| 1 | /**
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| 2 | * @file comm_mpi.cpp
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| 3 | * @author Julian Iseringhausen <isering@ins.uni-bonn.de>
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| 4 | * @date Wed Jun 16 13:21:06 2010
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| 5 | *
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| 6 | * @brief Class for MPI-based communication.
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| 7 | *
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| 8 | */
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| 9 |
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| 10 | #ifdef HAVE_CONFIG_H
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| 11 | #include <config.h>
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| 12 | #endif
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| 13 |
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| 14 | #ifdef HAVE_MPI
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| 15 |
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| 16 | #include <mpi.h>
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| 17 |
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| 18 | #ifdef HAVE_BOOST_FILESYSTEM
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| 19 | #include <boost/filesystem.hpp>
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| 20 | namespace fs = boost::filesystem;
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| 21 | #endif
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| 22 |
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| 23 | #include <cstring>
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| 24 | #include <sstream>
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| 25 |
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| 26 | #include "base/helper.hpp"
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| 27 | #include "base/linked_cell_list.hpp"
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| 28 | #include "base/timer.hpp"
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| 29 | #include "comm/comm_mpi.hpp"
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| 30 | #include "grid/grid.hpp"
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| 31 | #include "grid/multigrid.hpp"
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| 32 | #include "grid/tempgrid.hpp"
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| 33 | #include "mg.hpp"
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| 34 |
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| 35 | static char print_buffer[512];
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| 36 |
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| 37 | using namespace VMG;
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| 38 |
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| 39 | void CommMPI::CommSubgrid(Grid& grid_old, Grid& grid_new)
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| 40 | {
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| 41 | Timer::Start("CommSubgrid");
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| 42 |
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| 43 | MPI_Comm comm = comm_info.GetUnionCommunicator(grid_old, grid_new);
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| 44 |
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| 45 | if (comm != MPI_COMM_NULL) {
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| 46 |
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| 47 | int comm_rank, comm_size;
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| 48 | MPI_Comm_rank(comm, &comm_rank);
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| 49 | MPI_Comm_size(comm, &comm_size);
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| 50 |
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| 51 | Index begin_local, end_local;
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| 52 | Index begin_remote, end_remote;
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| 53 | Index sizes, subsizes, starts;
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| 54 | Index offset_new, offset_old;
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| 55 | int* buffer = new int[6*comm_size];
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| 56 |
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| 57 | for (int i=0; i<3; ++i) {
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| 58 |
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| 59 | offset_old[i] = (grid_old.Local().HaloEnd1()[i] > 0 ? grid_old.Local().Begin()[i] : 0);
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| 60 | offset_new[i] = (grid_new.Local().HaloEnd1()[i] > 0 ? grid_new.Local().Begin()[i] : 0);
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| 61 |
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| 62 | buffer[6*comm_rank + i ] = grid_new.Global().BeginLocal()[i];
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| 63 | buffer[6*comm_rank + i+3] = grid_new.Global().EndLocal()[i];
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| 64 |
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| 65 | }
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| 66 |
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| 67 | //TODO: Create LUT to avoid global communication here
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| 68 | MPI_Allgather(MPI_IN_PLACE, 6, MPI_INT, buffer, 6, MPI_INT, comm);
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| 69 |
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| 70 | for (int i=0; i<comm_size; ++i) {
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| 71 |
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| 72 | for (int j=0; j<3; ++j) {
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| 73 |
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| 74 | begin_remote[j] = buffer[6*i + j];
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| 75 | end_remote[j] = buffer[6*i + j+3];
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| 76 |
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| 77 | }
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| 78 |
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| 79 | begin_remote = begin_remote.Clamp(grid_old.Global().BeginLocal(), grid_old.Global().EndLocal());
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| 80 | end_remote = end_remote.Clamp(grid_old.Global().BeginLocal(), grid_old.Global().EndLocal());
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| 81 |
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| 82 | if ((end_remote - begin_remote).Product() > 0) {
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| 83 |
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| 84 | MPI_Datatype dt_temp;
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| 85 |
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| 86 | sizes = grid_old.Local().SizeTotal();
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| 87 | subsizes = end_remote - begin_remote;
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| 88 | starts = begin_remote - grid_old.Global().BeginLocal() + offset_old;
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| 89 |
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| 90 | MPI_Type_create_subarray(3, sizes.vec(), subsizes.vec(), starts.vec(), MPI_ORDER_C, MPI_DOUBLE, &dt_temp);
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| 91 |
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| 92 | MPI_Type_commit(&dt_temp);
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| 93 |
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| 94 | MPI_Isend(&grid_old(0), 1, dt_temp, i, 0, comm, &Request());
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| 95 |
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| 96 | MPI_Type_free(&dt_temp);
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| 97 |
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| 98 | }
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| 99 |
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| 100 | }
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| 101 |
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| 102 | for (int i=0; i<3; ++i) {
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| 103 |
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| 104 | buffer[6*comm_rank + i ] = grid_old.Global().BeginLocal()[i];
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| 105 | buffer[6*comm_rank + i+3] = grid_old.Global().EndLocal()[i];
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| 106 |
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| 107 | }
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| 108 |
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| 109 | //TODO: Create LUT to avoid global communication here
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| 110 | MPI_Allgather(MPI_IN_PLACE, 6, MPI_INT, buffer, 6, MPI_INT, comm);
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| 111 |
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| 112 | for (int i=0; i<comm_size; ++i) {
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| 113 |
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| 114 | for (int j=0; j<3; ++j) {
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| 115 |
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| 116 | begin_remote[j] = buffer[6*i + j];
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| 117 | end_remote[j] = buffer[6*i + j+3];
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| 118 |
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| 119 | }
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| 120 |
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| 121 | begin_remote = begin_remote.Clamp(grid_new.Global().BeginLocal(), grid_new.Global().EndLocal());
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| 122 | end_remote = end_remote.Clamp(grid_new.Global().BeginLocal(), grid_new.Global().EndLocal());
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| 123 |
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| 124 | if ((end_remote - begin_remote).Product() > 0) {
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| 125 |
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| 126 | MPI_Datatype dt_temp;
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| 127 |
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| 128 | sizes = grid_new.Local().SizeTotal();
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| 129 | subsizes = end_remote - begin_remote;
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| 130 | starts = begin_remote - grid_new.Global().BeginLocal() + offset_new;
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| 131 |
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| 132 | MPI_Type_create_subarray(3, sizes.vec(), subsizes.vec(), starts.vec(), MPI_ORDER_C, MPI_DOUBLE, &dt_temp);
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| 133 |
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| 134 | MPI_Type_commit(&dt_temp);
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| 135 |
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| 136 | MPI_Irecv(&grid_new(0), 1, dt_temp, i, 0, comm, &Request());
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| 137 |
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| 138 | MPI_Type_free(&dt_temp);
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| 139 |
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| 140 | }
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| 141 |
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| 142 | }
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| 143 |
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| 144 | ClearRequests();
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| 145 |
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| 146 | delete [] buffer;
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| 147 |
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| 148 | }
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| 149 |
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| 150 | CommToGhosts(grid_new);
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| 151 |
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| 152 | Timer::Stop("CommSubgrid");
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| 153 | }
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| 154 |
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| 155 | void CommMPI::CommAddSubgrid(Grid& grid_old, Grid& grid_new)
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| 156 | {
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| 157 | Timer::Start("CommAddSubgrid");
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| 158 |
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| 159 | MPI_Comm comm = comm_info.GetUnionCommunicator(grid_old, grid_new);
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| 160 |
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| 161 | if (comm != MPI_COMM_NULL) {
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| 162 |
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| 163 | int comm_rank, comm_size;
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| 164 | MPI_Comm_rank(comm, &comm_rank);
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| 165 | MPI_Comm_size(comm, &comm_size);
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| 166 |
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| 167 | Index begin_local, end_local;
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| 168 | Index begin_remote, end_remote;
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| 169 | Index sizes, subsizes, starts;
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| 170 | int* buffer = new int[6*comm_size];
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| 171 |
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| 172 | for (int i=0; i<3; ++i) {
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| 173 |
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| 174 | buffer[6*comm_rank + i ] = grid_new.Global().BeginLocal()[i];
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| 175 | buffer[6*comm_rank + i+3] = grid_new.Global().EndLocal()[i];
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| 176 |
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| 177 | }
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| 178 |
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| 179 | //TODO: Create LUT to avoid global communication here
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| 180 | MPI_Allgather(MPI_IN_PLACE, 6, MPI_INT, buffer, 6, MPI_INT, comm);
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| 181 |
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| 182 | for (int i=0; i<comm_size; ++i) {
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| 183 | for (int j=0; j<3; ++j) {
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| 184 |
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| 185 | begin_remote[j] = buffer[6*i + j];
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| 186 | end_remote[j] = buffer[6*i + j+3];
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| 187 |
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| 188 | }
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| 189 |
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| 190 | begin_remote = begin_remote.Clamp(grid_old.Global().BeginLocal(), grid_old.Global().EndLocal());
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| 191 | end_remote = end_remote.Clamp(grid_old.Global().BeginLocal(), grid_old.Global().EndLocal());
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| 192 |
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| 193 | if ((end_remote - begin_remote).Product() > 0) {
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| 194 |
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| 195 | MPI_Datatype dt_temp;
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| 196 |
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| 197 | sizes = grid_old.Local().SizeTotal();
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| 198 | subsizes = end_remote - begin_remote;
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| 199 | starts = begin_remote - grid_old.Global().BeginLocal();
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| 200 |
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| 201 | MPI_Type_create_subarray(3, sizes.vec(), subsizes.vec(), starts.vec(), MPI_ORDER_C, MPI_DOUBLE, &dt_temp);
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| 202 |
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| 203 | MPI_Type_commit(&dt_temp);
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| 204 |
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| 205 | MPI_Isend(&grid_old(0), 1, dt_temp, i, 0, comm, &Request());
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| 206 |
