, dim - 1, 0, 1, 2>(gr.getSize(), domain);
+ sub_g = dist_g_factory.template construct<NO_EDGE, T, dim - 1, 0, 1, 2>(gr.getSize(), domain);
sub_g.getDecompositionVector(vtxdist);
- for(size_t i=0; i< sub_g.getNVertex(); i++)
- sub_g.vertex(i).template get<nm_v::x>()[2] = 0;
+
+ if (dim == 2)
+ for (size_t i = 0; i < sub_g.getNVertex(); i++)
+ sub_g.vertex(i).template get<nm_v::x>()[2] = 0;
}
@@ -120,13 +122,12 @@ public:
//! Get result partition for this processors
idx_t *partition = parmetis_graph.getPartition();
- for (size_t i = 0; i < sub_g.getNVertex(); ++i)
+ for (size_t i = 0, j = sub_g.firstId(); i < sub_g.getNVertex() && j <= sub_g.lastId(); i++, j++)
{
if (partition[i] != v_cl.getProcessUnitID())
- sub_g.q_move(i, partition[i]);
+ sub_g.q_move(sub_g.nodeById(j), partition[i]);
}
sub_g.redistribute();
-
}
/*! \brief Refine current decomposition
@@ -146,27 +147,12 @@ public:
//! Get result partition for this processors
idx_t *partition = parmetis_graph.getPartition();
- for (size_t i = 0; i < sub_g.getNVertex(); ++i)
+ for (size_t i = 0, j = sub_g.firstId(); i < sub_g.getNVertex() && j <= sub_g.lastId(); i++, j++)
{
if (partition[i] != v_cl.getProcessUnitID())
- sub_g.q_move(i, partition[i]);
+ sub_g.q_move(sub_g.nodeById(j), partition[i]);
}
-
sub_g.redistribute();
-
- /*
- for (size_t i = 0; i < sub_g.getNVertex(); i++)
- {
- // Add weight to vertex and migration cost
- std::cout << "g " << sub_g.vertex(i).template get<nm_v::global_id>() << "-" << sub_g.vertex(i).template get<nm_v::id>() << " -> ";
-
- // Create the adjacency list and the weights for edges
- for (size_t s = 0; s < sub_g.getNChilds(i); s++)
- {
- std::cout << sub_g.getChild(i, s) << " ";
- }
- std::cout << "\n";
- }*/
}
/*! \brief Compute the unbalance value
@@ -175,13 +161,11 @@ public:
*/
float getUnbalance()
{
- long t_cost = 0;
+ long t_cost = getProcessorLoad();
long min, max, sum;
float unbalance;
- t_cost = getProcessorLoad();
-
min = t_cost;
max = t_cost;
sum = t_cost;
@@ -191,7 +175,7 @@ public:
v_cl.sum(sum);
v_cl.execute();
- unbalance = ((float) (max - min)) / (float) sum;
+ unbalance = ((float) (max - min)) / (((float) sum) / v_cl.getProcessingUnits());
return unbalance * 100;
}
@@ -221,8 +205,7 @@ public:
*/
inline void setVertexWeight(size_t id, size_t weight)
{
- if (!verticesGotWeights)
- verticesGotWeights = true;
+ verticesGotWeights = true;
if (id >= sub_g.getNVertex())
std::cerr << "Weight - Such vertex doesn't exist (id = " << id << ", " << "total size = " << sub_g.getNVertex() << ")\n";
@@ -344,25 +327,8 @@ public:
*/
void printCurrentDecomposition(int id)
{
- if (v_cl.getProcessUnitID() == 0)
- {
- sub_g.deleteGhosts();
-
- for (size_t i = 0; i < sub_g.getTotNVertex(); ++i)
- {
- sub_g.reqVertex(i);
- }
- }
-
- sub_g.sync();
-
- if (v_cl.getProcessUnitID() == 0)
- {
- VTKWriter<DistGraph_CSR<nm_v, nm_e>, DIST_GRAPH> gv2(sub_g);
- gv2.write("test_dist_graph_" + std::to_string(id) + ".vtk");
-
- sub_g.deleteGhosts();
- }
+ VTKWriter<DistGraph_CSR<nm_v, nm_e>, DIST_GRAPH> gv2(sub_g);
+ gv2.write("test_dist_graph_" + std::to_string(id) + ".vtk");
}
};
diff --git a/src/Decomposition/ParMetisDistribution.hpp b/src/Decomposition/ParMetisDistribution.hpp
index f915f5d6..cb0df5c0 100644
--- a/src/Decomposition/ParMetisDistribution.hpp
+++ b/src/Decomposition/ParMetisDistribution.hpp
@@ -398,6 +398,7 @@ public:
unbalance = ((float) (max - min)) / (float) sum;
+ std::cout << std::endl;
return unbalance * 100;
}
diff --git a/src/Graph/CartesianGraphFactory_unit_test.hpp b/src/Graph/CartesianGraphFactory_unit_test.hpp
index bbba04e4..08690f90 100644
--- a/src/Graph/CartesianGraphFactory_unit_test.hpp
+++ b/src/Graph/CartesianGraphFactory_unit_test.hpp
@@ -4,7 +4,7 @@
#include "Graph/CartesianGraphFactory.hpp"
#include "Graph/map_graph.hpp"
-#define GS_SIZE 8
+#define GS_SIZE 64
/*!
