[7448] | 1 | ######################################################### |
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| 2 | # |
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| 3 | # |
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| 4 | # Read in a data file and subdivide the triangle list |
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| 5 | # |
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| 6 | # |
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| 7 | # The final routine, pmesh_divide_metis, does automatic |
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| 8 | # grid partitioning. Once testing has finished on this |
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| 9 | # routine the others should be removed. |
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| 10 | # |
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| 11 | # Authors: Linda Stals and Matthew Hardy, June 2005 |
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| 12 | # Modified: Linda Stals, Nov 2005 |
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| 13 | # Jack Kelly, Nov 2005 |
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| 14 | # Steve Roberts, Aug 2009 (updating to numpy) |
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| 15 | # |
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| 16 | # |
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| 17 | ######################################################### |
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| 18 | |
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[7461] | 19 | |
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[7448] | 20 | import sys |
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| 21 | from os import sep |
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| 22 | from sys import path |
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| 23 | from math import floor |
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| 24 | |
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| 25 | import numpy as num |
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| 26 | |
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| 27 | from anuga.abstract_2d_finite_volumes.neighbour_mesh import Mesh |
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| 28 | |
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| 29 | ######################################################### |
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| 30 | # |
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| 31 | # If the triangles list is reordered, the quantities |
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| 32 | # assigned to the triangles must also be reorded. |
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| 33 | # |
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| 34 | # *) quantities contain the quantites in the old ordering |
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| 35 | # *) proc_sum[i] contains the number of triangles in |
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| 36 | # processor i |
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| 37 | # *) tri_index is a map from the old triangle ordering to |
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| 38 | # the new ordering, where the new number for triangle |
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| 39 | # i is proc_sum[tri_index[i][0]]+tri_index[i][1] |
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| 40 | # |
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| 41 | # ------------------------------------------------------- |
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| 42 | # |
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| 43 | # *) The quantaties are returned in the new ordering |
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| 44 | # |
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| 45 | ######################################################### |
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| 46 | |
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| 47 | def reorder(quantities, tri_index, proc_sum): |
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| 48 | |
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| 49 | # Find the number triangles |
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| 50 | |
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| 51 | N = len(tri_index) |
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| 52 | |
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| 53 | # Temporary storage area |
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| 54 | |
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| 55 | index = num.zeros(N, num.int) |
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| 56 | q_reord = {} |
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| 57 | |
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| 58 | # Find the new ordering of the triangles |
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| 59 | |
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| 60 | for i in range(N): |
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| 61 | bin = tri_index[i][0] |
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| 62 | bin_off_set = tri_index[i][1] |
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| 63 | index[i] = proc_sum[bin]+bin_off_set |
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| 64 | |
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| 65 | # Reorder each quantity according to the new ordering |
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| 66 | |
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| 67 | for k in quantities: |
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| 68 | q_reord[k] = num.zeros((N, 3), num.float) |
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| 69 | for i in range(N): |
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| 70 | q_reord[k][index[i]]=quantities[k].vertex_values[i] |
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| 71 | del index |
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| 72 | |
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| 73 | return q_reord |
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| 74 | |
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| 75 | |
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| 76 | ######################################################### |
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| 77 | # |
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| 78 | # Divide the mesh using a call to metis, through pymetis. |
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| 79 | # |
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| 80 | # ------------------------------------------------------- |
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| 81 | # |
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| 82 | # *) The nodes, triangles, boundary, and quantities are |
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| 83 | # returned. triangles_per_proc defines the subdivision. |
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| 84 | # The first triangles_per_proc[0] triangles are assigned |
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| 85 | # to processor 0, the next triangles_per_proc[1] are |
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| 86 | # assigned to processor 1 etc. The boundary and quantites |
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| 87 | # are ordered the same way as the triangles |
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| 88 | # |
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| 89 | ######################################################### |
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| 90 | |
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| 91 | #path.append('..' + sep + 'pymetis') |
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| 92 | |
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| 93 | try: |
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| 94 | from pymetis.metis import partMeshNodal |
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| 95 | except ImportError: |
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| 96 | print "***************************************************" |
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| 97 | print " Metis is probably not compiled." |
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| 98 | print " Read \anuga_core\source\pymetis\README" |
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| 99 | print "***************************************************" |
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| 100 | raise ImportError |
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| 101 | |
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| 102 | def pmesh_divide_metis(domain, n_procs): |
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| 103 | |
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| 104 | # Initialise the lists |
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| 105 | # List, indexed by processor of # triangles. |
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| 106 | |
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| 107 | triangles_per_proc = [] |
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| 108 | |
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| 109 | # List of lists, indexed by processor of vertex numbers |
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| 110 | |
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| 111 | tri_list = [] |
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| 112 | |
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| 113 | # List indexed by processor of cumulative total of triangles allocated. |
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| 114 | |
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| 115 | proc_sum = [] |