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| 207 | MPI_Type_free(&dt_temp);
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| 208 |
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| 209 | }
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| 210 |
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| 211 | }
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| 212 |
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| 213 | for (int i=0; i<3; ++i) {
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| 214 |
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| 215 | buffer[6*comm_rank + i ] = grid_old.Global().BeginLocal()[i];
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| 216 | buffer[6*comm_rank + i+3] = grid_old.Global().EndLocal()[i];
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| 217 |
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| 218 | }
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| 219 |
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| 220 | //TODO: Create LUT to avoid global communication here
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| 221 | MPI_Allgather(MPI_IN_PLACE, 6, MPI_INT, buffer, 6, MPI_INT, comm);
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| 222 |
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| 223 | for (int i=0; i<comm_size; ++i) {
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| 224 |
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| 225 | for (int j=0; j<3; ++j) {
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| 226 |
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| 227 | begin_remote[j] = buffer[6*i + j];
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| 228 | end_remote[j] = buffer[6*i + j+3];
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| 229 |
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| 230 | }
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| 231 |
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| 232 | begin_remote = begin_remote.Clamp(grid_new.Global().BeginLocal(), grid_new.Global().EndLocal());
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| 233 | end_remote = end_remote.Clamp(grid_new.Global().BeginLocal(), grid_new.Global().EndLocal());
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| 234 |
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| 235 | if ((end_remote - begin_remote).Product() > 0) {
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| 236 |
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| 237 | MPI_Datatype dt_temp;
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| 238 |
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| 239 | sizes = grid_new.Local().SizeTotal();
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| 240 | subsizes = end_remote - begin_remote;
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| 241 | starts = begin_remote - grid_old.Global().BeginLocal();
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| 242 |
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| 243 | MPI_Type_create_subarray(3, sizes.vec(), subsizes.vec(), starts.vec(), MPI_ORDER_C, MPI_DOUBLE, &dt_temp);
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| 244 |
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| 245 | MPI_Type_commit(&dt_temp);
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| 246 |
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| 247 | ReceiveAndAddSubgrid(grid_new, comm, dt_temp, i, 0);
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| 248 |
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| 249 | MPI_Type_free(&dt_temp);
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| 250 |
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| 251 | }
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| 252 |
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| 253 | }
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| 254 |
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| 255 | ClearRequests();
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| 256 |
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| 257 | delete [] buffer;
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| 258 |
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| 259 | }
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| 260 |
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| 261 | CommToGhosts(grid_new);
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| 262 |
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| 263 | Timer::Stop("CommAddSubgrid");
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| 264 | }
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| 265 |
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| 266 | void CommMPI::CommFromGhosts(Grid& grid)
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| 267 | {
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| 268 | Timer::Start("CommFromGhosts");
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| 269 |
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| 270 | MPI_Comm comm = comm_info.GetCommunicator(grid);
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| 271 |
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| 272 | if (comm != MPI_COMM_NULL) {
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| 273 |
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| 274 | const Index has_halo_1 = grid.Local().HasHalo1();
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| 275 | const Index has_halo_2 = grid.Local().HasHalo2();
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| 276 | Tuple<int> neighbors;
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| 277 |
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| 278 | for (int i=0; i<3; ++i) {
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| 279 |
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| 280 | MPI_Cart_shift(comm, i, 1, &neighbors.Left(), &neighbors.Right());
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| 281 |
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| 282 | if (has_halo_1[i]) {
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| 283 | MPI_Datatype dts1 = comm_info.GetDatatypeSubarray(grid, grid.Iterators().Halo1()[i]);
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| 284 | MPI_Isend(&grid(0), 1, dts1, neighbors.Left(), 1, comm, &Request());
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| 285 | }
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| 286 |
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| 287 | if (has_halo_2[i]) {
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| 288 |
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| 289 | MPI_Datatype dts2 = comm_info.GetDatatypeSubarray(grid, grid.Iterators().Halo2()[i]);
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| 290 | MPI_Isend(&grid(0), 1, dts2, neighbors.Right(), 2, comm, &Request());
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| 291 |
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| 292 | MPI_Datatype dtr1 = comm_info.GetDatatypeSubarray(grid, grid.Iterators().NearBoundary2()[i]);
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| 293 | ReceiveAndAddSubgrid(grid, comm, dtr1, neighbors.Right(), 1);
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| 294 |
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| 295 | }
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| 296 |
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| 297 | if (has_halo_1[i]) {
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| 298 | MPI_Datatype dtr2 = comm_info.GetDatatypeSubarray(grid, grid.Iterators().NearBoundary1()[i]);
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| 299 | ReceiveAndAddSubgrid(grid, comm, dtr2, neighbors.Left(), 2);
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| 300 | }
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| 301 |
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| 302 | }
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| 303 |
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| 304 | ClearRequests();
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| 305 |
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| 306 | }
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| 307 |
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| 308 | Timer::Stop("CommFromGhosts");
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| 309 | }
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| 310 |
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| 311 | void CommMPI::CommToGhosts(Grid& grid)
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| 312 | {
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| 313 | Timer::Start("CommToGhosts");
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| 314 |
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| 315 | MPI_Comm comm = comm_info.GetCommunicator(grid);
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| 316 |
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| 317 | if (comm != MPI_COMM_NULL) {
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| 318 |
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| 319 | const Index has_halo_1 = grid.Local().HasHalo1();
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| 320 | const Index has_halo_2 = grid.Local().HasHalo2();
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| 321 | Tuple<int> neighbors;
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| 322 |
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| 323 | for (int i=2; i>=0; --i) {
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| 324 |
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| 325 | MPI_Cart_shift(comm, i, 1, &neighbors.Left(), &neighbors.Right());
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| 326 |
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| 327 | MPI_Datatype dts_left, dts_right;
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| 328 | MPI_Datatype dtr_left, dtr_right;
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| 329 | int num_left, num_right;
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| 330 |
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| 331 | if (has_halo_1[i]) {
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| 332 | dts_left = comm_info.GetDatatypeSubarray(grid, grid.Iterators().NearBoundary1()[i]);
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| 333 | dtr_left = comm_info.GetDatatypeSubarray(grid, grid.Iterators().Halo1()[i]);
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| 334 | num_left = 1;
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| 335 | }else {
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| 336 | dts_left = MPI_INT;
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| 337 | dtr_left = MPI_INT;
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| 338 | num_left = 0;
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| 339 | }
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| 340 |
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| 341 | if (has_halo_2[i]) {
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| 342 | dts_right = comm_info.GetDatatypeSubarray(grid, grid.Iterators().NearBoundary2()[i]);
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| 343 | dtr_right = comm_info.GetDatatypeSubarray(grid, grid.Iterators().Halo2()[i]);
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| 344 | num_right = 1;
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| 345 | }else {
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| 346 | dts_right = MPI_INT;
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| 347 | dtr_right = MPI_INT;
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| 348 | num_right = 0;
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| 349 | }
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| 350 |
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| 351 | Timer::Start("MPI_Sendrecv");
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| 352 | MPI_Sendrecv(&(grid(0)), num_right, dts_right, neighbors.Right(), 3,
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| 353 | &(grid(0)), num_left, dtr_left, neighbors.Left(), 3,
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| 354 | comm, MPI_STATUS_IGNORE);
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| 355 | MPI_Sendrecv(&(grid(0)), num_left, dts_left, neighbors.Left(), 4,
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| 356 | &(grid(0)), num_right, dtr_right, neighbors.Right(), 4,
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| 357 | comm, MPI_STATUS_IGNORE);
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| 358 | Timer::Stop("MPI_Sendrecv");
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| 359 |
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| 360 | }
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| 361 | }
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| 362 |
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| 363 | Timer::Stop("CommToGhosts");
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| 364 | }
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| 365 |
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| 366 | Grid& CommMPI::GetCoarserGrid(Multigrid& multigrid)
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| 367 | {
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| 368 | std::map<const Grid*, TempGrid*>::iterator iter = coarser_grids.find(&multigrid());
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| 369 |
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| 370 | if (iter == coarser_grids.end()) {
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| 371 | TempGrid* temp_grid = new TempGrid();
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| 372 | temp_grid->SetPropertiesToCoarser(multigrid(), BoundaryConditions());
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| 373 | iter = coarser_grids.insert(std::make_pair(&multigrid(), temp_grid)).first;
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| 374 | }
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| 375 |
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| 376 | TempGrid& grid_coarser = *iter->second;
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| 377 |
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| 378 | CommSubgrid(multigrid(multigrid.Level()-1), grid_coarser);
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| 379 |
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| 380 | return grid_coarser;
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| 381 | }
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| 382 |
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| 383 | Grid& CommMPI::GetFinerGrid(Multigrid& multigrid)
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| 384 | {
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| 385 | std::map<const Grid*, TempGrid*>::iterator iter = finer_grids.find(&multigrid());
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| 386 |
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| 387 | if (iter == finer_grids.end()) {
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| 388 | TempGrid* temp_grid = new TempGrid();
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| 389 | temp_grid->SetPropertiesToFiner(multigrid(), BoundaryConditions());
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| 390 | iter = finer_grids.insert(std::make_pair(&multigrid(), temp_grid)).first;
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| 391 | }
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| 392 |
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| 393 | TempGrid& grid_finer = *iter->second;
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| 394 |
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| 395 | CommSubgrid(multigrid(multigrid.Level()+1), grid_finer);
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| 396 |
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| 397 | return grid_finer;
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| 398 | }
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| 399 |
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| 400 | Grid& CommMPI::GetGlobalCoarseGrid(Multigrid& multigrid)
|
|---|
| 401 | {
|
|---|
| 402 | if (global_coarse_grid == NULL) {
|
|---|
| 403 |
|
|---|
| 404 | global_coarse_grid = new TempGrid();
|
|---|
| 405 | global_coarse_grid->SetPropertiesToGlobalCoarseGrid();
|
|---|
| 406 |
|
|---|
| 407 | }
|
|---|
| 408 |
|
|---|
| 409 | CommSubgrid(multigrid(multigrid.MinLevel()), *global_coarse_grid);
|
|---|
| 410 |
|
|---|
| 411 | return *global_coarse_grid;
|
|---|
| 412 | }
|
|---|
| 413 |
|
|---|
| 414 | //
|
|---|
| 415 | // Decodes a derived datatype created by MPI_Type_create_subarray
|
|---|
| 416 | // and adds values to grid.
|
|---|
| 417 | // I chose this approach since MPI neither supports a point-to-point reduce nor
|
|---|
| 418 | // a non-blocking global reduce.