*
diff --git a/src/Graph/DistCartesianGraphFactory_unit_test.hpp b/src/Graph/DistCartesianGraphFactory_unit_test.hpp
index 82f5ef17..a2beccaf 100644
--- a/src/Graph/DistCartesianGraphFactory_unit_test.hpp
+++ b/src/Graph/DistCartesianGraphFactory_unit_test.hpp
@@ -225,7 +225,6 @@ BOOST_AUTO_TEST_CASE( DistCartesianGraphFactory_2D_use)
// try to pack
Packer<size_t,HeapMemory>::pack(mem, 3, sts);
- node n = gd.vertex(0);
Packer<decltype(gd.vertex(0)),HeapMemory>::pack(mem,gd.vertex(0), sts);
Packer<decltype(gd.vertex(0)),HeapMemory>::pack(mem,gd.vertex(1), sts);
Packer<decltype(gd.vertex(0)),HeapMemory>::pack(mem,gd.vertex(2), sts);
@@ -312,7 +311,7 @@ BOOST_AUTO_TEST_CASE( DistCartesianGraphFactory_2D_use)
v.resize(size);
- for(int i = 0; i < size; i++){
+ for(size_t i = 0; i < size; i++){
node v_n;
Unpacker<node,HeapMemory>::unpack(mem,v_n,ps);
v.set(i, v_n);
@@ -336,7 +335,7 @@ BOOST_AUTO_TEST_CASE( DistCartesianGraphFactory_2D_use)
v.resize(size);
- for(int i = 0; i < size; i++){
+ for(size_t i = 0; i < size; i++){
node v_n;
Unpacker<node,HeapMemory>::unpack(mem,v_n,ps);
v.set(i, v_n);
diff --git a/src/Graph/dist_map_graph.hpp b/src/Graph/dist_map_graph.hpp
index 93f2c0f4..ee67614a 100644
--- a/src/Graph/dist_map_graph.hpp
+++ b/src/Graph/dist_map_graph.hpp
@@ -429,7 +429,7 @@ class DistGraph_CSR
{
if (sgp.size() == vcl.getProcessingUnits())
{
- for (int p = 0; p < vcl.getProcessingUnits(); ++p)
+ for (size_t p = 0; p < vcl.getProcessingUnits(); ++p)
{
sgp.get(p).send_v.clear();
sgp.get(p).send_v_m.clear();
@@ -444,7 +444,7 @@ class DistGraph_CSR
{
sgp.resize(vcl.getProcessingUnits());
- for (int p = 0; p < vcl.getProcessingUnits(); ++p)
+ for (size_t p = 0; p < vcl.getProcessingUnits(); ++p)
{
openfpm::vector<V> s_v;
openfpm::vector<v_info> s_v_m;
@@ -524,7 +524,7 @@ class DistGraph_CSR
*/
size_t getVProcessor(size_t v)
{
- for (int i = 1; i < vtxdist.size() - 1; ++i)
+ for (size_t i = 1; i < vtxdist.size() - 1; ++i)
{
if (v < vtxdist.get(i))
{
@@ -577,7 +577,7 @@ class DistGraph_CSR
// prepare slot for number of vertices
Packer<size_t, HeapMemory>::packRequest(pap_prp);
- for (int j = 0; j < vp_size; j++)
+ for (size_t j = 0; j < vp_size; j++)
{
// prepare slot for vertex
Packer<V, HeapMemory>::packRequest(pap_prp);
@@ -589,7 +589,7 @@ class DistGraph_CSR
Packer<size_t, HeapMemory>::packRequest(pap_prp);
// prepare slots for the children
- for (int k = 0; k < sgp.get(pc).send_es.get(j); k++)
+ for (size_t k = 0; k < sgp.get(pc).send_es.get(j); k++)
{
// prepare slot for edge
Packer<E, HeapMemory>::packRequest(pap_prp);
@@ -617,7 +617,7 @@ class DistGraph_CSR
// Pack total size
Packer<size_t, HeapMemory>::pack(mem, vp_size, sts);
- for (int j = 0; j < vp_size; j++)
+ for (size_t j = 0; j < vp_size; j++)
{
// Pack the vertex
Packer<decltype(sgp.get(pc).send_v.get(0)), HeapMemory>::pack(mem, sgp.get(pc).send_v.get(j), sts);
@@ -629,7 +629,7 @@ class DistGraph_CSR
Packer<size_t, HeapMemory>::pack(mem, sgp.get(pc).send_es.get(j), sts);