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| 116 | for i in range(n_procs): |
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| 117 | tri_list.append([]) |
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| 118 | triangles_per_proc.append(0) |
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| 119 | proc_sum.append([]) |
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| 120 | |
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| 121 | # Prepare variables for the metis call |
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| 122 | |
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| 123 | n_tri = len(domain.triangles) |
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| 124 | if n_procs != 1: #Because metis chokes on it... |
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| 125 | n_vert = domain.get_number_of_nodes() |
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| 126 | t_list = domain.triangles.copy() |
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| 127 | t_list = num.reshape(t_list, (-1,)) |
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| 128 | |
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| 129 | # The 1 here is for triangular mesh elements. |
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| 130 | edgecut, epart, npart = partMeshNodal(n_tri, n_vert, t_list, 1, n_procs) |
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| 131 | # print edgecut |
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| 132 | # print npart |
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| 133 | # print epart |
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| 134 | del edgecut |
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| 135 | del npart |
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| 136 | |
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| 137 | # Sometimes (usu. on x86_64), partMeshNodal returnes an array of zero |
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| 138 | # dimensional arrays. Correct this. |
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| 139 | if type(epart[0]) == num.ndarray: |
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| 140 | epart_new = num.zeros(len(epart), num.int) |
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| 141 | for i in range(len(epart)): |
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| 142 | epart_new[i] = epart[i][0] |
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| 143 | epart = epart_new |
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| 144 | del epart_new |
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| 145 | # Assign triangles to processes, according to what metis told us. |
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| 146 | |
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| 147 | # tri_index maps triangle number -> processor, new triangle number |
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| 148 | # (local to the processor) |
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| 149 | |
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| 150 | tri_index = {} |
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| 151 | triangles = [] |
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| 152 | for i in range(n_tri): |
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| 153 | triangles_per_proc[epart[i]] = triangles_per_proc[epart[i]] + 1 |
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| 154 | tri_list[epart[i]].append(domain.triangles[i]) |
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| 155 | tri_index[i] = ([epart[i], len(tri_list[epart[i]]) - 1]) |
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| 156 | |
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| 157 | # Order the triangle list so that all of the triangles belonging |
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| 158 | # to processor i are listed before those belonging to processor |
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| 159 | # i+1 |
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| 160 | |
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| 161 | for i in range(n_procs): |
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| 162 | for t in tri_list[i]: |
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| 163 | triangles.append(t) |
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| 164 | |
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| 165 | # The boundary labels have to changed in accoradance with the |
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| 166 | # new triangle ordering, proc_sum and tri_index help with this |
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| 167 | |
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| 168 | proc_sum[0] = 0 |
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| 169 | for i in range(n_procs - 1): |
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| 170 | proc_sum[i+1]=proc_sum[i]+triangles_per_proc[i] |
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| 171 | |
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| 172 | # Relabel the boundary elements to fit in with the new triangle |
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| 173 | # ordering |
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| 174 | |
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| 175 | boundary = {} |
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| 176 | for b in domain.boundary: |
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| 177 | t = tri_index[b[0]] |
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| 178 | boundary[proc_sum[t[0]]+t[1], b[1]] = domain.boundary[b] |
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| 179 | |
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| 180 | quantities = reorder(domain.quantities, tri_index, proc_sum) |
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| 181 | else: |
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| 182 | boundary = domain.boundary.copy() |
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| 183 | triangles_per_proc[0] = n_tri |
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| 184 | triangles = domain.triangles.copy() |
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| 185 | |
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| 186 | # This is essentially the same as a chunk of code from reorder. |
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| 187 | |
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| 188 | quantities = {} |
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| 189 | for k in domain.quantities: |
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| 190 | quantities[k] = num.zeros((n_tri, 3), num.float) |
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| 191 | for i in range(n_tri): |
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| 192 | quantities[k][i] = domain.quantities[k].vertex_values[i] |
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| 193 | |
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| 194 | # Extract the node list |
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| 195 | |
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| 196 | nodes = domain.get_nodes().copy() |
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| 197 | |
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| 198 | # Convert the triangle datastructure to be an array type, |
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| 199 | # this helps with the communication |
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| 200 | |
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| 201 | ttriangles = num.zeros((len(triangles), 3), num.int) |
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| 202 | for i in range(len(triangles)): |
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| 203 | ttriangles[i] = triangles[i] |
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| 204 | |
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| 205 | return nodes, ttriangles, boundary, triangles_per_proc, quantities |
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| 206 | |
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| 207 | |
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| 208 | ######################################################### |
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| 209 | # |
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| 210 | # Subdivide the domain. This module is primarily |
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| 211 | # responsible for building the ghost layer and |
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| 212 | # communication pattern |
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| 213 | # |
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| 214 | # |
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| 215 | # Author: Linda Stals, June 2005 |
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| 216 | # Modified: Linda Stals, Nov 2005 (optimise python code) |
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| 217 | # Steve Roberts, Aug 2009 (convert to numpy) |
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| 218 | # |
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| 219 | # |
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| 220 | ######################################################### |
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| 221 | |
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| 222 | |
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| 223 | |
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| 224 | ######################################################### |
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| 225 | # |
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| 226 | # Subdivide the triangles into non-overlapping domains. |
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| 227 | # |
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| 228 | # *) The subdivision is controlled by triangles_per_proc. |