|
|---|
| 419 | // For more information see Chapter 4.1 "DERIVED DATATYPES" of the MPI standard
|
|---|
| 420 | //
|
|---|
| 421 | void CommMPI::ReceiveAndAddSubgrid(Grid& grid, const MPI_Comm& comm, MPI_Datatype& type,
|
|---|
| 422 | const int& rank, const int& tag)
|
|---|
| 423 | {
|
|---|
| 424 | int counter = 0;
|
|---|
| 425 | int ibuffer[11];
|
|---|
| 426 | Index i;
|
|---|
| 427 | MPI_Datatype base_type;
|
|---|
| 428 | MPI_Aint address;
|
|---|
| 429 |
|
|---|
| 430 | MPI_Type_get_contents(type, 11, 0, 1, ibuffer, &address, &base_type);
|
|---|
| 431 |
|
|---|
| 432 | if (static_cast<int>(receive_buffer.size()) < ibuffer[4]*ibuffer[5]*ibuffer[6])
|
|---|
| 433 | receive_buffer.resize(ibuffer[4]*ibuffer[5]*ibuffer[6]);
|
|---|
| 434 |
|
|---|
| 435 | MPI_Recv(&(receive_buffer.front()), ibuffer[4]*ibuffer[5]*ibuffer[6], MPI_DOUBLE, rank, tag, comm, MPI_STATUS_IGNORE);
|
|---|
| 436 |
|
|---|
| 437 | for (i.X()=ibuffer[7]; i.X()<ibuffer[7]+ibuffer[4]; ++i.X())
|
|---|
| 438 | for (i.Y()=ibuffer[8]; i.Y()<ibuffer[8]+ibuffer[5]; ++i.Y())
|
|---|
| 439 | for (i.Z()=ibuffer[9]; i.Z()<ibuffer[9]+ibuffer[6]; ++i.Z())
|
|---|
| 440 | grid(i) += receive_buffer[counter++];
|
|---|
| 441 | }
|
|---|
| 442 |
|
|---|
| 443 | void CommMPI::CommParticles(const Grid& grid, std::list<Particle::Particle>& particles)
|
|---|
| 444 | {
|
|---|
| 445 | Timer::Start("CommParticles");
|
|---|
| 446 |
|
|---|
| 447 | Factory& factory = MG::GetFactory();
|
|---|
| 448 |
|
|---|
| 449 | const vmg_int& num_particles_local = factory.GetObjectStorageVal<vmg_int>("PARTICLE_NUM_LOCAL");
|
|---|
| 450 | vmg_float* x = factory.GetObjectStorageArray<vmg_float>("PARTICLE_POS_ARRAY");
|
|---|
| 451 | vmg_float* q = factory.GetObjectStorageArray<vmg_float>("PARTICLE_CHARGE_ARRAY");
|
|---|
| 452 |
|
|---|
| 453 | int rank, size;
|
|---|
| 454 | MPI_Comm_rank(comm_global, &rank);
|
|---|
| 455 | MPI_Comm_size(comm_global, &size);
|
|---|
| 456 |
|
|---|
| 457 | Index index;
|
|---|
| 458 | int global_extent[6*size], send_sizes[size], recv_sizes[size];
|
|---|
| 459 | Index begin_remote[size], end_remote[size];
|
|---|
| 460 | std::vector<int> pos_indices[size], charge_indices[size];
|
|---|
| 461 | MPI_Datatype dt_temp;
|
|---|
| 462 | std::vector<vmg_float> buffer_x, buffer_q;
|
|---|
| 463 | std::vector<vmg_int> buffer_ind;
|
|---|
| 464 |
|
|---|
| 465 | std::memcpy(&global_extent[6*rank], grid.Global().BeginLocal().vec(), 3*sizeof(vmg_float));
|
|---|
| 466 | std::memcpy(&global_extent[6*rank+3], grid.Global().EndLocal().vec(), 3*sizeof(vmg_float));
|
|---|
| 467 |
|
|---|
| 468 | MPI_Allgather(MPI_IN_PLACE, 6, MPI_INT, global_extent, 6, MPI_INT, MPI_COMM_WORLD);
|
|---|
| 469 |
|
|---|
| 470 | for (int i=0; i<size; ++i) {
|
|---|
| 471 | begin_remote[i] = static_cast<Vector>(&global_extent[6*i]);
|
|---|
| 472 | end_remote[i] = static_cast<Vector>(&global_extent[6*i+3]);
|
|---|
| 473 | }
|
|---|
| 474 |
|
|---|
| 475 | for (int i=0; i<num_particles_local; ++i) {
|
|---|
| 476 | index = static_cast<Index>((Vector(&x[3*i]) - grid.Extent().Begin()) / grid.Extent().MeshWidth());
|
|---|
| 477 | for (int j=0; j<size; ++j)
|
|---|
| 478 | if (index.IsInBounds(begin_remote[j], end_remote[j])) {
|
|---|
| 479 | pos_indices[j].push_back(3*i);
|
|---|
| 480 | charge_indices[j].push_back(i);
|
|---|
| 481 | break;
|
|---|
| 482 | }
|
|---|
| 483 | }
|
|---|
| 484 |
|
|---|
| 485 | /*
|
|---|
| 486 | * Communicate which process gets how many particles
|
|---|
| 487 | */
|
|---|
| 488 | for (int i=0; i<size; ++i)
|
|---|
| 489 | send_sizes[i] = charge_indices[i].size();
|
|---|
| 490 |
|
|---|
| 491 | MPI_Alltoall(send_sizes, 1, MPI_INT, recv_sizes, 1, MPI_INT, comm_global);
|
|---|
| 492 |
|
|---|
| 493 | /*
|
|---|
| 494 | * Send particles
|
|---|
| 495 | */
|
|---|
| 496 | for (int i=0; i<size; ++i) {
|
|---|
| 497 |
|
|---|
| 498 | if (pos_indices[i].size() > 0) {
|
|---|
| 499 |
|
|---|
| 500 | MPI_Type_create_indexed_block(pos_indices[i].size(), 3, &pos_indices[i].front(), MPI_DOUBLE, &dt_temp);
|
|---|
| 501 | MPI_Type_commit(&dt_temp);
|
|---|
| 502 | MPI_Isend(x, 1, dt_temp, i, 0, MPI_COMM_WORLD, &Request());
|
|---|
| 503 | MPI_Type_free(&dt_temp);
|
|---|
| 504 |
|
|---|
| 505 | MPI_Type_create_indexed_block(charge_indices[i].size(), 1, &charge_indices[i].front(), MPI_DOUBLE, &dt_temp);
|
|---|
| 506 | MPI_Type_commit(&dt_temp);
|
|---|
| 507 | MPI_Isend(q, 1, dt_temp, i, 1, MPI_COMM_WORLD, &Request());
|
|---|
| 508 | MPI_Type_free(&dt_temp);
|
|---|
| 509 |
|
|---|
| 510 | MPI_Isend(&charge_indices[i].front(), charge_indices[i].size(), MPI_INT, i, 2, MPI_COMM_WORLD, &Request());
|
|---|
| 511 |
|
|---|
| 512 | }
|
|---|
| 513 |
|
|---|
| 514 | }
|
|---|
| 515 |
|
|---|
| 516 | /*
|
|---|
| 517 | * Receive particles
|
|---|
| 518 | */
|
|---|
| 519 | for (int i=0; i<size; ++i) {
|
|---|
| 520 |
|
|---|
| 521 | if (recv_sizes[i] > 0) {
|
|---|
| 522 |
|
|---|
| 523 | buffer_x.resize(3*recv_sizes[i]);
|
|---|
| 524 | buffer_q.resize(recv_sizes[i]);
|
|---|
| 525 | buffer_ind.resize(recv_sizes[i]);
|
|---|
| 526 |
|
|---|
| 527 | MPI_Recv(&buffer_x.front(), 3*recv_sizes[i], MPI_DOUBLE, i, 0, MPI_COMM_WORLD, MPI_STATUS_IGNORE);
|
|---|
| 528 | MPI_Recv(&buffer_q.front(), recv_sizes[i], MPI_DOUBLE, i, 1, MPI_COMM_WORLD, MPI_STATUS_IGNORE);
|
|---|
| 529 | MPI_Recv(&buffer_ind.front(), recv_sizes[i], MPI_INT, i, 2, MPI_COMM_WORLD, MPI_STATUS_IGNORE);
|
|---|
| 530 |
|
|---|
| 531 | particles.clear();
|
|---|
| 532 |
|
|---|
| 533 | for (int j=0; j<recv_sizes[i]; ++j)
|
|---|
| 534 | particles.push_back(Particle::Particle(&buffer_x[3*j], buffer_q[j], 0.0, 0.0, i, buffer_ind[j]));
|
|---|
| 535 |
|
|---|
| 536 | }
|
|---|
| 537 |
|
|---|
| 538 | }
|
|---|
| 539 |
|
|---|
| 540 | ClearRequests();
|
|---|
| 541 |
|
|---|
| 542 | Timer::Stop("CommParticles");
|
|---|
| 543 | }
|
|---|
| 544 |
|
|---|
| 545 | void CommMPI::CommLCListGhosts(const Grid& grid, Particle::LinkedCellList& lc)
|
|---|
| 546 | {
|
|---|
| 547 | Timer::Start("CommLCListGhosts");
|
|---|
| 548 |
|
|---|
| 549 | std::vector<vmg_float> send_buffer_1, send_buffer_2, recv_buffer;
|
|---|
| 550 | vmg_int send_size_1, send_size_2, recv_size;
|
|---|
| 551 | std::list<Particle::Particle>::iterator p_iter;
|
|---|
| 552 | Grid::iterator g_iter;
|
|---|
| 553 |
|
|---|
| 554 | Tuple<int> neighbors;
|
|---|
| 555 |
|
|---|
| 556 | for (int i=2; i>=0; --i) {
|
|---|
| 557 |
|
|---|
| 558 | /*
|
|---|
| 559 | * Get ranks of neighbors
|
|---|
| 560 | */
|
|---|
| 561 | MPI_Cart_shift(comm_global, i, 1, &neighbors.Left(), &neighbors.Right());
|
|---|
| 562 |
|
|---|
| 563 | /*
|
|---|
| 564 | * Send to left
|
|---|
| 565 | */
|
|---|
| 566 | send_buffer_1.clear();
|
|---|
| 567 |
|
|---|
| 568 | for (g_iter=lc.Iterators().Boundary1()[i].Begin(); g_iter!=lc.Iterators().Boundary1()[i].End(); ++g_iter)
|
|---|
| 569 | lc(*g_iter).clear();
|
|---|
| 570 |
|
|---|
| 571 | for (g_iter=lc.Iterators().NearBoundary1()[i].Begin(); g_iter!=lc.Iterators().NearBoundary1()[i].End(); ++g_iter)
|
|---|
| 572 | for (p_iter=lc(*g_iter).begin(); p_iter!=lc(*g_iter).end(); ++p_iter) {
|
|---|
| 573 |
|
|---|
| 574 | if (grid.Global().BeginLocal()[i] == 0)
|
|---|
| 575 | for (int j=0; j<3; ++j)
|
|---|