// Pack children
- for (int k = 0; k < sgp.get(pc).send_es.get(j); k++)
+ for (size_t k = 0; k < sgp.get(pc).send_es.get(j); k++)
{
// Pack the edge
Packer<decltype(sgp.get(pc).send_e.get(0)), HeapMemory>::pack(mem, sgp.get(pc).send_e.get(e_it), sts);
@@ -668,7 +668,7 @@ class DistGraph_CSR
// take previous last item
size_t prev = getNVertex();
- for (int j = prev; j < prev + r_size; j++)
+ for (size_t j = prev; j < prev + r_size; j++)
{
// unpack the vertex
V v_n;
@@ -689,7 +689,7 @@ class DistGraph_CSR
Unpacker<size_t, HeapMemory>::unpack(mem, s, ps);
// prepare slots for the children
- for (int k = 0; k < s; k++)
+ for (size_t k = 0; k < s; k++)
{
// unpack edge
E e_n;
@@ -882,7 +882,7 @@ class DistGraph_CSR
openfpm::vector<openfpm::vector<size_t>> resp_rmi(vcl.getProcessingUnits());
// Prepare re-mapping info response
- for (int i = 0; i < req_rmi.size(); ++i)
+ for (size_t i = 0; i < req_rmi.size(); ++i)
{
for (size_t j = 0; j < req_rmi.get(i).size(); ++j)
{
@@ -944,7 +944,7 @@ class DistGraph_CSR
*/
size_t getInfoProc(size_t vid)
{
- for (int i = 0; i < fvtxdist.size() - 1; ++i)
+ for (size_t i = 0; i < fvtxdist.size() - 1; ++i)
{
if (vid >= fvtxdist.get(i) && vid < fvtxdist.get(i + 1))
{
@@ -1017,6 +1017,7 @@ public:
dup.id2glb = id2glb;
dup.glb2loc = glb2loc;
dup.e.swap(e.duplicate());
+ dup.e_m.swap(e_m.duplicate());
dup.e_l.swap(e_l.duplicate());
dup.e_invalid.swap(e_invalid.duplicate());
dup.vtxdist.swap(vtxdist.duplicate());
@@ -1096,7 +1097,7 @@ public:
{
v.resize(vtxdist.size());
- for (int i = 0; i < vtxdist.size(); ++i)
+ for (size_t i = 0; i < vtxdist.size(); ++i)
{
v.get(i) = vtxdist.get(i);
}
@@ -1120,7 +1121,7 @@ public:
vtxdist.resize(vcl.getProcessingUnits() + 1);
fvtxdist.resize(vcl.getProcessingUnits() + 1);
- for (int i = 0; i < vtxdist.size(); ++i)
+ for (size_t i = 0; i < vtxdist.size(); ++i)
{
vtxdist.get(i) = v.get(i);
fvtxdist.get(i) = v.get(i);
@@ -1136,7 +1137,7 @@ public:
fvtxdist.resize(vcl.getProcessingUnits() + 1);
- for (int i = 0; i < vtxdist.size(); ++i)
+ for (size_t i = 0; i < vtxdist.size(); ++i)
{
fvtxdist.get(i) = vtxdist.get(i);
}
@@ -1316,7 +1317,14 @@ public:
*/
size_t nodeById(size_t id) const
{
- return glb2loc.at(id2glb.at(id));
+ try
+ {
+ return glb2loc.at(id2glb.at(id));
+ }
+ catch (const std::out_of_range& oor)
+ {
+ std::cout << "Node not found by glb: "<< id <<std::endl;
+ }
}
/*! /brief Get the first id of the graph
@@ -1635,32 +1643,6 @@ public:
return e_l.template get<e_map::vid>(v.get() * v_slot + i);
}
- /*! \brief add vertex
- *
- * \param vrt Vertex properties
- *
- */
- inline void addVertex(const V & vrt)
- {
- // Add the vertex
- v.add(vrt);
-
- // Update id to global map
- id2glb.insert( { vrt.template get<V::id>(), vrt.template get<V::global_id>() });
-
- // Update global id to local index
- glb2loc.insert( { vrt.template get<V::global_id>(), v.size() - 1 });
-
- // Update global id to id
- glb2id.insert( { vrt.template get<V::global_id>(), vrt.template get<V::id>() });