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| 229 | # The first triangles_per_proc[0] triangles are assigned |
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| 230 | # to the first processor, the second triangles_per_proc[1] |
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| 231 | # are assigned to the second processor etc. |
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| 232 | # |
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| 233 | # *) nodes, triangles and boundary contains all of the |
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| 234 | # nodes, triangles and boundary tag information for the |
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| 235 | # whole domain. The triangles should be orientated in the |
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| 236 | # correct way and the nodes number consecutively from 0. |
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| 237 | # |
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| 238 | # ------------------------------------------------------- |
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| 239 | # |
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| 240 | # *) A dictionary containing the full_nodes, full_triangles |
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| 241 | # and full_boundary information for each processor is |
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| 242 | # returned. The node information consists of |
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| 243 | # [global_id, x_coord, y_coord]. |
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| 244 | # |
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| 245 | ######################################################### |
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| 246 | |
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| 247 | def submesh_full(nodes, triangles, boundary, triangles_per_proc): |
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| 248 | |
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| 249 | # Initialise |
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| 250 | |
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| 251 | tlower = 0 |
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| 252 | nproc = len(triangles_per_proc) |
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| 253 | nnodes = len(nodes) |
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| 254 | node_list = [] |
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| 255 | triangle_list = [] |
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| 256 | boundary_list = [] |
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| 257 | submesh = {} |
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| 258 | node_range = num.reshape(num.arange(nnodes),(nnodes,1)) |
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| 259 | |
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| 260 | #print node_range |
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| 261 | tsubnodes = num.concatenate((node_range, nodes), 1) |
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| 262 | |
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| 263 | |
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| 264 | # Loop over processors |
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| 265 | |
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| 266 | for p in range(nproc): |
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| 267 | |
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| 268 | # Find triangles on processor p |
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| 269 | |
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| 270 | tupper = triangles_per_proc[p]+tlower |
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| 271 | subtriangles = triangles[tlower:tupper] |
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| 272 | triangle_list.append(subtriangles) |
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| 273 | |
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| 274 | # Find the boundary edges on processor p |
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| 275 | |
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| 276 | subboundary = {} |
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| 277 | for k in boundary: |
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| 278 | if (k[0] >=tlower and k[0] < tupper): |
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| 279 | subboundary[k]=boundary[k] |
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| 280 | boundary_list.append(subboundary) |
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| 281 | |
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| 282 | # Find nodes in processor p |
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| 283 | |
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| 284 | nodemap = num.zeros(nnodes, 'i') |
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| 285 | for t in subtriangles: |
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| 286 | nodemap[t[0]]=1 |
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| 287 | nodemap[t[1]]=1 |
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| 288 | nodemap[t[2]]=1 |
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| 289 | |
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| 290 | |
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| 291 | node_list.append(tsubnodes.take(num.flatnonzero(nodemap),axis=0)) |
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| 292 | |
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| 293 | # Move to the next processor |
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| 294 | |
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| 295 | tlower = tupper |
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| 296 | |
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| 297 | # Put the results in a dictionary |
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| 298 | |
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| 299 | submesh["full_nodes"] = node_list |
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| 300 | submesh["full_triangles"] = triangle_list |
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| 301 | submesh["full_boundary"] = boundary_list |
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| 302 | |
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| 303 | # Clean up before exiting |
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| 304 | |
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| 305 | del (nodemap) |
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| 306 | |
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| 307 | return submesh |
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| 308 | |
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| 309 | |
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| 310 | ######################################################### |
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| 311 | # |
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| 312 | # Build the ghost layer of triangles |
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| 313 | # |
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| 314 | # *) Given the triangle subpartion for the processor |
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| 315 | # build a ghost layer of triangles. The ghost layer |
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| 316 | # consists of two layers of neighbouring triangles. |
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| 317 | # |
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| 318 | # *) The vertices in the ghost triangles must also |
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| 319 | # be added to the node list for the current processor |
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| 320 | # |
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| 321 | # |
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| 322 | # ------------------------------------------------------- |
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| 323 | # |
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| 324 | # *) The extra triangles and nodes are returned. |
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| 325 | # |
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| 326 | # *) The node information consists of |
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| 327 | # [global_id, x_coord, y_coord]. |
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| 328 | # |
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| 329 | # *) The triangle information consists of |
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| 330 | # [triangle number, t], where t = [v1, v2, v3]. |
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| 331 | # |
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| 332 | ######################################################### |
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| 333 | |
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| 334 | def ghost_layer(submesh, mesh, p, tupper, tlower): |
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| 335 | |
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| 336 | ncoord = mesh.number_of_nodes |
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| 337 | ntriangles = mesh.number_of_triangles |
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| 338 | |
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| 339 | # Find the first layer of boundary triangles |
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| 340 | |
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| 341 | trianglemap = num.zeros(ntriangles, 'i') |
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| 342 | for t in range(tlower, tupper): |
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| 343 | |
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| 344 | n = mesh.neighbours[t, 0] |