| 576 | send_buffer_1.push_back(p_iter->Pos()[j] + grid.Extent().Size()[j]);
|
|---|
| 577 | else
|
|---|
| 578 | for (int j=0; j<3; ++j)
|
|---|
| 579 | send_buffer_1.push_back(p_iter->Pos()[j]);
|
|---|
| 580 |
|
|---|
| 581 | send_buffer_1.push_back(p_iter->Charge());
|
|---|
| 582 |
|
|---|
| 583 | }
|
|---|
| 584 |
|
|---|
| 585 | send_size_1 = send_buffer_1.size();
|
|---|
| 586 |
|
|---|
| 587 | MPI_Isend(&send_size_1, 1, MPI_INT, neighbors.Left(), 0, comm_global, &Request());
|
|---|
| 588 |
|
|---|
| 589 | if (send_size_1 > 0)
|
|---|
| 590 | MPI_Isend(&send_buffer_1.front(), send_size_1, MPI_DOUBLE, neighbors.Left(), 1, comm_global, &Request());
|
|---|
| 591 |
|
|---|
| 592 | /*
|
|---|
| 593 | * Send to right
|
|---|
| 594 | */
|
|---|
| 595 | send_buffer_2.clear();
|
|---|
| 596 |
|
|---|
| 597 | for (g_iter=lc.Iterators().Boundary2()[i].Begin(); g_iter!=lc.Iterators().Boundary2()[i].End(); ++g_iter)
|
|---|
| 598 | lc(*g_iter).clear();
|
|---|
| 599 |
|
|---|
| 600 | for (g_iter=lc.Iterators().NearBoundary2()[i].Begin(); g_iter!=lc.Iterators().NearBoundary2()[i].End(); ++g_iter)
|
|---|
| 601 | for (p_iter=lc(*g_iter).begin(); p_iter!=lc(*g_iter).end(); ++p_iter) {
|
|---|
| 602 |
|
|---|
| 603 | if (grid.Global().EndLocal()[i] == grid.Global().SizeGlobal()[i])
|
|---|
| 604 | for (int j=0; j<3; ++j)
|
|---|
| 605 | send_buffer_2.push_back(p_iter->Pos()[j] - grid.Extent().Size()[j]);
|
|---|
| 606 | else
|
|---|
| 607 | for (int j=0; j<3; ++j)
|
|---|
| 608 | send_buffer_2.push_back(p_iter->Pos()[j]);
|
|---|
| 609 |
|
|---|
| 610 | send_buffer_2.push_back(p_iter->Charge());
|
|---|
| 611 |
|
|---|
| 612 | }
|
|---|
| 613 |
|
|---|
| 614 | send_size_2 = send_buffer_2.size();
|
|---|
| 615 |
|
|---|
| 616 | MPI_Isend(&send_size_2, 1, MPI_INT, neighbors.Right(), 2, comm_global, &Request());
|
|---|
| 617 |
|
|---|
| 618 | if (send_size_2 > 0)
|
|---|
| 619 | MPI_Isend(&send_buffer_2.front(), send_size_2, MPI_DOUBLE, neighbors.Right(), 3, comm_global, &Request());
|
|---|
| 620 |
|
|---|
| 621 | /*
|
|---|
| 622 | * Receive from right
|
|---|
| 623 | */
|
|---|
| 624 | MPI_Recv(&recv_size, 1, MPI_INT, neighbors.Right(), 0, comm_global, MPI_STATUS_IGNORE);
|
|---|
| 625 |
|
|---|
| 626 | if (recv_size > 0) {
|
|---|
| 627 |
|
|---|
| 628 | recv_buffer.resize(recv_size);
|
|---|
| 629 | MPI_Recv(&recv_buffer.front(), recv_size, MPI_DOUBLE, neighbors.Right(), 1, comm_global, MPI_STATUS_IGNORE);
|
|---|
| 630 |
|
|---|
| 631 | for (vmg_int i=0; i<recv_size; i+=4)
|
|---|
| 632 | lc.AddParticleToComplete(&recv_buffer[i], recv_buffer[i+3]);
|
|---|
| 633 |
|
|---|
| 634 | }
|
|---|
| 635 |
|
|---|
| 636 | /*
|
|---|
| 637 | * Receive from left
|
|---|
| 638 | */
|
|---|
| 639 | MPI_Recv(&recv_size, 1, MPI_INT, neighbors.Left(), 2, comm_global, MPI_STATUS_IGNORE);
|
|---|
| 640 |
|
|---|
| 641 | if (recv_size > 0) {
|
|---|
| 642 |
|
|---|
| 643 | recv_buffer.resize(recv_size);
|
|---|
| 644 | MPI_Recv(&recv_buffer.front(), recv_size, MPI_DOUBLE, neighbors.Left(), 3, comm_global, MPI_STATUS_IGNORE);
|
|---|
| 645 |
|
|---|
| 646 | for (vmg_int i=0; i<recv_size; i+=4)
|
|---|
| 647 | lc.AddParticleToComplete(&recv_buffer[i], recv_buffer[i+3]);
|
|---|
| 648 |
|
|---|
| 649 | }
|
|---|
| 650 |
|
|---|
| 651 |
|
|---|
| 652 | ClearRequests();
|
|---|
| 653 | }
|
|---|
| 654 |
|
|---|
| 655 | Timer::Stop("CommLCListGhosts");
|
|---|
| 656 | }
|
|---|
| 657 |
|
|---|
| 658 | void CommMPI::CommAddPotential(std::list<Particle::Particle>& particles)
|
|---|
| 659 | {
|
|---|
| 660 | Timer::Start("CommAddPotential");
|
|---|
| 661 |
|
|---|
| 662 | std::list<Particle::Particle>::iterator iter;
|
|---|
| 663 |
|
|---|
| 664 | if (!win_created) {
|
|---|
| 665 | vmg_float* p = MG::GetFactory().GetObjectStorageArray<vmg_float>("PARTICLE_POTENTIAL_ARRAY");
|
|---|
| 666 | const vmg_int& num_particles_local = MG::GetFactory().GetObjectStorageVal<vmg_int>("PARTICLE_NUM_LOCAL");
|
|---|
| 667 | MPI_Win_create(p, num_particles_local*sizeof(vmg_float), sizeof(vmg_float), info, comm_global, &win);
|
|---|
| 668 | win_created = true;
|
|---|
| 669 | }
|
|---|
| 670 |
|
|---|
| 671 | MPI_Win_fence(MPI_MODE_NOPRECEDE, win);
|
|---|
| 672 |
|
|---|
| 673 | for (iter=particles.begin(); iter!=particles.end(); ++iter)
|
|---|
| 674 | MPI_Accumulate(&iter->Pot(), 1, MPI_DOUBLE, iter->Rank(), iter->Index(), 1, MPI_DOUBLE, MPI_SUM, win);
|
|---|
| 675 |
|
|---|
| 676 | MPI_Win_fence(MPI_MODE_NOSTORE | MPI_MODE_NOSUCCEED, win);
|
|---|
| 677 |
|
|---|
| 678 | Timer::Stop("CommAddPotential");
|
|---|
| 679 | }
|
|---|
| 680 |
|
|---|
| 681 | void CommMPI::CommAddPotential(Particle::LinkedCellList& lc)
|
|---|
| 682 | {
|
|---|
| 683 | Timer::Start("CommAddPotential");
|
|---|
| 684 |
|
|---|
| 685 | Grid::iterator g_iter;
|
|---|
| 686 | std::list<Particle::Particle>::iterator p_iter;
|
|---|
| 687 |
|
|---|
| 688 | if (!win_created) {
|
|---|
| 689 | vmg_float* p = MG::GetFactory().GetObjectStorageArray<vmg_float>("PARTICLE_POTENTIAL_ARRAY");
|
|---|
| 690 | const vmg_int& num_particles_local = MG::GetFactory().GetObjectStorageVal<vmg_int>("PARTICLE_NUM_LOCAL");
|
|---|
| 691 | MPI_Win_create(p, num_particles_local*sizeof(vmg_float), sizeof(vmg_float), info, comm_global, &win);
|
|---|
| 692 | win_created = true;
|
|---|
| 693 | }
|
|---|
| 694 |
|
|---|
| 695 | MPI_Win_fence(MPI_MODE_NOPRECEDE, win);
|
|---|
| 696 |
|
|---|
| 697 | for (g_iter=lc.Iterators().Local().Begin(); g_iter!=lc.Iterators().Local().End(); ++g_iter)
|
|---|
| 698 | for (p_iter=lc(*g_iter).begin(); p_iter!=lc(*g_iter).end(); ++p_iter)
|
|---|
| 699 | MPI_Accumulate(&p_iter->Pot(), 1, MPI_DOUBLE, p_iter->Rank(), p_iter->Index(), 1, MPI_DOUBLE, MPI_SUM, win);
|
|---|
| 700 |
|
|---|
| 701 | MPI_Win_fence(MPI_MODE_NOSTORE | MPI_MODE_NOSUCCEED, win);
|
|---|
| 702 |
|
|---|
| 703 | Timer::Stop("CommAddPotential");
|
|---|
| 704 | }
|
|---|
| 705 |
|
|---|
| 706 | vmg_float CommMPI::GlobalSum(const vmg_float& value)
|
|---|
| 707 | {
|
|---|
| 708 | vmg_float result = value;
|
|---|
| 709 |
|
|---|
| 710 | MPI_Allreduce(MPI_IN_PLACE, &result, 1, MPI_DOUBLE, MPI_SUM, comm_global);
|
|---|
| 711 |
|
|---|
| 712 | return result;
|
|---|
| 713 | }
|
|---|
| 714 |
|
|---|
| 715 | vmg_float CommMPI::GlobalSumRoot(const vmg_float& value)
|
|---|
| 716 | {
|
|---|
| 717 | vmg_float recv_buffer;
|
|---|
| 718 | vmg_float send_buffer = value;
|
|---|
| 719 |
|
|---|
| 720 | MPI_Reduce(&send_buffer, &recv_buffer, 1, MPI_DOUBLE, MPI_SUM, 0, comm_global);
|
|---|
| 721 |
|
|---|
| 722 | return recv_buffer;
|
|---|
| 723 | }
|
|---|
| 724 |
|
|---|
| 725 | void CommMPI::GlobalSumArray(vmg_float* array, const vmg_int& size)
|
|---|
| 726 | {
|
|---|
| 727 | MPI_Allreduce(MPI_IN_PLACE, array, size, MPI_DOUBLE, MPI_SUM, comm_global);
|
|---|
| 728 | }
|
|---|
| 729 |
|
|---|
| 730 | void CommMPI::PrintString(const char* format, ...)
|
|---|
| 731 | {
|
|---|
| 732 | va_list args;
|
|---|
| 733 | va_start(args, format);
|
|---|
| 734 | vsprintf(print_buffer, format, args);
|
|---|
| 735 | printf("VMG: Rank %d: %s\n", GlobalRank(), print_buffer);
|
|---|
| 736 | va_end(args);
|
|---|
| 737 | }
|
|---|
| 738 |
|
|---|
| 739 | void CommMPI::PrintStringOnce(const char* format, ...)