-
- // Set the number of adjacent vertex for this vertex to 0
- v_l.add(0ul);
-
- // Add a slot for the vertex adjacency list
- e_l.resize(e_l.size() + v_slot);
- }
-
/*! \brief Add vertex vrt with global id and id properties
*
* \param vrt vertex object to add
@@ -1939,6 +1921,7 @@ public:
v.swap(g.v);
v_m.swap(g.v_m);
e.swap(g.e);
+ e_m.swap(g.e_m);
v_l.swap(g.v_l);
glb2id = g.glb2id;
id2glb = g.id2glb;
@@ -1964,6 +1947,7 @@ public:
v.swap(g.v);
v_m.swap(g.v_m);
e.swap(g.e);
+ e_m.swap(g.e_m);
v_l.swap(g.v_l);
glb2id = g.glb2id;
id2glb = g.id2glb;
@@ -2076,9 +2060,10 @@ public:
for (auto gh : ghs_map)
{
epos += getNChilds(glb2loc.at(gh.first));
+ id2glb.erase(glb2id.at(gh.first));
glb2loc.erase(gh.first);
glb2id.erase(gh.first);
- id2glb.erase(gh.first);
+
}
//resize all structures to delete the ghosts
@@ -2103,6 +2088,8 @@ public:
template<bool toRemove = true> //TODO make it private and create wrapper in public
void q_move(size_t i, size_t t)
{
+ //std::cout << vcl.getProcessUnitID() <<" moving " << getVertexId(i) << " local " << i << " to " << t << std::endl;
+
// Check if a 'useless' move has been requested
if (t == vcl.getProcessUnitID())
{
@@ -2161,16 +2148,16 @@ public:
if (glbi_map.size() == 0)
initGlbimap();
- //std::cout<< "TEMP DBG::deleteGhosts\n";
+ //std::cout << "TEMP DBG::deleteGhosts\n";
deleteGhosts();
- //std::cout<< "TEMP DBG::exchangeVertices\n";
+ //std::cout << "TEMP DBG::exchangeVertices\n";
exchangeVertices<false>();
- //std::cout<< "TEMP DBG::updateVtxdist\n";
+ //std::cout << "TEMP DBG::updateVtxdist\n";
updateVtxdist();
- //std::cout<< "TEMP DBG::remap\n";
+ //std::cout << "TEMP DBG::remap\n";
remap();
}
diff --git a/src/Graph/dist_map_graph_unit_test.hpp b/src/Graph/dist_map_graph_unit_test.hpp
index 125ce7e3..c68f97c6 100644
--- a/src/Graph/dist_map_graph_unit_test.hpp
+++ b/src/Graph/dist_map_graph_unit_test.hpp
@@ -152,26 +152,16 @@ BOOST_AUTO_TEST_CASE( dist_map_graph_use_4p)
//! [Request some vertices given global ids]
- //gd.deleteGhosts();
-
gd.reqVertex(13);
gd.reqVertex(1);
gd.reqVertex(14);
gd.sync();
- //BOOST_REQUIRE_EQUAL(gd.getVertex(13).template get<vx::global_id>(), 13);
- //BOOST_REQUIRE_EQUAL(gd.getVertex(1).template get<vx::global_id>(), 1);
- //BOOST_REQUIRE_EQUAL(gd.getVertex(14).template get<vx::global_id>(), 14);
-
gd.reqVertex(15);
gd.reqVertex(2);
gd.reqVertex(10);
gd.sync();
- //BOOST_REQUIRE_EQUAL(gd.getVertex(15).template get<vx::global_id>(), 15);
- //BOOST_REQUIRE_EQUAL(gd.getVertex(2).template get<vx::global_id>(), 2);
- //BOOST_REQUIRE_EQUAL(gd.getVertex(10).template get<vx::global_id>(), 10);
-
gd.deleteGhosts();
//! [Exchange n vertices and edges packed]
@@ -254,11 +244,14 @@ BOOST_AUTO_TEST_CASE( dist_map_graph_use_4p)
}
}
-BOOST_AUTO_TEST_CASE( dist_map_graph_use_4p_redistribution)
+BOOST_AUTO_TEST_CASE( dist_map_graph_use_redistribution)
{
//! Vcluster
Vcluster & vcl = *global_v_cluster;
+ if(vcl.getProcessingUnits() != 4)