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| 345 | |
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| 346 | if n >= 0: |
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| 347 | if n < tlower or n >= tupper: |
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| 348 | trianglemap[n] = 1 |
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| 349 | n = mesh.neighbours[t, 1] |
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| 350 | if n >= 0: |
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| 351 | if n < tlower or n >= tupper: |
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| 352 | trianglemap[n] = 1 |
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| 353 | n = mesh.neighbours[t, 2] |
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| 354 | if n >= 0: |
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| 355 | if n < tlower or n >= tupper: |
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| 356 | trianglemap[n] = 1 |
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| 357 | |
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| 358 | # Find the second layer of boundary triangles |
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| 359 | |
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| 360 | for t in range(len(trianglemap)): |
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| 361 | if trianglemap[t]==1: |
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| 362 | n = mesh.neighbours[t, 0] |
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| 363 | if n >= 0: |
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| 364 | if (n < tlower or n >= tupper) and trianglemap[n] == 0: |
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| 365 | trianglemap[n] = 2 |
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| 366 | n = mesh.neighbours[t, 1] |
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| 367 | if n >= 0: |
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| 368 | if (n < tlower or n >= tupper) and trianglemap[n] == 0: |
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| 369 | trianglemap[n] = 2 |
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| 370 | n = mesh.neighbours[t, 2] |
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| 371 | if n >= 0: |
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| 372 | if (n < tlower or n >= tupper) and trianglemap[n] == 0: |
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| 373 | trianglemap[n] = 2 |
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| 374 | |
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| 375 | # Build the triangle list and make note of the vertices |
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| 376 | |
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| 377 | nodemap = num.zeros(ncoord, 'i') |
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| 378 | fullnodes = submesh["full_nodes"][p] |
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| 379 | |
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| 380 | subtriangles = [] |
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| 381 | for i in range(len(trianglemap)): |
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| 382 | if trianglemap[i] != 0: |
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| 383 | t = list(mesh.triangles[i]) |
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| 384 | nodemap[t[0]] = 1 |
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| 385 | nodemap[t[1]] = 1 |
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| 386 | nodemap[t[2]] = 1 |
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| 387 | |
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| 388 | trilist = num.reshape(num.arange(ntriangles),(ntriangles,1)) |
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| 389 | tsubtriangles = num.concatenate((trilist, mesh.triangles), 1) |
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| 390 | subtriangles = tsubtriangles.take(num.flatnonzero(trianglemap),axis=0) |
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| 391 | |
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| 392 | |
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| 393 | # Keep a record of the triangle vertices, if they are not already there |
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| 394 | |
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| 395 | subnodes = [] |
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| 396 | for n in fullnodes: |
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| 397 | nodemap[int(n[0])] = 0 |
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| 398 | |
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| 399 | nodelist = num.reshape(num.arange(ncoord),(ncoord,1)) |
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| 400 | tsubnodes = num.concatenate((nodelist, mesh.get_nodes()), 1) |
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| 401 | subnodes = tsubnodes.take(num.flatnonzero(nodemap),axis=0) |
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| 402 | |
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| 403 | # Clean up before exiting |
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| 404 | |
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| 405 | del (nodelist) |
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| 406 | del (trilist) |
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| 407 | del (tsubnodes) |
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| 408 | del (nodemap) |
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| 409 | del (trianglemap) |
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| 410 | |
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| 411 | # Return the triangles and vertices sitting on the boundary layer |
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| 412 | |
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| 413 | return subnodes, subtriangles |
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| 414 | |
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| 415 | ######################################################### |
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| 416 | # |
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| 417 | # Find the edges of the ghost trianlges that do not |
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| 418 | # have a neighbour in the current cell. These are |
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| 419 | # treated as a special type of boundary edge. |
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| 420 | # |
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| 421 | # *) Given the ghost triangles in a particular |
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| 422 | # triangle, use the mesh to find its neigbours. If |
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| 423 | # the neighbour is not in the processor set it to |
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| 424 | # be a boundary edge |
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| 425 | # |
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| 426 | # *) The vertices in the ghost triangles must also |
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| 427 | # be added to the node list for the current processor |
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| 428 | # |
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| 429 | # *) The boundary edges for the ghost triangles are |
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| 430 | # ignored. |
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| 431 | # |
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| 432 | # ------------------------------------------------------- |
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| 433 | # |
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| 434 | # *) The type assigned to the ghost boundary edges is 'ghost' |
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| 435 | # |
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| 436 | # *) The boundary information is returned as a directorier |
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| 437 | # with the key = (triangle id, edge no) and the values |
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| 438 | # assigned to the key is 'ghost' |
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| 439 | # |
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| 440 | # |
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| 441 | ######################################################### |
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| 442 | def is_in_processor(ghost_list, tlower, tupper, n): |
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| 443 | |
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| 444 | return num.equal(ghost_list,n).any() or (tlower <= n and tupper > n) |
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| 445 | |
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| 446 | |
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| 447 | def ghost_bnd_layer(ghosttri, tlower, tupper, mesh, p): |
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| 448 | |
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| 449 | ghost_list = [] |
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| 450 | subboundary = {} |
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| 451 | |
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| 452 | |
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| 453 | for t in ghosttri: |
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| 454 | ghost_list.append(t[0]) |
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| 455 | |
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| 456 | for t in ghosttri: |
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| 457 | |
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| 458 | n = mesh.neighbours[t[0], 0] |
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| 459 | if not is_in_processor(ghost_list, tlower, tupper, n): |