|
|---|
| 740 | {
|
|---|
| 741 | if (GlobalRank() == 0) {
|
|---|
| 742 | va_list args;
|
|---|
| 743 | va_start(args, format);
|
|---|
| 744 | vsprintf(print_buffer, format, args);
|
|---|
| 745 | printf("VMG: Rank %d: %s\n", GlobalRank(), print_buffer);
|
|---|
| 746 | va_end(args);
|
|---|
| 747 | }
|
|---|
| 748 | }
|
|---|
| 749 |
|
|---|
| 750 | void CommMPI::PrintXML(const std::string& filename, const std::string& xml_data)
|
|---|
| 751 | {
|
|---|
| 752 | MPI_File file;
|
|---|
| 753 | std::stringstream path, xml_header;
|
|---|
| 754 |
|
|---|
| 755 | pugi::xml_document doc;
|
|---|
| 756 | pugi::xml_node node_data = doc.append_child("Global").append_child("NumProcesses").append_child(pugi::node_pcdata);
|
|---|
| 757 | node_data.set_value(Helper::ToString(GlobalProcs().Product()).c_str());
|
|---|
| 758 | doc.save(xml_header);
|
|---|
| 759 |
|
|---|
| 760 | path << OutputPath() << filename;
|
|---|
| 761 |
|
|---|
| 762 | char* filename_array = Helper::GetCharArray(path.str());
|
|---|
| 763 | char* xml_header_array = Helper::GetCharArray(xml_header.str());
|
|---|
| 764 | char* str_array = Helper::GetCharArray(xml_data);
|
|---|
| 765 |
|
|---|
| 766 | MPI_File_open(MPI_COMM_SELF, filename_array, MPI_MODE_WRONLY|MPI_MODE_CREATE, MPI_INFO_NULL, &file);
|
|---|
| 767 | MPI_File_set_size(file, 0);
|
|---|
| 768 | MPI_File_write(file, xml_header_array, xml_header.str().size(), MPI_CHAR, MPI_STATUS_IGNORE);
|
|---|
| 769 | MPI_File_write(file, str_array, xml_data.size(), MPI_CHAR, MPI_STATUS_IGNORE);
|
|---|
| 770 | MPI_File_close(&file);
|
|---|
| 771 |
|
|---|
| 772 | delete [] filename_array;
|
|---|
| 773 | delete [] xml_header_array;
|
|---|
| 774 | delete [] str_array;
|
|---|
| 775 | }
|
|---|
| 776 |
|
|---|
| 777 | void CommMPI::PrintXMLAll(const std::string& filename, const std::string& xml_data)
|
|---|
| 778 | {
|
|---|
| 779 | MPI_File file;
|
|---|
| 780 | std::stringstream path;
|
|---|
| 781 |
|
|---|
| 782 | path << OutputPath() << filename;
|
|---|
| 783 |
|
|---|
| 784 | char* filename_array = Helper::GetCharArray(path.str());
|
|---|
| 785 | char* str_array = Helper::GetCharArray(xml_data);
|
|---|
| 786 |
|
|---|
| 787 | MPI_File_open(comm_global, filename_array, MPI_MODE_WRONLY|MPI_MODE_CREATE, MPI_INFO_NULL, &file);
|
|---|
| 788 | MPI_File_set_size(file, 0);
|
|---|
| 789 |
|
|---|
| 790 | if (GlobalRank() == 0) {
|
|---|
| 791 | std::stringstream xml_header;
|
|---|
| 792 | pugi::xml_document doc;
|
|---|
| 793 | pugi::xml_node node_data = doc.append_child("Global").append_child("NumProcesses").append_child(pugi::node_pcdata);
|
|---|
| 794 | node_data.set_value(Helper::ToString(GlobalProcs().Product()).c_str());
|
|---|
| 795 | doc.save(xml_header);
|
|---|
| 796 |
|
|---|
| 797 | char* xml_header_array = Helper::GetCharArray(xml_header.str());
|
|---|
| 798 |
|
|---|
| 799 | MPI_File_write_shared(file, xml_header_array, xml_header.str().size(), MPI_CHAR, MPI_STATUS_IGNORE);
|
|---|
| 800 |
|
|---|
| 801 | delete [] xml_header_array;
|
|---|
| 802 | }
|
|---|
| 803 |
|
|---|
| 804 | MPI_File_write_ordered(file, str_array, xml_data.size(), MPI_CHAR, MPI_STATUS_IGNORE);
|
|---|
| 805 | MPI_File_close(&file);
|
|---|
| 806 |
|
|---|
| 807 | delete [] filename_array;
|
|---|
| 808 | delete [] str_array;
|
|---|
| 809 | }
|
|---|
| 810 |
|
|---|
| 811 | void CommMPI::PrintAllSettings()
|
|---|
| 812 | {
|
|---|
| 813 | std::stringstream buf;
|
|---|
| 814 | MPI_File file;
|
|---|
| 815 | MPI_Status status;
|
|---|
| 816 |
|
|---|
| 817 | Multigrid* mg = MG::GetFactory().Get("SOL")->Cast<Multigrid>();
|
|---|
| 818 |
|
|---|
| 819 | buf << OutputPath() << "settings.txt";
|
|---|
| 820 | char *filename = Helper::GetCharArray(buf.str());
|
|---|
| 821 |
|
|---|
| 822 | MPI_File_open(comm_global, filename, MPI_MODE_WRONLY|MPI_MODE_CREATE, MPI_INFO_NULL, &file);
|
|---|
| 823 | MPI_File_set_size(file, 0);
|
|---|
| 824 | MPI_File_close(&file);
|
|---|
| 825 |
|
|---|
| 826 | for (int i=mg->MinLevel(); i<=mg->MaxLevel(); ++i) {
|
|---|
| 827 |
|
|---|
| 828 | MPI_Comm comm = comm_info.GetCommunicator((*mg)(i));
|
|---|
| 829 |
|
|---|
| 830 | if (comm != MPI_COMM_NULL) {
|
|---|
| 831 |
|
|---|
| 832 | MPI_File_open(comm, filename, MPI_MODE_WRONLY|MPI_MODE_CREATE|MPI_MODE_APPEND, MPI_INFO_NULL, &file);
|
|---|
| 833 |
|
|---|
| 834 | int comm_rank;
|
|---|
| 835 | MPI_Comm_rank(comm, &comm_rank);
|
|---|
| 836 |
|
|---|
| 837 | if (comm_rank == 0) {
|
|---|
| 838 |
|
|---|
| 839 | buf.str("");
|
|---|
| 840 | buf << "PROCESS INDEPENDENT INFORMATION:" << std::endl
|
|---|
| 841 | << "GRID LEVEL " << i << std::endl
|
|---|
| 842 | << "BEGINFINEST: " << (*mg)(i).Global().BeginFinest() << std::endl
|
|---|
| 843 | << "ENDFINEST: " << (*mg)(i).Global().EndFinest() << std::endl
|
|---|
| 844 | << "SIZEFINEST: " << (*mg)(i).Global().SizeFinest() << std::endl
|
|---|
| 845 | << "SIZEGLOBAL: " << (*mg)(i).Global().SizeGlobal() << std::endl
|
|---|
| 846 | << "BOUNDARYTYPE: " << (*mg)(i).Global().BoundaryType() << std::endl
|
|---|
| 847 | << "EXTENT" << std::endl
|
|---|
| 848 | << "SIZE: " << (*mg)(i).Extent().Size() << std::endl
|
|---|
| 849 | << "SIZEFACTOR: " << (*mg)(i).Extent().SizeFactor() << std::endl
|
|---|
| 850 | << "BEGIN: " << (*mg)(i).Extent().Begin() << std::endl
|
|---|
| 851 | << "END: " << (*mg)(i).Extent().End() << std::endl
|
|---|
| 852 | << "MESHWIDTH: " << (*mg)(i).Extent().MeshWidth() << std::endl
|
|---|
| 853 | << std::endl
|
|---|
| 854 | << "PROCESS DEPENDENT INFORMATION:" << std::endl;
|
|---|
| 855 |
|
|---|
| 856 | char* char_buf = Helper::GetCharArray(buf.str());
|
|---|
| 857 |
|
|---|
| 858 | MPI_File_write_shared(file, char_buf, buf.str().size(), MPI_CHAR, &status);
|
|---|
| 859 |
|
|---|
| 860 | delete [] char_buf;
|
|---|
| 861 |
|
|---|
| 862 | }
|
|---|
| 863 |
|
|---|
| 864 | buf.str("");
|
|---|
| 865 | buf << "PROCESS " << comm_rank << ":" << std::endl
|
|---|
| 866 | << "GLOBAL" << std::endl
|
|---|
| 867 | << "BEGINLOCAL: " << (*mg)(i).Global().BeginLocal() << std::endl
|
|---|
| 868 | << "ENDLOCAL: " << (*mg)(i).Global().EndLocal() << std::endl
|
|---|
| 869 | << "SIZELOCAL: " << (*mg)(i).Global().SizeLocal() << std::endl
|
|---|
| 870 | << "LOCAL" << std::endl
|
|---|
| 871 | << "SIZE: " << (*mg)(i).Local().Size() << std::endl
|
|---|
| 872 | << "SIZETOTAL: " << (*mg)(i).Local().SizeTotal() << std::endl
|
|---|
| 873 | << "BEGIN: " << (*mg)(i).Local().Begin() << std::endl
|
|---|
| 874 | << "END: " << (*mg)(i).Local().End() << std::endl
|
|---|
| 875 | << "HALOBEGIN1: " << (*mg)(i).Local().HaloBegin1() << std::endl
|
|---|
| 876 | << "HALOEND1: " << (*mg)(i).Local().HaloEnd1() << std::endl
|
|---|
| 877 | << "HALOBEGIN2: " << (*mg)(i).Local().HaloBegin2() << std::endl
|
|---|
| 878 | << "HALOEND2: " << (*mg)(i).Local().HaloEnd2() << std::endl
|
|---|
| 879 | << "BOUNDARYBEGIN1: " << (*mg)(i).Local().BoundaryBegin1() << std::endl
|
|---|
| 880 | << "BOUNDARYEND1: " << (*mg)(i).Local().BoundaryEnd1() << std::endl
|
|---|
| 881 | << "BOUNDARYBEGIN2: " << (*mg)(i).Local().BoundaryBegin2() << std::endl
|
|---|
| 882 | << "BOUNDARYEND2: " << (*mg)(i).Local().BoundaryEnd2() << std::endl