+ return;
+
//! Initialize the global VCluster
init_global_v_cluster(&boost::unit_test::framework::master_test_suite().argc,&boost::unit_test::framework::master_test_suite().argv);
@@ -277,11 +270,6 @@ BOOST_AUTO_TEST_CASE( dist_map_graph_use_4p_redistribution)
for(size_t i=0; i< gd.getNVertex(); i++)
gd.vertex(i).template get<vx::x>()[2] = 0;
- for(size_t i=0; i< gd.getNVertex(); i++)
- std::cout << gd.getVertexId(i) << " ";
-
- std::cout << "\n";
-
if (vcl.getProcessUnitID() == 0)
{
gd.q_move(0,1);
@@ -308,27 +296,13 @@ BOOST_AUTO_TEST_CASE( dist_map_graph_use_4p_redistribution)
gd.redistribute();
- if (vcl.getProcessUnitID() == 0)
- {
- gd.deleteGhosts();
-
- for (size_t i = 0; i < gd.getTotNVertex(); ++i)
- {
- gd.reqVertex(i);
- }
- }
+ VTKWriter<DistGraph_CSR<vx, ed>, DIST_GRAPH> gv2(gd);
+ gv2.write("dist_graph_redistribution_0.vtk");
- gd.sync();
-
- if (vcl.getProcessUnitID() == 0)
+ if(vcl.getProcessUnitID() == 0)
{
- VTKWriter<DistGraph_CSR<vx, ed>, GRAPH> gv2(gd);
- gv2.write("dist_graph_0.vtk");
-
- bool test = compare("dist_graph_0.vtk","dist_graph_0_test.vtk");
- //BOOST_REQUIRE_EQUAL(true,test);
-
- gd.deleteGhosts();
+ bool test = compare("dist_graph_redistribution_0.vtk", "dist_graph_redistribution_0_test.vtk");
+ BOOST_REQUIRE_EQUAL(true,test);
}
if (vcl.getProcessUnitID() == 2)
@@ -345,36 +319,24 @@ BOOST_AUTO_TEST_CASE( dist_map_graph_use_4p_redistribution)
gd.redistribute();
- if (vcl.getProcessUnitID() == 0)
- {
- gd.deleteGhosts();
-
- for (size_t i = 0; i < gd.getTotNVertex(); ++i)
- {
- gd.reqVertex(i);
- }
- }
-
- gd.sync();
+ gv2.write("dist_graph_redistribution_1.vtk");
- if (vcl.getProcessUnitID() == 0)
+ if(vcl.getProcessUnitID() == 0)
{
- VTKWriter<DistGraph_CSR<vx, ed>, DIST_GRAPH> gv2(gd);
- gv2.write("dist_graph_1.vtk");
-
- bool test = compare("dist_graph_1.vtk","dist_graph_1_test.vtk");
- //BOOST_REQUIRE_EQUAL(true,test);
-
- gd.deleteGhosts();
+ bool test = compare("dist_graph_redistribution_1.vtk","dist_graph_redistribution_1_test.vtk");
+ BOOST_REQUIRE_EQUAL(true,test);
}
}
-BOOST_AUTO_TEST_CASE( dist_map_graph_use_4p_free_add)
+BOOST_AUTO_TEST_CASE( dist_map_graph_use_free_add)
{
//! Vcluster
Vcluster & vcl = *global_v_cluster;
+ if(vcl.getProcessingUnits() != 4)
+ return;
+
//! Initialize the global VCluster
init_global_v_cluster(&boost::unit_test::framework::master_test_suite().argc,&boost::unit_test::framework::master_test_suite().argv);
@@ -442,17 +404,6 @@ BOOST_AUTO_TEST_CASE( dist_map_graph_use_4p_free_add)
}
}
- std::cout << vcl.getProcessUnitID()<< " ";
- for(size_t i = 0; i < gd.getNVertex(); i++)
- {
-
- for(size_t j =0; j< gd.getNChilds(i); j++)
- {
- std::cout << gd.getChildDstGid(i, j) << " ";
- }
- }
- std::cout << "\n\n";
-
if(vcl.getProcessUnitID() == 0)
gd.reqVertex(5);
@@ -486,44 +437,13 @@ BOOST_AUTO_TEST_CASE( dist_map_graph_use_4p_free_add)
gd.redistribute();
- for (int i = 0; i < gd.getNVertex(); ++i)
- {
- std::cout << gd.getVertexId(i) << " ";
- }
- std::cout << "\n";