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| 460 | subboundary[t[0], 0] = 'ghost' |
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| 461 | |
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| 462 | n = mesh.neighbours[t[0], 1] |
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| 463 | if not is_in_processor(ghost_list, tlower, tupper, n): |
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| 464 | subboundary[t[0], 1] = 'ghost' |
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| 465 | |
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| 466 | n = mesh.neighbours[t[0], 2] |
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| 467 | if not is_in_processor(ghost_list, tlower, tupper, n): |
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| 468 | subboundary[t[0], 2] = 'ghost' |
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| 469 | |
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| 470 | return subboundary |
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| 471 | |
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| 472 | ######################################################### |
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| 473 | # |
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| 474 | # The ghost triangles on the current processor will need |
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| 475 | # to get updated information from the neighbouring |
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| 476 | # processor containing the corresponding full triangles. |
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| 477 | # |
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| 478 | # *) The tri_per_proc is used to determine which |
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| 479 | # processor contains the full node copy. |
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| 480 | # |
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| 481 | # ------------------------------------------------------- |
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| 482 | # |
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| 483 | # *) The ghost communication pattern consists of |
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| 484 | # [global node number, neighbour processor number]. |
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| 485 | # |
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| 486 | ######################################################### |
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| 487 | |
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| 488 | def ghost_commun_pattern(subtri, p, tri_per_proc): |
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| 489 | |
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| 490 | # Loop over the ghost triangles |
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| 491 | |
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| 492 | ghost_commun = num.zeros((len(subtri), 2), num.int) |
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| 493 | |
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| 494 | for i in range(len(subtri)): |
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| 495 | global_no = subtri[i][0] |
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| 496 | |
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| 497 | # Find which processor contains the full triangle |
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| 498 | |
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| 499 | nproc = len(tri_per_proc) |
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| 500 | neigh = nproc-1 |
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| 501 | sum = 0 |
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| 502 | for q in range(nproc-1): |
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| 503 | if (global_no < sum+tri_per_proc[q]): |
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| 504 | neigh = q |
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| 505 | break |
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| 506 | sum = sum+tri_per_proc[q] |
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| 507 | |
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| 508 | # Keep a copy of the neighbour processor number |
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| 509 | |
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| 510 | ghost_commun[i] = [global_no, neigh] |
---|
| 511 | |
---|
| 512 | return ghost_commun |
---|
| 513 | |
---|
| 514 | ######################################################### |
---|
| 515 | # |
---|
| 516 | # The full triangles in this processor must communicate |
---|
| 517 | # updated information to neighbouring processor that |
---|
| 518 | # contain ghost triangles |
---|
| 519 | # |
---|
| 520 | # *) The ghost communication pattern for all of the |
---|
| 521 | # processor must be built before calling this processor. |
---|
| 522 | # |
---|
| 523 | # *) The full communication pattern is found by looping |
---|
| 524 | # through the ghost communication pattern for all of the |
---|
| 525 | # processors. Recall that this information is stored in |
---|
| 526 | # the form [global node number, neighbour processor number]. |
---|
| 527 | # The full communication for the neighbour processor is |
---|
| 528 | # then updated. |
---|
| 529 | # |
---|
| 530 | # ------------------------------------------------------- |
---|
| 531 | # |
---|
| 532 | # *) The full communication pattern consists of |
---|
| 533 | # [global id, [p1, p2, ...]], where p1, p2 etc contain |
---|
| 534 | # a ghost node copy of the triangle global id. |
---|
| 535 | # |
---|
| 536 | ######################################################### |
---|
| 537 | |
---|
| 538 | def full_commun_pattern(submesh, tri_per_proc): |
---|
| 539 | tlower = 0 |
---|
| 540 | nproc = len(tri_per_proc) |
---|
| 541 | full_commun = [] |
---|
| 542 | |
---|
| 543 | # Loop over the processor |
---|
| 544 | |
---|
| 545 | for p in range(nproc): |
---|
| 546 | |
---|
| 547 | # Loop over the full triangles in the current processor |
---|
| 548 | # and build an empty dictionary |
---|
| 549 | |
---|
| 550 | fcommun = {} |
---|
| 551 | tupper = tri_per_proc[p]+tlower |
---|
| 552 | for i in range(tlower, tupper): |
---|
| 553 | fcommun[i] = [] |
---|
| 554 | full_commun.append(fcommun) |
---|
| 555 | tlower = tupper |
---|
| 556 | |
---|
| 557 | # Loop over the processor again |
---|
| 558 | |
---|
| 559 | for p in range(nproc): |
---|
| 560 | |
---|
| 561 | # Loop over the ghost triangles in the current processor, |
---|
| 562 | # find which processor contains the corresponding full copy |
---|
| 563 | # and note that the processor must send updates to this |
---|
| 564 | # processor |
---|
| 565 | |
---|
| 566 | for g in submesh["ghost_commun"][p]: |
---|
| 567 | neigh = g[1] |
---|
| 568 | full_commun[neigh][g[0]].append(p) |
---|
| 569 | |
---|
| 570 | return full_commun |
---|
| 571 | |
---|
| 572 | |
---|
| 573 | ######################################################### |
---|
| 574 | # |
---|
| 575 | # Given the non-overlapping grid partition, an extra layer |
---|
| 576 | # of triangles are included to help with the computations. |
---|
| 577 | # The triangles in this extra layer are not updated by |
---|
| 578 | # the processor, their updated values must be sent by the |
---|
| 579 | # processor containing the original, full, copy of the |
---|
| 580 | # triangle. The communication pattern that controls these |
---|
| 581 | # updates must also be built. |
---|
| 582 | # |
---|
| 583 | # *) Assumes that full triangles, nodes etc have already |
---|
| 584 | # been found and stored in submesh |
---|
| 585 | # |
---|
| 586 | # *) See the documentation for ghost_layer, |
---|
| 587 | # ghost_commun_pattern and full_commun_pattern |
---|
| 588 | # |
---|
| 589 | # ------------------------------------------------------- |
---|
| 590 | # |
---|
| 591 | # *) The additional information is added to the submesh |
---|
| 592 | # dictionary. See the documentation for ghost_layer, |
---|
| 593 | # ghost_commun_pattern and full_commun_pattern |
---|
| 594 | # |
---|
| 595 | # *) The ghost_triangles, ghost_nodes, ghost_boundary, |
---|
| 596 | # ghost_commun and full_commun is added to submesh |
---|
| 597 | ######################################################### |
---|
| 598 | |
---|
| 599 | def submesh_ghost(submesh, mesh, triangles_per_proc): |
---|
| 600 | |
---|
| 601 | nproc = len(triangles_per_proc) |
---|
| 602 | tlower = 0 |
---|
| 603 | ghost_triangles = [] |
---|
| 604 | ghost_nodes = [] |
---|
| 605 | ghost_commun = [] |
---|
| 606 | ghost_bnd = [] |
---|
| 607 | |
---|
| 608 | # Loop over the processors |
---|
| 609 | |
---|
| 610 | for p in range(nproc): |
---|
| 611 | |
---|
| 612 | # Find the full triangles in this processor |
---|
| 613 | |
---|
| 614 | tupper = triangles_per_proc[p]+tlower |
---|
| 615 | |
---|
| 616 | # Build the ghost boundary layer |
---|
| 617 | |
---|
| 618 | [subnodes, subtri] = \ |
---|
| 619 | ghost_layer(submesh, mesh, p, tupper, tlower) |
---|
| 620 | ghost_triangles.append(subtri) |
---|
| 621 | ghost_nodes.append(subnodes) |
---|
| 622 | |
---|
| 623 | |
---|
| 624 | # Find the boundary layer formed by the ghost triangles |
---|
| 625 | |
---|
| 626 | subbnd = ghost_bnd_layer(subtri, tlower, tupper, mesh, p) |
---|
| 627 | ghost_bnd.append(subbnd) |
---|
| 628 | |
---|
| 629 | # Build the communication pattern for the ghost nodes |
---|
| 630 | |
---|
| 631 | gcommun = \ |
---|
| 632 | ghost_commun_pattern(subtri, p, triangles_per_proc) |
---|
| 633 | ghost_commun.append(gcommun) |
---|
| 634 | |
---|
| 635 | # Move to the next processor |
---|
| 636 | |
---|
| 637 | tlower = tupper |
---|
| 638 | |
---|
| 639 | |
---|
| 640 | # Record the ghost layer and communication pattern |
---|
| 641 | |
---|
| 642 | submesh["ghost_nodes"] = ghost_nodes |
---|
| 643 | submesh["ghost_triangles"] = ghost_triangles |