|
|---|
| 883 | << "ALIGNMENTBEGIN: " << (*mg)(i).Local().AlignmentBegin() << std::endl
|
|---|
| 884 | << "ALIGNMENTEND: " << (*mg)(i).Local().AlignmentEnd() << std::endl
|
|---|
| 885 | << std::endl;
|
|---|
| 886 |
|
|---|
| 887 | char* char_buf = Helper::GetCharArray(buf.str());
|
|---|
| 888 |
|
|---|
| 889 | MPI_File_write_ordered(file, char_buf, buf.str().size(), MPI_CHAR, &status);
|
|---|
| 890 |
|
|---|
| 891 | delete [] char_buf;
|
|---|
| 892 |
|
|---|
| 893 | MPI_File_close(&file);
|
|---|
| 894 |
|
|---|
| 895 | }
|
|---|
| 896 | }
|
|---|
| 897 |
|
|---|
| 898 | delete [] filename;
|
|---|
| 899 |
|
|---|
| 900 | }
|
|---|
| 901 |
|
|---|
| 902 | void CommMPI::PrintDefect(Grid& sol, Grid& rhs, const char* information)
|
|---|
| 903 | {
|
|---|
| 904 | TempGrid *temp = MG::GetTempGrid();
|
|---|
| 905 | temp->SetProperties(sol);
|
|---|
| 906 | temp->ImportFromResidual(sol, rhs);
|
|---|
| 907 |
|
|---|
| 908 | PrintInnerGrid(*temp, information);
|
|---|
| 909 | }
|
|---|
| 910 |
|
|---|
| 911 | void CommMPI::PrintGrid(Grid& grid, const char* information)
|
|---|
| 912 | {
|
|---|
| 913 | Index i;
|
|---|
| 914 | std::stringstream buf;
|
|---|
| 915 |
|
|---|
| 916 | Index begin = 0;
|
|---|
| 917 | Index end = grid.Local().End();
|
|---|
| 918 | Index begin_local, end_local, begin_global, end_global;
|
|---|
| 919 |
|
|---|
| 920 | CommToGhosts(grid);
|
|---|
| 921 |
|
|---|
| 922 | for (int j=0; j<3; ++j)
|
|---|
| 923 | if (grid.Global().EndLocal()[j] == grid.Global().SizeGlobal()[j])
|
|---|
| 924 | end[j] = grid.Local().SizeTotal()[j];
|
|---|
| 925 |
|
|---|
| 926 | for (i.Z()=begin.Z(); i.Z()<end.Z(); ++i.Z())
|
|---|
| 927 | for (i.Y()=begin.Y(); i.Y()<end.Y(); ++i.Y())
|
|---|
| 928 | for (i.X()=begin.X(); i.X()<end.X(); ++i.X())
|
|---|
| 929 | buf << std::scientific << grid.GetVal(i) << " ";
|
|---|
| 930 |
|
|---|
| 931 | begin_local = grid.Global().BeginLocal();
|
|---|
| 932 | end_local = grid.Global().EndLocal();
|
|---|
| 933 | begin_global = 0;
|
|---|
| 934 |
|
|---|
| 935 | for (int i=0; i<3; ++i) {
|
|---|
| 936 |
|
|---|
| 937 | if (BoundaryConditions()[i] == Dirichlet ||
|
|---|
| 938 | BoundaryConditions()[i] == Open) {
|
|---|
| 939 |
|
|---|
| 940 | if (begin_local[i] != 0)
|
|---|
| 941 | begin_local[i] -= grid.Local().HaloEnd1()[i] - grid.Local().HaloBegin1()[i];
|
|---|
| 942 |
|
|---|
| 943 | end_global[i] = grid.Global().SizeGlobal()[i];
|
|---|
| 944 |
|
|---|
| 945 | }else if (BoundaryConditions()[i] == Periodic) {
|
|---|
| 946 |
|
|---|
| 947 | if (end_local[i] == grid.Global().SizeGlobal()[i])
|
|---|
| 948 | end_local[i] += grid.Local().HaloEnd1()[i] - grid.Local().HaloBegin1()[i] + grid.Local().HaloEnd2()[i] - grid.Local().HaloBegin2()[i];
|
|---|
| 949 | else
|
|---|
| 950 | end_local[i] += grid.Local().HaloEnd1()[i] - grid.Local().HaloBegin1()[i];
|
|---|
| 951 |
|
|---|
| 952 | end_global[i] = grid.Global().SizeGlobal()[i] +
|
|---|
| 953 | grid.Local().HaloEnd1()[i] - grid.Local().HaloBegin1()[i] +
|
|---|
| 954 | grid.Local().HaloEnd2()[i] - grid.Local().HaloBegin2()[i];
|
|---|
| 955 |
|
|---|
| 956 | }
|
|---|
| 957 |
|
|---|
| 958 | }
|
|---|
| 959 |
|
|---|
| 960 | CreateOutputFiles(grid, buf, information,
|
|---|
| 961 | begin_global, end_global,
|
|---|
| 962 | begin_local, end_local);
|
|---|
| 963 | }
|
|---|
| 964 |
|
|---|
| 965 | void CommMPI::PrintCorrectedGrid(Grid& grid, const char* information)
|
|---|
| 966 | {
|
|---|
| 967 | Index i;
|
|---|
| 968 |
|
|---|
| 969 | std::stringstream buf;
|
|---|
| 970 |
|
|---|
| 971 | Index begin = 0;
|
|---|
| 972 | Index end = grid.Local().End();
|
|---|
| 973 | Index begin_local, end_local, begin_global, end_global;
|
|---|
| 974 |
|
|---|
| 975 | CommToGhosts(grid);
|
|---|
| 976 |
|
|---|
| 977 | for (int j=0; j<3; ++j)
|
|---|
| 978 | if (grid.Global().EndLocal()[j] == grid.Global().SizeGlobal()[j])
|
|---|
| 979 | end[j] = grid.Local().SizeTotal()[j];
|
|---|
| 980 |
|
|---|
| 981 | for (i.Z()=begin.Z(); i.Z()<end.Z(); ++i.Z())
|
|---|
| 982 | for (i.Y()=begin.Y(); i.Y()<end.Y(); ++i.Y())
|
|---|
| 983 | for (i.X()=begin.X(); i.X()<end.X(); ++i.X())
|
|---|
| 984 | buf << std::scientific << grid.GetVal(i) - Grid::Correction() << " ";
|
|---|
| 985 |
|
|---|
| 986 | begin_local = grid.Global().BeginLocal();
|
|---|
| 987 | end_local = grid.Global().EndLocal();
|
|---|
| 988 | begin_global = 0;
|
|---|
| 989 |
|
|---|
| 990 | for (int i=0; i<3; ++i) {
|
|---|
| 991 |
|
|---|
| 992 | if (BoundaryConditions()[i] == Dirichlet ||
|
|---|
| 993 | BoundaryConditions()[i] == Open) {
|
|---|
| 994 |
|
|---|
| 995 | if (begin_local[i] != 0)
|
|---|
| 996 | --begin_local[i];
|
|---|
| 997 |
|
|---|
| 998 | end_global[i] = grid.Global().SizeGlobal()[i];
|
|---|
| 999 |
|
|---|
| 1000 | }else if (BoundaryConditions()[i] == Periodic) {
|
|---|
| 1001 |
|
|---|
| 1002 | if (begin_local[i] != 0)
|
|---|
| 1003 | --begin_local[i];
|
|---|
| 1004 |
|
|---|
| 1005 | if (end_local[i] == grid.Global().SizeGlobal()[i])
|
|---|
| 1006 | end_local[i] += 2;
|
|---|
| 1007 |
|
|---|
| 1008 | end_global[i] = grid.Global().SizeGlobal()[i] + 2;
|
|---|
| 1009 |
|
|---|
| 1010 | }
|
|---|
| 1011 |
|
|---|
| 1012 | }
|
|---|
| 1013 |
|
|---|
| 1014 | CreateOutputFiles(grid, buf, information,
|
|---|
| 1015 | 0, grid.Global().SizeGlobal()+2,
|
|---|
| 1016 | begin, end);
|
|---|
| 1017 | }
|
|---|
| 1018 |
|
|---|
| 1019 | void CommMPI::PrintInnerGrid(Grid& grid, const char* information)
|
|---|
| 1020 | {
|
|---|
| 1021 | Index i;
|
|---|
| 1022 | Index begin_local, end_local, begin_global, end_global;
|
|---|
| 1023 | std::stringstream buf;
|
|---|
| 1024 |
|
|---|
| 1025 | CommToGhosts(grid);
|
|---|
| 1026 |
|
|---|
| 1027 | Index begin = 0;
|
|---|
| 1028 | Index end = grid.Local().End();
|
|---|
| 1029 |
|
|---|
| 1030 | /* VTK parallel ImageData files seem to require some overlap. */
|
|---|
| 1031 | for (int j=0; j<3; ++j)
|
|---|
| 1032 | if (grid.Global().BeginLocal()[j] == 0)
|
|---|
| 1033 | ++begin[j];
|
|---|
| 1034 |
|
|---|
| 1035 | /* Write grid values into buffer */
|
|---|
| 1036 | for (i.Z()=begin.Z(); i.Z()<end.Z(); ++i.Z())
|
|---|
| 1037 | for (i.Y()=begin.Y(); i.Y()<end.Y(); ++i.Y())
|
|---|
| 1038 | for (i.X()=begin.X(); i.X()<end.X(); ++i.X())
|
|---|
| 1039 | buf << std::scientific << grid.GetVal(i) << " ";
|
|---|
| 1040 |
|
|---|
| 1041 | for (int j=0; j<3; ++j) {
|
|---|
| 1042 |
|
|---|
| 1043 | if (BoundaryConditions()[j] == Dirichlet ||
|
|---|
| 1044 | BoundaryConditions()[j] == Open) {
|
|---|
| 1045 |
|
|---|
| 1046 | begin_global[j] = 1;
|
|---|
| 1047 | end_global[j] = grid.Global().SizeGlobal()[j] - 1;
|
|---|
| 1048 |
|
|---|
| 1049 | if (grid.Global().BeginLocal()[j] == 0)
|
|---|
| 1050 | begin_local[j] = 1;
|
|---|
| 1051 | else
|
|---|
| 1052 | begin_local[j] = grid.Global().BeginLocal()[j] - 1;
|
|---|
| 1053 |
|
|---|
| 1054 | if (grid.Global().EndLocal()[j] == grid.Global().SizeGlobal()[j])
|
|---|
| 1055 | end_local[j] = grid.Global().EndLocal()[j] - 1;
|
|---|
| 1056 | else
|
|---|
| 1057 | end_local[j] = grid.Global().EndLocal()[j];
|
|---|
| 1058 |
|
|---|