-
- std::cout << vcl.getProcessUnitID()<< " ";
- for(size_t i = 0; i < gd.getNVertex(); i++)
- {
-
- for(size_t j =0; j< gd.getNChilds(i); j++)
- {
- std::cout << gd.getChildDstGid(i, j) << " ";
- }
- }
- std::cout << "\n\n";
-
- if (vcl.getProcessUnitID() == 0)
- {
- gd.deleteGhosts();
-
- for (size_t i = 0; i < gd.getTotNVertex(); ++i)
- {
- gd.reqVertex(i);
- }
- }
-
- gd.sync();
+ VTKWriter<DistGraph_CSR<vx, ed>, DIST_GRAPH> gv2(gd);
+ gv2.write("dist_graph_free_0.vtk");
- if (vcl.getProcessUnitID() == 0)
+ if(vcl.getProcessUnitID() == 0)
{
- VTKWriter<DistGraph_CSR<vx, ed>, DIST_GRAPH> gv2(gd);
- gv2.write("dist_graph_0_free.vtk");
-
- bool test = compare("dist_graph_0_free.vtk","dist_graph_0_free_test.vtk");
- //BOOST_REQUIRE_EQUAL(true,test);
-
- gd.deleteGhosts();
+ bool test = compare("dist_graph_free_0.vtk", "dist_graph_free_0_test.vtk");
+ BOOST_REQUIRE_EQUAL(true,test);
}
if (vcl.getProcessUnitID() == 2)
@@ -540,29 +460,13 @@ BOOST_AUTO_TEST_CASE( dist_map_graph_use_4p_free_add)
gd.redistribute();
- if (vcl.getProcessUnitID() == 0)
- {
- gd.deleteGhosts();
+ gv2.write("dist_graph_free_1.vtk");
- for (size_t i = 0; i < gd.getTotNVertex(); ++i)
- {
- gd.reqVertex(i);
- }
- }
-
- gd.sync();
-
- if (vcl.getProcessUnitID() == 0)
+ if(vcl.getProcessUnitID() == 0)
{
- VTKWriter<DistGraph_CSR<vx, ed>, DIST_GRAPH> gv2(gd);
- gv2.write("dist_graph_1_free.vtk");
-
- bool test = compare("dist_graph_1_free.vtk","dist_graph_1_free_test.vtk");
- //BOOST_REQUIRE_EQUAL(true,test);
-
- gd.deleteGhosts();
+ bool test = compare("dist_graph_free_1.vtk", "dist_graph_free_1_test.vtk");
+ BOOST_REQUIRE_EQUAL(true,test);
}
-
}
BOOST_AUTO_TEST_SUITE_END()
diff --git a/src/main.cpp b/src/main.cpp
index c50c14f1..a1415740 100644
--- a/src/main.cpp
+++ b/src/main.cpp
@@ -29,5 +29,6 @@
#include "Grid/grid_dist_id_unit_test.hpp"
#include "Vector/vector_dist_unit_test.hpp"
//#include "Decomposition/DLB_unit_test.hpp"
-//#include "Graph/dist_map_graph_unit_test.hpp"
+#include "Graph/dist_map_graph_unit_test.hpp"
#include "Graph/DistGraphFactory.hpp"
+#include "parmetis_dist_util_unit_test.hpp"
diff --git a/src/parmetis_dist_util.hpp b/src/parmetis_dist_util.hpp
index 5ca62734..a9713995 100755
--- a/src/parmetis_dist_util.hpp
+++ b/src/parmetis_dist_util.hpp
@@ -141,46 +141,34 @@ class DistParmetis
// actual position
size_t id = 0;
- // for each vertex calculate the position of the starting point in the adjacency list
for (size_t i = 0, j = sub_g.firstId(); i < sub_g.getNVertex() && j <= sub_g.lastId(); i++, j++)
{
+ size_t idx = sub_g.nodeById(j);
+
// Add weight to vertex and migration cost
- Mg.vwgt[i] = sub_g.vertex(sub_g.nodeById(j)).template get<nm_v::computation>();
- Mg.vsize[i] = sub_g.vertex(sub_g.nodeById(j)).template get<nm_v::migration>();
+ Mg.vwgt[i] = sub_g.vertex(idx).template get<nm_v::computation>();
+ Mg.vsize[i] = sub_g.vertex(idx).template get<nm_v::migration>();
// Calculate the starting point in the adjacency list