---|
| 644 | submesh["ghost_commun"] = ghost_commun |
---|
| 645 | submesh["ghost_boundary"] = ghost_bnd |
---|
| 646 | |
---|
| 647 | # Build the communication pattern for the full triangles |
---|
| 648 | |
---|
| 649 | full_commun = full_commun_pattern(submesh, triangles_per_proc) |
---|
| 650 | submesh["full_commun"] = full_commun |
---|
| 651 | |
---|
| 652 | # Return the submesh |
---|
| 653 | |
---|
| 654 | return submesh |
---|
| 655 | |
---|
| 656 | |
---|
| 657 | ######################################################### |
---|
| 658 | # |
---|
| 659 | # Certain quantities may be assigned to the triangles, |
---|
| 660 | # these quantities must be subdivided in the same way |
---|
| 661 | # as the triangles |
---|
| 662 | # |
---|
| 663 | # *) The quantities are ordered in the same way as the |
---|
| 664 | # triangles |
---|
| 665 | # |
---|
| 666 | # ------------------------------------------------------- |
---|
| 667 | # |
---|
| 668 | # *) The quantites attached to the full triangles are |
---|
| 669 | # stored in full_quan |
---|
| 670 | # |
---|
| 671 | # *) The quantities attached to the ghost triangles are |
---|
| 672 | # stored in ghost_quan |
---|
| 673 | ######################################################### |
---|
| 674 | |
---|
| 675 | def submesh_quantities(submesh, quantities, triangles_per_proc): |
---|
| 676 | |
---|
| 677 | nproc = len(triangles_per_proc) |
---|
| 678 | |
---|
| 679 | lower = 0 |
---|
| 680 | |
---|
| 681 | # Build an empty dictionary to hold the quantites |
---|
| 682 | |
---|
| 683 | submesh["full_quan"] = {} |
---|
| 684 | submesh["ghost_quan"] = {} |
---|
| 685 | for k in quantities: |
---|
| 686 | submesh["full_quan"][k] = [] |
---|
| 687 | submesh["ghost_quan"][k] = [] |
---|
| 688 | |
---|
| 689 | # Loop trough the subdomains |
---|
| 690 | |
---|
| 691 | for p in range(nproc): |
---|
| 692 | upper = lower+triangles_per_proc[p] |
---|
| 693 | |
---|
| 694 | # Find the global ID of the ghost triangles |
---|
| 695 | |
---|
| 696 | global_id = [] |
---|
| 697 | M = len(submesh["ghost_triangles"][p]) |
---|
| 698 | for j in range(M): |
---|
| 699 | global_id.append(submesh["ghost_triangles"][p][j][0]) |
---|
| 700 | |
---|
| 701 | # Use the global ID to extract the quantites information from |
---|
| 702 | # the full domain |
---|
| 703 | |
---|
| 704 | for k in quantities: |
---|
| 705 | submesh["full_quan"][k].append(quantities[k][lower:upper]) |
---|
| 706 | submesh["ghost_quan"][k].append(num.zeros( (M,3) , num.float)) |
---|
| 707 | for j in range(M): |
---|
| 708 | submesh["ghost_quan"][k][p][j] = \ |
---|
| 709 | quantities[k][global_id[j]] |
---|
| 710 | |
---|
| 711 | lower = upper |
---|
| 712 | |
---|
| 713 | return submesh |
---|
| 714 | |
---|
| 715 | ######################################################### |
---|
| 716 | # |
---|
| 717 | # Build the grid partition on the host. |
---|
| 718 | # |
---|
| 719 | # *) See the documentation for submesh_ghost and |
---|
| 720 | # submesh_full |
---|
| 721 | # |
---|
| 722 | # ------------------------------------------------------- |
---|
| 723 | # |
---|
| 724 | # *) A dictionary containing the full_triangles, |
---|
| 725 | # full_nodes, full_boundary, ghost_triangles, ghost_nodes, |
---|
| 726 | # ghost_boundary, ghost_commun and full_commun and true boundary polygon is returned. |
---|
| 727 | # |
---|
| 728 | ######################################################### |
---|
| 729 | |
---|
| 730 | def build_submesh(nodes, triangles, edges, quantities, |
---|
| 731 | triangles_per_proc): |
---|
| 732 | |
---|
| 733 | # Temporarily build the mesh to find the neighbouring |
---|
| 734 | # triangles and true boundary polygon |
---|
| 735 | |
---|
| 736 | mesh = Mesh(nodes, triangles) |
---|
| 737 | boundary_polygon = mesh.get_boundary_polygon() |
---|
| 738 | |
---|
| 739 | |
---|
| 740 | # Subdivide into non-overlapping partitions |
---|
| 741 | |
---|
| 742 | submeshf = submesh_full(nodes, triangles, edges, \ |
---|
| 743 | triangles_per_proc) |
---|
| 744 | |
---|
| 745 | # Add any extra ghost boundary layer information |
---|
| 746 | |
---|
| 747 | submeshg = submesh_ghost(submeshf, mesh, triangles_per_proc) |
---|
| 748 | |
---|
| 749 | # Order the quantities information to be the same as the triangle |
---|
| 750 | # information |
---|
| 751 | |
---|
| 752 | submesh = submesh_quantities(submeshg, quantities, \ |
---|
| 753 | triangles_per_proc) |
---|
| 754 | |
---|
| 755 | submesh["boundary_polygon"] = boundary_polygon |
---|
| 756 | return submesh |
---|
| 757 | |
---|
| 758 | ######################################################### |
---|
| 759 | # |
---|
| 760 | # Given the subdivision of the grid assigned to the |
---|
| 761 | # current processor convert it into a form that is |
---|
| 762 | # appropriate for the GA datastructure. |
---|
| 763 | # |
---|
| 764 | # The main function of these modules is to change the |
---|
| 765 | # node numbering. The GA datastructure assumes they |
---|
| 766 | # are numbered consecutively from 0. |
---|
| 767 | # |
---|
| 768 | # The module also changes the communication pattern |
---|
| 769 | # datastructure into a form needed by parallel_advection |
---|
| 770 | # |
---|
| 771 | # Authors: Linda Stals and Matthew Hardy, June 2005 |
---|
| 772 | # Modified: Linda Stals, Nov 2005 (optimise python code) |
---|
| 773 | # Steve Roberts, Aug 2009 (updating to numpy) |
---|
| 774 | # |
---|
| 775 | # |
---|
| 776 | ######################################################### |
---|
| 777 | |
---|
| 778 | |
---|
| 779 | ######################################################### |
---|
| 780 | # Convert the format of the data to that used by ANUGA |
---|
| 781 | # |
---|
| 782 | # |
---|
| 783 | # *) Change the nodes global ID's to an integer value, |
---|
| 784 | #starting from 0. |
---|
| 785 | # |
---|
| 786 | # *) The triangles and boundary edges must also be |
---|
| 787 | # updated accordingly. |
---|
| 788 | # |
---|
| 789 | # ------------------------------------------------------- |
---|
| 790 | # |
---|
| 791 | # *) The nodes, triangles and boundary edges defined by |
---|
| 792 | # the new numbering scheme are returned |
---|
| 793 | # |
---|
| 794 | ######################################################### |
---|
| 795 | |
---|
| 796 | def build_local_GA(nodes, triangles, boundaries, tri_index): |
---|
| 797 | |
---|
| 798 | Nnodes =len(nodes) |
---|
| 799 | Ntriangles = len(triangles) |
---|
| 800 | |
---|
| 801 | # Extract the nodes (using the local ID) |
---|
| 802 | |
---|
| 803 | GAnodes = num.take(nodes, (1, 2), 1) |
---|
| 804 | |
---|
| 805 | # Build a global ID to local ID mapping |
---|
| 806 | |
---|
| 807 | NGlobal = 0 |
---|
| 808 | for i in range(Nnodes): |
---|
| 809 | if nodes[i][0] > NGlobal: |
---|
| 810 | NGlobal = nodes[i][0] |
---|
| 811 | index = num.zeros(int(NGlobal)+1, num.int) |
---|
| 812 | num.put(index, num.take(nodes, (0,), 1).astype(num.int), \ |
---|
| 813 | num.arange(Nnodes)) |
---|
| 814 | |
---|
| 815 | # Change the global IDs in the triangles to the local IDs |
---|
| 816 | |
---|
| 817 | GAtriangles = num.zeros((Ntriangles, 3), num.int) |
---|
| 818 | GAtriangles[:,0] = num.take(index, triangles[:,0]) |
---|
| 819 | GAtriangles[:,1] = num.take(index, triangles[:,1]) |
---|
| 820 | GAtriangles[:,2] = num.take(index, triangles[:,2]) |
---|
| 821 | |
---|
| 822 | # Change the triangle numbering in the boundaries |
---|
| 823 | |
---|
| 824 | GAboundaries = {} |
---|
| 825 | for b in boundaries: |
---|
| 826 | GAboundaries[tri_index[b[0]], b[1]] = boundaries[b] |
---|
| 827 | |
---|
| 828 | del (index) |
---|
| 829 | |
---|
| 830 | return GAnodes, GAtriangles, GAboundaries |
---|
| 831 | |
---|
| 832 | |
---|
| 833 | ######################################################### |
---|
| 834 | # Change the communication format to that needed by the |
---|
| 835 | # parallel advection file. |
---|
| 836 | # |
---|
| 837 | # *) The index contains [global triangle no, |
---|
| 838 | # local triangle no.] |
---|
| 839 | # |
---|
| 840 | # ------------------------------------------------------- |
---|
| 841 | # |
---|
| 842 | # *) The ghost_recv and full_send dictionaries are |
---|
| 843 | # returned. |
---|
| 844 | # |
---|
| 845 | # *) ghost_recv dictionary is local id, global id, value |
---|
| 846 | # |
---|
| 847 | # *) full_recv dictionary is local id, global id, value |
---|
| 848 | # |
---|
| 849 | # *) The information is ordered by the global id. This |
---|
| 850 | # means that the communication order is predetermined and |
---|
| 851 | # local and global id do not need to be |
---|
| 852 | # compared when the information is sent/received. |
---|
| 853 | # |
---|
| 854 | ######################################################### |
---|
| 855 | |
---|
| 856 | def build_local_commun(index, ghostc, fullc, nproc): |
---|
| 857 | |
---|
| 858 | # Initialise |
---|
| 859 | |
---|
| 860 | full_send = {} |
---|
| 861 | ghost_recv = {} |
---|
| 862 | |
---|
| 863 | # Build the ghost_recv dictionary (sort the |
---|
| 864 | # information by the global numbering) |
---|
| 865 | |
---|
| 866 | ghostc = num.sort(ghostc, 0) |
---|
| 867 | |
---|
| 868 | for c in range(nproc): |
---|
| 869 | s = ghostc[:,0] |
---|
| 870 | d = num.compress(num.equal(ghostc[:,1],c), s) |
---|
| 871 | if len(d) > 0: |
---|
| 872 | ghost_recv[c] = [0, 0] |
---|
| 873 | ghost_recv[c][1] = d |
---|
| 874 | ghost_recv[c][0] = num.take(index, d) |
---|
| 875 | |
---|
| 876 | # Build a temporary copy of the full_send dictionary |
---|
| 877 | # (this version allows the information to be stored |
---|
| 878 | # by the global numbering) |
---|
| 879 | |
---|
| 880 | tmp_send = {} |
---|
| 881 | for global_id in fullc: |
---|
| 882 | for i in range(len(fullc[global_id])): |
---|
| 883 | neigh = fullc[global_id][i] |
---|
| 884 | if not tmp_send.has_key(neigh): |
---|
| 885 | tmp_send[neigh] = [] |
---|
| 886 | tmp_send[neigh].append([global_id, \ |
---|
| 887 | index[global_id]]) |
---|
| 888 | |
---|
| 889 | # Extract the full send information and put it in the form |
---|