| 1059 | }else if (BoundaryConditions()[j] == Periodic) {
|
|---|
| 1060 |
|
|---|
| 1061 | begin_global[j] = 0;
|
|---|
| 1062 | end_global[j] = grid.Global().SizeGlobal()[j];
|
|---|
| 1063 |
|
|---|
| 1064 | if (grid.Global().BeginLocal()[j] == 0)
|
|---|
| 1065 | begin_local[j] = grid.Global().BeginLocal()[j];
|
|---|
| 1066 | else
|
|---|
| 1067 | begin_local[j] = grid.Global().BeginLocal()[j] - 1;
|
|---|
| 1068 |
|
|---|
| 1069 | end_local[j] = grid.Global().EndLocal()[j];
|
|---|
| 1070 |
|
|---|
| 1071 | }else {
|
|---|
| 1072 |
|
|---|
| 1073 | assert(0 == "Boundary condition not handled properly.");
|
|---|
| 1074 |
|
|---|
| 1075 | }
|
|---|
| 1076 |
|
|---|
| 1077 | }
|
|---|
| 1078 |
|
|---|
| 1079 | CreateOutputFiles(grid, buf, information,
|
|---|
| 1080 | begin_global, end_global,
|
|---|
| 1081 | begin_local, end_local);
|
|---|
| 1082 | }
|
|---|
| 1083 |
|
|---|
| 1084 | void CommMPI::PrintInnerCorrectedGrid(Grid& grid, const char* information)
|
|---|
| 1085 | {
|
|---|
| 1086 | Index i;
|
|---|
| 1087 | const Index begin = grid.Local().Begin();
|
|---|
| 1088 | const Index end = grid.Local().End();
|
|---|
| 1089 | std::stringstream buf;
|
|---|
| 1090 |
|
|---|
| 1091 | for (i.Z()=begin.Z(); i.Z()<end.Z(); ++i.Z())
|
|---|
| 1092 | for (i.Y()=begin.Y(); i.Y()<end.Y(); ++i.Y())
|
|---|
| 1093 | for (i.X()=begin.X(); i.X()<end.X(); ++i.X())
|
|---|
| 1094 | buf << std::scientific << grid.GetVal(i) - Grid::Correction() << " ";
|
|---|
| 1095 |
|
|---|
| 1096 | CreateOutputFiles(grid, buf, information,
|
|---|
| 1097 | 0, grid.Global().SizeGlobal(),
|
|---|
| 1098 | grid.Global().BeginLocal(), grid.Global().EndLocal());
|
|---|
| 1099 | }
|
|---|
| 1100 |
|
|---|
| 1101 | void CommMPI::CreateOutputFiles(const Grid& grid, const std::stringstream& serial_data, const char* information,
|
|---|
| 1102 | const Index& begin_global, const Index& end_global,
|
|---|
| 1103 | const Index& begin_local, const Index& end_local)
|
|---|
| 1104 | {
|
|---|
| 1105 | int output_count = OutputCount();
|
|---|
| 1106 |
|
|---|
| 1107 | MPI_Comm comm = comm_info.GetCommunicator(grid);
|
|---|
| 1108 |
|
|---|
| 1109 | if (comm != MPI_COMM_NULL) {
|
|---|
| 1110 |
|
|---|
| 1111 | MPI_File file;
|
|---|
| 1112 | std::string conv_information = Helper::ReplaceWhitespaces(information, "_");
|
|---|
| 1113 |
|
|---|
| 1114 | CreateParallelOutputFile(grid, comm, output_count, conv_information.c_str(),
|
|---|
| 1115 | begin_global, end_global, begin_local, end_local);
|
|---|
| 1116 |
|
|---|
| 1117 | file = CreateSerialOutputFile(grid, comm, output_count, conv_information.c_str(),
|
|---|
| 1118 | begin_global, end_global, begin_local, end_local);
|
|---|
| 1119 |
|
|---|
| 1120 | char *char_buf = Helper::GetCharArray(serial_data.str());
|
|---|
| 1121 | MPI_File_write(file, char_buf, serial_data.str().size(), MPI_CHAR, MPI_STATUS_IGNORE);
|
|---|
| 1122 | delete [] char_buf;
|
|---|
| 1123 |
|
|---|
| 1124 | FinalizeSerialOutputFile(file);
|
|---|
| 1125 |
|
|---|
| 1126 | }
|
|---|
| 1127 | }
|
|---|
| 1128 |
|
|---|
| 1129 | void CommMPI::CreateParallelOutputFile(const Grid& grid, MPI_Comm& comm,
|
|---|
| 1130 | const int& output_count, const char* information,
|
|---|
| 1131 | const Index& begin_global, const Index& end_global,
|
|---|
| 1132 | const Index& begin_local, const Index& end_local)
|
|---|
| 1133 | {
|
|---|
| 1134 | int rank;
|
|---|
| 1135 | MPI_File file;
|
|---|
| 1136 | char parallel_filename[513], serial_filename[513];
|
|---|
| 1137 | std::stringstream buf;
|
|---|
| 1138 |
|
|---|
| 1139 | MPI_Comm_rank(comm, &rank);
|
|---|
| 1140 |
|
|---|
| 1141 | sprintf(parallel_filename, "%s%04d.pvti", OutputPath().c_str(), output_count);
|
|---|
| 1142 | sprintf(serial_filename, "%04d_%d.vti", output_count, rank);
|
|---|
| 1143 |
|
|---|
| 1144 | MPI_File_open(comm, parallel_filename, MPI_MODE_WRONLY|MPI_MODE_CREATE, MPI_INFO_NULL, &file);
|
|---|
| 1145 | MPI_File_set_size(file, 0);
|
|---|
| 1146 |
|
|---|
| 1147 | if (rank == 0) {
|
|---|
| 1148 |
|
|---|
| 1149 | buf << "<?xml version=\"1.0\"?>" << std::endl
|
|---|
| 1150 | << "<VTKFile type=\"PImageData\" version=\"0.1\" byte_order=\"LittleEndian\">" << std::endl
|
|---|
| 1151 | << " <PImageData WholeExtent=\"";
|
|---|
| 1152 |
|
|---|
| 1153 | for (int i=0; i<3; ++i)
|
|---|
| 1154 | buf << begin_global[i] << " " << end_global[i] - 1 << " ";
|
|---|
| 1155 |
|
|---|
| 1156 | buf << "\"" << std::endl
|
|---|
| 1157 | << " GhostLevel=\"0\" Origin=\"0 0 0\" Spacing=\"";
|
|---|
| 1158 |
|
|---|
| 1159 | for (int i=0; i<3; ++i)
|
|---|
| 1160 | buf << grid.Extent().MeshWidth()[i] << " ";
|
|---|
| 1161 |
|
|---|
| 1162 | buf << "\">" << std::endl
|
|---|
| 1163 | << " <PPointData Scalars=\"" << information << "\">" << std::endl
|
|---|
| 1164 | << " <PDataArray type=\"Float32\" Name=\"" << information << "\"/>" << std::endl
|
|---|
| 1165 | << " </PPointData>" << std::endl;
|
|---|
| 1166 |
|
|---|
| 1167 | char* char_buf = Helper::GetCharArray(buf.str());
|
|---|
| 1168 |
|
|---|
| 1169 | MPI_File_write_shared(file, char_buf, buf.str().size(), MPI_CHAR, MPI_STATUS_IGNORE);
|
|---|
| 1170 |
|
|---|
| 1171 | delete [] char_buf;
|
|---|
| 1172 | }
|
|---|
| 1173 |
|
|---|
| 1174 | buf.str("");
|
|---|
| 1175 | buf << " <Piece Extent=\"";
|
|---|
| 1176 |
|
|---|
| 1177 | for (int i=0; i<3; ++i)
|
|---|
| 1178 | buf << begin_local[i] << " " << end_local[i] - 1 << " ";
|
|---|
| 1179 |
|
|---|
| 1180 | buf << "\" Source=\"" << serial_filename << "\"/>" << std::endl;
|
|---|
| 1181 |
|
|---|
| 1182 | char* char_buf = Helper::GetCharArray(buf.str());
|
|---|
| 1183 |
|
|---|
| 1184 | MPI_File_write_ordered(file, char_buf, buf.str().size(), MPI_CHAR, MPI_STATUS_IGNORE);
|
|---|
| 1185 |
|
|---|
| 1186 | delete [] char_buf;
|
|---|
| 1187 |
|
|---|
| 1188 | if (rank == 0) {
|
|---|
| 1189 |
|
|---|
| 1190 | buf.str("");
|
|---|
| 1191 |
|
|---|
| 1192 | buf << " </PImageData>" << std::endl
|
|---|
| 1193 | << "</VTKFile>" << std::endl;
|
|---|
| 1194 |
|
|---|
| 1195 | char* char_buf = Helper::GetCharArray(buf.str());
|
|---|
| 1196 |
|
|---|
| 1197 | MPI_File_write_shared(file, char_buf, buf.str().size(), MPI_CHAR, MPI_STATUS_IGNORE);
|
|---|
| 1198 |
|
|---|
| 1199 | delete [] char_buf;
|
|---|
| 1200 | }
|
|---|
| 1201 |
|
|---|
| 1202 | MPI_File_close(&file);
|
|---|
| 1203 | }
|
|---|
| 1204 |
|
|---|
| 1205 | MPI_File CommMPI::CreateSerialOutputFile(const Grid& grid, MPI_Comm& comm,
|
|---|
| 1206 | const int& output_count, const char* information,
|
|---|
| 1207 | const Index& begin_global, const Index& end_global,
|
|---|
| 1208 | const Index& begin_local, const Index& end_local)
|
|---|
| 1209 | {
|
|---|
| 1210 | char serial_filename[513];
|
|---|
| 1211 | int rank;
|
|---|
| 1212 | MPI_File file;
|
|---|
| 1213 | std::stringstream buf;
|
|---|
| 1214 |
|
|---|
| 1215 | MPI_Comm_rank(comm_global, &rank);
|
|---|
| 1216 |
|
|---|
| 1217 | sprintf(serial_filename, "%s%04d_%d.vti", OutputPath().c_str(), output_count, rank);
|
|---|
| 1218 |
|
|---|
| 1219 | MPI_File_open(MPI_COMM_SELF, serial_filename, MPI_MODE_WRONLY|MPI_MODE_CREATE, MPI_INFO_NULL, &file);
|
|---|
| 1220 |
|