Mg.xadj[id] = prev;
// Create the adjacency list and the weights for edges
- for (size_t s = 0; s < sub_g.getNChilds(sub_g.nodeById(j)); s++)
+ for (size_t s = 0; s < sub_g.getNChilds(idx); s++)
{
- Mg.adjncy[prev + s] = sub_g.getChild(sub_g.nodeById(j), s);
+ Mg.adjncy[prev + s] = sub_g.getChild(idx, s);
- Mg.adjwgt[prev + s] = sub_g.getChildEdge(sub_g.nodeById(j), s).template get<nm_e::communication>();
+ Mg.adjwgt[prev + s] = sub_g.getChildEdge(idx, s).template get<nm_e::communication>();
}
// update the position for the next vertex
- prev += sub_g.getNChilds(sub_g.nodeById(j));
+ prev += sub_g.getNChilds(idx);
id++;
}
// Fill the last point
Mg.xadj[id] = prev;
- /*
- std::cout << p_id << "--------------------------------------\n";
- for (int i = 0; i <= sub_g.getNVertex(); i++)
- {
- std::cout << Mg.xadj[i] << " ";
- }
- std::cout << "\n\n";
-
- for (int i = 0; i < sub_g.getNEdge(); i++)
- {
- std::cout << Mg.adjncy[i] << " ";
- }
- std::cout << "-----------------------------------------------------\n\n";
- */
+
}
public:
@@ -347,7 +335,7 @@ public:
//! This is used to indicate if the graph is weighted.
Mg.wgtflag = new idx_t[1];
- Mg.wgtflag[0] = 2;
+ Mg.wgtflag[0] = 3;
}
/*! \brief Decompose the graph
@@ -371,13 +359,10 @@ public:
*/
// For each vertex store the processor that contain the data
- for (size_t j = 0, id = 0; j < sub_g.getNVertex(); j++, id++)
+ for (size_t id = 0, j = sub_g.firstId(); id < sub_g.getNVertex() && j <= sub_g.lastId(); id++, j++)
{
-
- sub_g.vertex(j).template get<i>() = Mg.part[id];
-
+ sub_g.vertex(sub_g.nodeById(j)).template get<i>() = Mg.part[id];
}
-
}
/*! \brief Refine the graph
@@ -390,20 +375,13 @@ public:
void refine(Graph & sub_g)
{
// Refine
- for (int j = 0; j < sub_g.getVtxdist()->size(); ++j) {
- std::cout << sub_g.getVtxdist()->get(j) << " ";
- }
- std::cout << "\n";
- ParMETIS_V3_PartKway((idx_t *) sub_g.getVtxdist()->getPointer(), Mg.xadj, Mg.adjncy, Mg.vwgt, Mg.adjwgt, Mg.wgtflag, Mg.numflag, Mg.ncon, Mg.nparts, Mg.tpwgts, Mg.ubvec, Mg.options, Mg.edgecut, Mg.part, &comm);
- //ParMETIS_V3_AdaptiveRepart((idx_t *) sub_g.getVtxdist()->getPointer(), Mg.xadj, Mg.adjncy, Mg.vwgt, Mg.vsize, Mg.adjwgt, Mg.wgtflag, Mg.numflag, Mg.ncon, Mg.nparts, Mg.tpwgts, Mg.ubvec, Mg.itr, Mg.options, Mg.edgecut, Mg.part, &comm);
+ //ParMETIS_V3_PartKway((idx_t *) sub_g.getVtxdist()->getPointer(), Mg.xadj, Mg.adjncy, Mg.vwgt, Mg.adjwgt, Mg.wgtflag, Mg.numflag, Mg.ncon, Mg.nparts, Mg.tpwgts, Mg.ubvec, Mg.options, Mg.edgecut, Mg.part, &comm);
+ ParMETIS_V3_AdaptiveRepart((idx_t *) sub_g.getVtxdist()->getPointer(), Mg.xadj, Mg.adjncy, Mg.vwgt, Mg.vsize, Mg.adjwgt, Mg.wgtflag, Mg.numflag, Mg.ncon, Mg.nparts, Mg.tpwgts, Mg.ubvec, Mg.itr, Mg.options, Mg.edgecut, Mg.part, &comm);
// For each vertex store the processor that contain the data
-
- for (size_t j = 0, id = 0; j < sub_g.getNVertex(); j++, id++)
+ for (size_t id = 0, j = sub_g.firstId(); id < sub_g.getNVertex() && j <= sub_g.lastId(); id++, j++)