| 890 | # required for the full_send dictionary |
---|
| 891 | |
---|
| 892 | for neigh in tmp_send: |
---|
| 893 | neigh_commun = num.sort(tmp_send[neigh], 0) |
---|
| 894 | full_send[neigh] = [0, 0] |
---|
| 895 | full_send[neigh][0] = neigh_commun[:,1] |
---|
| 896 | full_send[neigh][1] = neigh_commun[:,0] |
---|
| 897 | |
---|
| 898 | return ghost_recv, full_send |
---|
| 899 | |
---|
| 900 | |
---|
| 901 | ######################################################### |
---|
| 902 | # Convert the format of the data to that used by ANUGA |
---|
| 903 | # |
---|
| 904 | # |
---|
| 905 | # *) Change the nodes global ID's to an integer value, |
---|
| 906 | # starting from 0. The node numbering in the triangles |
---|
| 907 | # must also be updated to take this into account. |
---|
| 908 | # |
---|
| 909 | # *) The triangle number will also change, which affects |
---|
| 910 | # the boundary tag information and the communication |
---|
| 911 | # pattern. |
---|
| 912 | # |
---|
| 913 | # ------------------------------------------------------- |
---|
| 914 | # |
---|
| 915 | # *) The nodes, triangles, boundary edges and communication |
---|
| 916 | # pattern defined by the new numbering scheme are returned |
---|
| 917 | # |
---|
| 918 | ######################################################### |
---|
| 919 | |
---|
| 920 | def build_local_mesh(submesh, lower_t, upper_t, nproc): |
---|
| 921 | |
---|
| 922 | # Combine the full nodes and ghost nodes |
---|
| 923 | |
---|
| 924 | nodes = num.concatenate((submesh["full_nodes"], \ |
---|
| 925 | submesh["ghost_nodes"])) |
---|
| 926 | |
---|
| 927 | # Combine the full triangles and ghost triangles |
---|
| 928 | |
---|
| 929 | gtri = num.take(submesh["ghost_triangles"],(1, 2, 3),1) |
---|
| 930 | triangles = num.concatenate((submesh["full_triangles"], gtri)) |
---|
| 931 | |
---|
| 932 | # Combine the full boundaries and ghost boundaries |
---|
| 933 | |
---|
| 934 | boundaries = submesh["full_boundary"] |
---|
| 935 | for b in submesh["ghost_boundary"]: |
---|
| 936 | boundaries[b]=submesh["ghost_boundary"][b] |
---|
| 937 | |
---|
| 938 | # Make note of the new triangle numbers, including the ghost |
---|
| 939 | # triangles |
---|
| 940 | |
---|
| 941 | NGlobal = upper_t |
---|
| 942 | for i in range(len(submesh["ghost_triangles"])): |
---|
| 943 | id = submesh["ghost_triangles"][i][0] |
---|
| 944 | if id > NGlobal: |
---|
| 945 | NGlobal = id |
---|
| 946 | index = num.zeros(int(NGlobal)+1, num.int) |
---|
| 947 | index[lower_t:upper_t]=num.arange(upper_t-lower_t) |
---|
| 948 | for i in range(len(submesh["ghost_triangles"])): |
---|
| 949 | index[submesh["ghost_triangles"][i][0]] = i+upper_t-lower_t |
---|
| 950 | |
---|
| 951 | # Change the node numbering (and update the numbering in the |
---|
| 952 | # triangles) |
---|
| 953 | |
---|
| 954 | [GAnodes, GAtriangles, GAboundary] = build_local_GA(nodes, triangles, boundaries, index) |
---|
| 955 | |
---|
| 956 | # Extract the local quantities |
---|
| 957 | |
---|
| 958 | quantities ={} |
---|
| 959 | for k in submesh["full_quan"]: |
---|
| 960 | Nf = len(submesh["full_quan"][k]) |
---|
| 961 | Ng = len(submesh["ghost_quan"][k]) |
---|
| 962 | quantities[k] = num.zeros((Nf+Ng, 3), num.float) |
---|
| 963 | quantities[k][0:Nf] = submesh["full_quan"][k] |
---|
| 964 | quantities[k][Nf:Nf+Ng] = submesh["ghost_quan"][k] |
---|
| 965 | |
---|
| 966 | # Change the communication pattern into a form needed by |
---|
| 967 | # the parallel_adv |
---|
| 968 | |
---|
| 969 | gcommun = submesh["ghost_commun"] |
---|
| 970 | fcommun = submesh["full_commun"] |
---|
| 971 | [ghost_rec, full_send] = \ |
---|
| 972 | build_local_commun(index, gcommun, fcommun, nproc) |
---|
| 973 | |
---|
| 974 | # Clean up before exiting |
---|
| 975 | |
---|
| 976 | del(index) |
---|
| 977 | |
---|
| 978 | return GAnodes, GAtriangles, GAboundary, quantities, ghost_rec, \ |
---|
| 979 | full_send |
---|
| 980 | |
---|
| 981 | |
---|
| 982 | ######################################################### |
---|
| 983 | # |
---|
| 984 | # Handle the communication between the host machine |
---|
| 985 | # (processor 0) and the processors. The host machine is |
---|
| 986 | # responsible for the doing the initial grid partitioning. |
---|
| 987 | # |
---|
| 988 | # The routines given below should be moved to the |
---|
| 989 | # build_submesh.py and build_local.py file to allow |
---|
| 990 | # overlapping of communication and computation. |
---|
| 991 | # This should be done after more debugging. |
---|
| 992 | # |
---|
| 993 | # |
---|
| 994 | # Author: Linda Stals, June 2005 |
---|
| 995 | # Modified: Linda Stals, Nov 2005 (optimise python code) |
---|
| 996 | # Steve Roberts, Aug 2009 (update to numpy) |
---|
| 997 | # |
---|
| 998 | # |
---|
| 999 | ######################################################### |
---|
| 1000 | |
---|
| 1001 | |
---|
| 1002 | ######################################################### |
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| 1003 | # |
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| 1004 | # Send the submesh to processor p. |
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| 1005 | # |
---|
| 1006 | # *) The order and form is strongly coupled with |
---|
| 1007 | # rec_submesh. |
---|
| 1008 | # |
---|
| 1009 | # ------------------------------------------------------- |
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| 1010 | # |
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| 1011 | # *) All of the information has been sent to processor p. |
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| 1012 | # |
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| 1013 | ######################################################### |
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| 1014 | |
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| 1015 | def send_submesh(submesh, triangles_per_proc, p, verbose=True): |
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| 1016 | |
---|
| 1017 | import pypar |
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| 1018 | |
---|
| 1019 | myid = pypar.rank() |
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| 1020 | |
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| 1021 | if verbose: print 'process %d sending submesh to process %d' %(myid, p) |
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| 1022 | |
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| 1023 | # build and send the tagmap for the boundary conditions |
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| 1024 | |
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| 1025 | tagmap = {} |
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| 1026 | counter = 1 |
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| 1027 | for b in submesh["full_boundary"][p]: |
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| 1028 | bkey = submesh["full_boundary"][p][b] |
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| 1029 | if not tagmap.has_key(bkey): |
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| 1030 | tagmap[bkey] = counter |
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| 1031 | counter = counter+1 |
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| 1032 | for b in submesh["ghost_boundary"][p]: |
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| 1033 | bkey = submesh["ghost_boundary"][p][b] |
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| 1034 | if not tagmap.has_key(bkey): |
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| 1035 | tagmap[bkey] = counter |
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| 1036 | counter = counter+1 |
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| 1037 | |
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| 1038 | pypar.send(tagmap, p) |
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| 1039 | |
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| 1040 | # send the quantities key information |
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| 1041 | |
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| 1042 | pypar.send(submesh["full_quan"].keys(), p) |
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| 1043 | |
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| 1044 | # send the number of triangles per processor |
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| 1045 | |
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| 1046 | pypar.send(triangles_per_proc, p) |
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| 1047 | |
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| 1048 | # compress full_commun |
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| 1049 | |
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| 1050 | flat_full_commun = [] |
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| 1051 | |
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| 1052 | for c in submesh["full_commun"][p]: |
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| 1053 | for i in range(len(submesh["full_commun"][p][c])): |
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| 1054 | flat_full_commun.append([c,submesh["full_commun"][p][c][i]]) |
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| 1055 | |
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| 1056 | # send the array sizes so memory can be allocated |
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| 1057 | |
---|
| 1058 | setup_array = num.zeros((9,),num.int) |
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| 1059 | setup_array[0] = len(submesh["full_nodes"][p]) |
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| 1060 | setup_array[1] = len(submesh["ghost_nodes"][p]) |
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| 1061 | setup_array[2] = len(submesh["full_triangles"][p]) |
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| 1062 | setup_array[3] = len(submesh["ghost_triangles"][p]) |
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| 1063 | setup_array[4] = len(submesh["full_boundary"][p]) |