|---|
| 1221 | buf << "<?xml version=\"1.0\"?>" << std::endl
|
|---|
| 1222 | << "<VTKFile type=\"ImageData\" version=\"0.1\" byte_order=\"LittleEndian\">" << std::endl
|
|---|
| 1223 | << " <ImageData WholeExtent=\"";
|
|---|
| 1224 |
|
|---|
| 1225 | for (int i=0; i<3; ++i)
|
|---|
| 1226 | buf << begin_global[i] << " " << end_global[i] - 1 << " ";
|
|---|
| 1227 |
|
|---|
| 1228 | buf << "\"" << std::endl
|
|---|
| 1229 | << " Origin=\"0 0 0\" Spacing=\"";
|
|---|
| 1230 |
|
|---|
| 1231 | for (int i=0; i<3; ++i)
|
|---|
| 1232 | buf << grid.Extent().MeshWidth()[i] << " ";
|
|---|
| 1233 |
|
|---|
| 1234 | buf << "\">" << std::endl
|
|---|
| 1235 | << " <Piece Extent=\"";
|
|---|
| 1236 |
|
|---|
| 1237 | for (int i=0; i<3; ++i)
|
|---|
| 1238 | buf << begin_local[i] << " " << end_local[i] - 1 << " ";
|
|---|
| 1239 |
|
|---|
| 1240 | buf << "\">" << std::endl
|
|---|
| 1241 | << " <PointData Scalars=\"" << information << "\">" << std::endl
|
|---|
| 1242 | << " <DataArray type=\"Float32\" Name=\"" << information << "\" format=\"ascii\">" << std::endl
|
|---|
| 1243 | << " ";
|
|---|
| 1244 |
|
|---|
| 1245 | char* char_buf = Helper::GetCharArray(buf.str());
|
|---|
| 1246 | MPI_File_write(file, char_buf, buf.str().size(), MPI_CHAR, MPI_STATUS_IGNORE);
|
|---|
| 1247 | delete [] char_buf;
|
|---|
| 1248 |
|
|---|
| 1249 | return file;
|
|---|
| 1250 | }
|
|---|
| 1251 |
|
|---|
| 1252 | void CommMPI::FinalizeSerialOutputFile(MPI_File& file)
|
|---|
| 1253 | {
|
|---|
| 1254 | std::stringstream buf;
|
|---|
| 1255 |
|
|---|
| 1256 | buf << std::endl
|
|---|
| 1257 | << " </DataArray>" << std::endl
|
|---|
| 1258 | << " </PointData>" << std::endl
|
|---|
| 1259 | << " </Piece>" << std::endl
|
|---|
| 1260 | << " </ImageData>" << std::endl
|
|---|
| 1261 | << "</VTKFile>" << std::endl;
|
|---|
| 1262 |
|
|---|
| 1263 | char* char_buf = Helper::GetCharArray(buf.str());
|
|---|
| 1264 | MPI_File_write(file, char_buf, buf.str().size(), MPI_CHAR, MPI_STATUS_IGNORE);
|
|---|
| 1265 | delete [] char_buf;
|
|---|
| 1266 |
|
|---|
| 1267 | MPI_File_close(&file);
|
|---|
| 1268 | }
|
|---|
| 1269 |
|
|---|
| 1270 | int CommMPI::GlobalRank() const
|
|---|
| 1271 | {
|
|---|
| 1272 | int rank;
|
|---|
| 1273 |
|
|---|
| 1274 | MPI_Comm_rank(comm_global, &rank);
|
|---|
| 1275 |
|
|---|
| 1276 | return rank;
|
|---|
| 1277 | }
|
|---|
| 1278 |
|
|---|
| 1279 | Index CommMPI::GlobalPos() const
|
|---|
| 1280 | {
|
|---|
| 1281 | Index dims, periods, coords;
|
|---|
| 1282 |
|
|---|
| 1283 | MPI_Cart_get(comm_global, 3, dims.vec(), periods.vec(), coords.vec());
|
|---|
| 1284 |
|
|---|
| 1285 | return coords;
|
|---|
| 1286 | }
|
|---|
| 1287 |
|
|---|
| 1288 | Index CommMPI::GlobalProcs() const
|
|---|
| 1289 | {
|
|---|
| 1290 | Index dims, periods, coords;
|
|---|
| 1291 |
|
|---|
| 1292 | MPI_Cart_get(comm_global, 3, dims.vec(), periods.vec(), coords.vec());
|
|---|
| 1293 |
|
|---|
| 1294 | return dims;
|
|---|
| 1295 | }
|
|---|
| 1296 |
|
|---|
| 1297 | void CommMPI::InitCommMPI(const MPI_Comm& comm)
|
|---|
| 1298 | {
|
|---|
| 1299 | int status, size, rank;
|
|---|
| 1300 | int dims[3] = {0, 0, 0};
|
|---|
| 1301 | int periods[3];
|
|---|
| 1302 |
|
|---|
| 1303 | global_coarse_grid = NULL;
|
|---|
| 1304 |
|
|---|
| 1305 | for (int i=0; i<3; ++i)
|
|---|
| 1306 | periods[i] = (BoundaryConditions()[i] == Periodic ? 1 : 0);
|
|---|
| 1307 |
|
|---|
| 1308 | MPI_Comm_size(comm, &size);
|
|---|
| 1309 | MPI_Comm_rank(comm, &rank);
|
|---|
| 1310 |
|
|---|
| 1311 | MPI_Topo_test(comm, &status);
|
|---|
| 1312 |
|
|---|
| 1313 | if (status == MPI_CART) {
|
|---|
| 1314 |
|
|---|
| 1315 | comm_global = comm;
|
|---|
| 1316 |
|
|---|
| 1317 | }else {
|
|---|
| 1318 |
|
|---|
| 1319 | MPI_Dims_create(size, 3, dims);
|
|---|
| 1320 |
|
|---|
| 1321 | MPI_Cart_create(comm, 3, dims, periods, 1, &comm_global);
|
|---|
| 1322 |
|
|---|
| 1323 | }
|
|---|
| 1324 |
|
|---|
| 1325 | comm_info.SetCommGlobal(comm_global);
|
|---|
| 1326 |
|
|---|
| 1327 | MPI_Info_create(&info);
|
|---|
| 1328 | char key[] = "no_locks";
|
|---|
| 1329 | char val[] = "true";
|
|---|
| 1330 | MPI_Info_set(info, key, val);
|
|---|
| 1331 |
|
|---|
| 1332 | }
|
|---|
| 1333 |
|
|---|
| 1334 | CommMPI::~CommMPI()
|
|---|
| 1335 | {
|
|---|
| 1336 | std::map<const Grid*, TempGrid*>::iterator iter;
|
|---|
| 1337 |
|
|---|
| 1338 | for (iter=finer_grids.begin(); iter!=finer_grids.end(); ++iter)
|
|---|
| 1339 | delete iter->second;
|
|---|
| 1340 |
|
|---|
| 1341 | for (iter=coarser_grids.begin(); iter!=coarser_grids.end(); ++iter)
|
|---|
| 1342 | delete iter->second;
|
|---|
| 1343 |
|
|---|
| 1344 | MPI_Comm_free(&comm_global);
|
|---|
| 1345 |
|
|---|
| 1346 | if (win_created)
|
|---|
| 1347 | MPI_Win_free(&win);
|
|---|
| 1348 |
|
|---|
| 1349 | MPI_Info_free(&info);
|
|---|
| 1350 |
|
|---|
| 1351 | delete global_coarse_grid;
|
|---|
| 1352 | }
|
|---|
| 1353 |
|
|---|
| 1354 | std::string CommMPI::CreateOutputDirectory()
|
|---|
| 1355 | {
|
|---|
| 1356 | #ifdef HAVE_BOOST_FILESYSTEM
|
|---|
| 1357 | std::string path, unique_path;
|
|---|
| 1358 | std::stringstream unique_suffix;
|
|---|
| 1359 | int suffix_counter = 0;
|
|---|
| 1360 | char buffer[129];
|
|---|
| 1361 | time_t rawtime;
|
|---|
| 1362 | struct tm *timeinfo;
|
|---|
| 1363 | int path_size;
|
|---|
| 1364 | char* path_array;
|
|---|
| 1365 |
|
|---|
| 1366 | if (GlobalRank() == 0) {
|
|---|
| 1367 |
|
|---|
| 1368 | time(&rawtime);
|
|---|
| 1369 | timeinfo = localtime(&rawtime);
|
|---|
| 1370 | strftime(buffer, 128, "./output/%Y_%m_%d_%H_%M_%S/", timeinfo);
|
|---|
| 1371 | path = buffer;
|
|---|
| 1372 |
|
|---|
| 1373 | if (!fs::exists("output"))
|
|---|
| 1374 | fs::create_directory("output");
|
|---|
| 1375 |
|
|---|
| 1376 | unique_path = path;
|
|---|
| 1377 |
|
|---|
| 1378 | while (fs::exists(unique_path.c_str())) {
|
|---|
| 1379 |
|
|---|
| 1380 | unique_suffix.str("");
|
|---|
| 1381 | unique_suffix << "_" << suffix_counter++ << "/";
|
|---|
| 1382 |
|
|---|
| 1383 | unique_path = path;
|
|---|
| 1384 | unique_path.replace(unique_path.size()-1, 1, unique_suffix.str());
|
|---|
| 1385 |
|
|---|
| 1386 | }
|
|---|
| 1387 |
|
|---|
| 1388 | fs::create_directory(unique_path.c_str());
|
|---|
| 1389 |
|
|---|
| 1390 | path_size = unique_path.size() + 1;
|
|---|
| 1391 | path_array = Helper::GetCharArray(unique_path);
|
|---|
| 1392 |
|
|---|
| 1393 | MPI_Bcast(&path_size, 1, MPI_INT, 0, comm_global);
|
|---|
| 1394 |
|
|---|
| 1395 | }else {
|
|---|
| 1396 |
|
|---|
| 1397 | MPI_Bcast(&path_size, 1, MPI_INT, 0, comm_global);
|
|---|
| 1398 | path_array = new char[path_size];
|
|---|
| 1399 |
|
|---|
| 1400 | }
|
|---|
| 1401 |
|
|---|
| 1402 | MPI_Bcast(path_array, path_size, MPI_CHAR, 0, comm_global);
|
|---|
| 1403 |
|
|---|
| 1404 | unique_path = path_array;
|
|---|
| 1405 |
|
|---|
| 1406 | delete [] path_array;
|
|---|
| 1407 |
|
|---|
| 1408 | return unique_path;
|
|---|
| 1409 |
|
|---|
| 1410 | #else
|
|---|
| 1411 |
|
|---|
| 1412 | return "./";
|
|---|
| 1413 |
|
|---|
| 1414 | #endif
|
|---|
| 1415 | }
|
|---|
| 1416 |
|
|---|
| 1417 |
|
|---|
| 1418 | #endif /* HAVE_MPI */
|
|---|