{
-
- sub_g.vertex(j).template get<i>() = Mg.part[id];
-
+ sub_g.vertex(sub_g.nodeById(j)).template get<i>() = Mg.part[id];
}
}
diff --git a/src/parmetis_util.hpp b/src/parmetis_util.hpp
index 62ef9576..89b34e75 100755
--- a/src/parmetis_util.hpp
+++ b/src/parmetis_util.hpp
@@ -191,92 +191,8 @@ class Parmetis
// Fill the last point
Mg.xadj[id] = prev;
-
- /*
- std::cout << p_id << " ------------";
- for (int i = 0; i <= sub_g.getNVertex(); i++) {
- std::cout << Mg.vwgt[i] << " ";
- }
- std::cout << "\n";
-
-
- if (p_id == 0) {
- std::cout << p_id << "\n";
- for (int i = 0; i <= sub_g.getNVertex(); i++) {
- std::cout << Mg.xadj[i] << " ";
- }
- std::cout << "\n\n";
-
- for (int i = 0; i < sub_g.getNEdge(); i++) {
- std::cout << Mg.adjwgt[i] << " ";
- }
- std::cout << "\n\n";
- */
-
-
}
- /*! \brief Construct Adjacency list
- *
- * \param g Reference graph to get informations
- *
- */
- /*
- void constructAdjList(Graph &refGraph, idx_t* &old_vtxdist ) {
- // create xadj and adjlist
- Mg.vwgt = new idx_t[g.getNVertex()];
- Mg.xadj = new idx_t[g.getNVertex() + 1];
- Mg.adjncy = new idx_t[g.getNEdge()];
-
- //! starting point in the adjacency list
- size_t prev = 0;
-
- // actual position
- size_t id = 0;
-
- // for each vertex calculate the position of the starting point in the adjacency list
- for (size_t i = 0; i < g.getNVertex(); i++) {
-
- // Add weight to vertex
- Mg.vwgt[i] = g.vertex(i).template get<nm_v::computation>();
-
- // Calculate the starting point in the adjacency list
- Mg.xadj[id] = prev;
-
- // Create the adjacency list and the weights for edges
- for (size_t s = 0; s < refGraph.getNChilds(i); s++) {
-
- size_t child = refGraph.getChild(i, s);
-
- // Check if child is not in this processor
- if(child > old_vtxdist[p_id+1] || child < old_vtxdist[p_id])
-
- Mg.adjncy[prev + s] = child;
- }
-
- // update the position for the next vertex
- prev += refGraph.getNChilds(i);
-
- id++;
- }
-
- // Fill the last point
- Mg.xadj[id] = prev;
-
-
- std::cout << p_id << "\n";
- for(int i=0; i<= g.getNVertex();i++){
- std::cout << Mg.xadj[i] << " ";
- }
- std::cout << "\n\n";
- for(int i=0; i< g.getNEdge();i++){
- std::cout << Mg.adjncy[i] << " ";
- }
- std::cout << "\n\n";
-
-
- }
- */
public:
/*! \brief Constructor
@@ -449,10 +365,10 @@ public:
//! This is used to indicate if the graph is weighted. wgtflag can take one of four values:
Mg.wgtflag = new idx_t[1];
- if(w)
- Mg.wgtflag[0] = 3;
- else
- Mg.wgtflag[0] = 0;
+ //if(w)
+ Mg.wgtflag[0] = 2;
+ //else
+ //Mg.wgtflag[0] = 0;
}
/*! \brief Decompose the graph
@@ -479,9 +395,7 @@ public:
// For each vertex store the processor that contain the data
for (size_t j = 0, id = 0; j < sub_g.getNVertex(); j++, id++)
{
-
sub_g.vertex(j).template get<i>() = Mg.part[id];
-
}
}
@@ -505,9 +419,7 @@ public:
for (size_t j = 0, id = 0; j < sub_g.getNVertex(); j++, id++)
{
-
sub_g.vertex(j).template get<i>() = Mg.part[id];
-
}
}
--
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