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| 1064 | setup_array[5] = len(submesh["ghost_boundary"][p]) |
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| 1065 | setup_array[6] = len(submesh["ghost_commun"][p]) |
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| 1066 | setup_array[7] = len(flat_full_commun) |
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| 1067 | setup_array[8] = len(submesh["full_quan"]) |
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| 1068 | |
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| 1069 | pypar.send(num.array(setup_array, num.int), p) |
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| 1070 | |
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| 1071 | # send the nodes |
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| 1072 | |
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| 1073 | pypar.send(num.array(submesh["full_nodes"][p], num.float), p) |
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| 1074 | pypar.send(num.array(submesh["ghost_nodes"][p], num.float),p) |
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| 1075 | |
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| 1076 | # send the triangles |
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| 1077 | |
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| 1078 | pypar.send(num.array(submesh["full_triangles"][p], num.int), p) |
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| 1079 | pypar.send(num.array(submesh["ghost_triangles"][p], num.int), p) |
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| 1080 | |
---|
| 1081 | # send the boundary |
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| 1082 | |
---|
| 1083 | bc = [] |
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| 1084 | for b in submesh["full_boundary"][p]: |
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| 1085 | bc.append([b[0], b[1], tagmap[submesh["full_boundary"][p][b]]]) |
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| 1086 | |
---|
| 1087 | |
---|
| 1088 | pypar.send(num.array(bc, num.int), p) |
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| 1089 | |
---|
| 1090 | bc = [] |
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| 1091 | for b in submesh["ghost_boundary"][p]: |
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| 1092 | bc.append([b[0], b[1], tagmap[submesh["ghost_boundary"][p][b]]]) |
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| 1093 | |
---|
| 1094 | pypar.send(num.array(bc, num.int), p) |
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| 1095 | |
---|
| 1096 | # send the communication pattern |
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| 1097 | |
---|
| 1098 | pypar.send(submesh["ghost_commun"][p], p) |
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| 1099 | |
---|
| 1100 | pypar.send(num.array(flat_full_commun, num.int), p) |
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| 1101 | |
---|
| 1102 | # send the quantities |
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| 1103 | |
---|
| 1104 | for k in submesh["full_quan"]: |
---|
| 1105 | pypar.send(num.array(submesh["full_quan"][k][p], num.float), p) |
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| 1106 | |
---|
| 1107 | for k in submesh["ghost_quan"]: |
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| 1108 | pypar.send(num.array(submesh["ghost_quan"][k][p], num.float),p) |
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| 1109 | |
---|
| 1110 | |
---|
| 1111 | ######################################################### |
---|
| 1112 | # |
---|
| 1113 | # Receive the submesh from processor p. |
---|
| 1114 | # |
---|
| 1115 | # *) The order and form is strongly coupled with |
---|
| 1116 | # send_submesh. |
---|
| 1117 | # |
---|
| 1118 | # ------------------------------------------------------- |
---|
| 1119 | # |
---|
| 1120 | # *) All of the information has been received by the |
---|
| 1121 | # processor p and passed into build_local. |
---|
| 1122 | # |
---|
| 1123 | # *) The information is returned in a form needed by the |
---|
| 1124 | # GA datastructure. |
---|
| 1125 | # |
---|
| 1126 | ######################################################### |
---|
| 1127 | |
---|
| 1128 | def rec_submesh_flat(p, verbose=True): |
---|
| 1129 | |
---|
| 1130 | import pypar |
---|
| 1131 | |
---|
| 1132 | numproc = pypar.size() |
---|
| 1133 | myid = pypar.rank() |
---|
| 1134 | |
---|
| 1135 | submesh_cell = {} |
---|
| 1136 | |
---|
| 1137 | if verbose: print 'process %d receiving submesh from process %d' %(myid, p) |
---|
| 1138 | |
---|
| 1139 | # receive the tagmap for the boundary conditions |
---|
| 1140 | |
---|
| 1141 | tagmap = pypar.receive(p) |
---|
| 1142 | |
---|
| 1143 | itagmap = {} |
---|
| 1144 | for t in tagmap: |
---|
| 1145 | itagmap[tagmap[t]]=t |
---|
| 1146 | |
---|
| 1147 | # receive the quantities key information |
---|
| 1148 | |
---|
| 1149 | qkeys = pypar.receive(p) |
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| 1150 | |
---|
| 1151 | # receive the number of triangles per processor |
---|
| 1152 | |
---|
| 1153 | triangles_per_proc = pypar.receive(p) |
---|
| 1154 | |
---|
| 1155 | # recieve information about the array sizes |
---|
| 1156 | |
---|
| 1157 | setup_array = pypar.receive(p) |
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| 1158 | |
---|
| 1159 | no_full_nodes = setup_array[0] |
---|
| 1160 | no_ghost_nodes = setup_array[1] |
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| 1161 | no_full_triangles = setup_array[2] |
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| 1162 | no_ghost_triangles = setup_array[3] |
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| 1163 | no_full_boundary = setup_array[4] |
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| 1164 | no_ghost_boundary = setup_array[5] |
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| 1165 | no_ghost_commun = setup_array[6] |
---|
| 1166 | no_full_commun = setup_array[7] |
---|
| 1167 | no_quantities = setup_array[8] |
---|
| 1168 | |
---|
| 1169 | # receive the full nodes |
---|
| 1170 | |
---|
| 1171 | submesh_cell["full_nodes"] = pypar.receive(p) |
---|
| 1172 | |
---|
| 1173 | # receive the ghost nodes |
---|
| 1174 | |
---|
| 1175 | submesh_cell["ghost_nodes"] = pypar.receive(p) |
---|
| 1176 | |
---|
| 1177 | # receive the full triangles |
---|
| 1178 | |
---|
| 1179 | submesh_cell["full_triangles"] = pypar.receive(p) |
---|
| 1180 | |
---|
| 1181 | # receive the ghost triangles |
---|
| 1182 | |
---|
| 1183 | submesh_cell["ghost_triangles"] = pypar.receive(p) |
---|
| 1184 | |
---|
| 1185 | # receive the full boundary |
---|
| 1186 | |
---|
| 1187 | bnd_c = pypar.receive(p) |
---|
| 1188 | |
---|
| 1189 | submesh_cell["full_boundary"] = {} |
---|
| 1190 | for b in bnd_c: |
---|
| 1191 | submesh_cell["full_boundary"][b[0],b[1]]=itagmap[b[2]] |
---|
| 1192 | |
---|
| 1193 | # receive the ghost boundary |
---|
| 1194 | |
---|
| 1195 | bnd_c = pypar.receive(p) |
---|
| 1196 | |
---|
| 1197 | submesh_cell["ghost_boundary"] = {} |
---|
| 1198 | for b in bnd_c: |
---|
| 1199 | submesh_cell["ghost_boundary"][b[0],b[1]]=itagmap[b[2]] |
---|
| 1200 | |
---|
| 1201 | # receive the ghost communication pattern |
---|
| 1202 | |
---|
| 1203 | submesh_cell["ghost_commun"] = pypar.receive(p) |
---|
| 1204 | |
---|
| 1205 | # receive the full communication pattern |
---|
| 1206 | |
---|
| 1207 | full_commun = pypar.receive(p) |
---|
| 1208 | |
---|
| 1209 | submesh_cell["full_commun"] = {} |
---|
| 1210 | for c in full_commun: |
---|
| 1211 | submesh_cell["full_commun"][c[0]] = [] |
---|
| 1212 | for c in full_commun: |
---|
| 1213 | submesh_cell["full_commun"][c[0]].append(c[1]) |
---|
| 1214 | |
---|
| 1215 | # receive the quantities |
---|
| 1216 | |
---|
| 1217 | submesh_cell["full_quan"]={} |
---|
| 1218 | |
---|
| 1219 | for i in range(no_quantities): |
---|
| 1220 | tmp = pypar.receive(p) |
---|
| 1221 | submesh_cell["full_quan"][qkeys[i]]=num.zeros((no_full_triangles,3), num.float) |
---|
| 1222 | submesh_cell["full_quan"][qkeys[i]][:] = tmp[:] |
---|
| 1223 | |
---|
| 1224 | submesh_cell["ghost_quan"]={} |
---|
| 1225 | for i in range(no_quantities): |
---|
| 1226 | tmp = pypar.receive(p) |
---|
| 1227 | submesh_cell["ghost_quan"][qkeys[i]]= num.zeros((no_ghost_triangles,3), num.float) |
---|
| 1228 | submesh_cell["ghost_quan"][qkeys[i]][:] = tmp[:] |
---|
| 1229 | |
---|
| 1230 | return submesh_cell, triangles_per_proc,\ |
---|
| 1231 | no_full_nodes, no_full_triangles |
---|
| 1232 | |
---|
| 1233 | |
---|
| 1234 | |
---|
| 1235 | ######################################################### |
---|
| 1236 | # |
---|
| 1237 | # Receive the submesh from processor p. |
---|
| 1238 | # |
---|
| 1239 | # *) The order and form is strongly coupled with |
---|
| 1240 | # send_submesh. |
---|
| 1241 | # |
---|
| 1242 | # ------------------------------------------------------- |
---|
| 1243 | # |
---|
| 1244 | # *) All of the information has been received by the |
---|
| 1245 | # processor p and passed into build_local. |
---|
| 1246 | # |
---|
| 1247 | # *) The information is returned in a form needed by the |
---|
| 1248 | # GA datastructure. |
---|
| 1249 | # |
---|
| 1250 | ######################################################### |
---|
| 1251 | |
---|
| 1252 | def rec_submesh(p, verbose=True): |
---|
| 1253 | |
---|
| 1254 | import pypar |
---|
| 1255 | |
---|
| 1256 | numproc = pypar.size() |
---|
| 1257 | myid = pypar.rank() |
---|
| 1258 | |
---|
| 1259 | [submesh_cell, triangles_per_proc,\ |
---|
| 1260 | number_of_full_nodes, number_of_full_triangles] = rec_submesh_flat(p,verbose) |
---|
| 1261 | |
---|
| 1262 | # find the full triangles assigned to this processor |
---|
| 1263 | |
---|
| 1264 | lower_t = 0 |
---|
| 1265 | for i in range(myid): |
---|
| 1266 | lower_t = lower_t+triangles_per_proc[i] |
---|
| 1267 | upper_t = lower_t+triangles_per_proc[myid] |
---|
| 1268 | |
---|
| 1269 | # convert the information into a form needed by the GA |
---|
| 1270 | # datastructure |
---|
| 1271 | |
---|
| 1272 | [GAnodes, GAtriangles, boundary, quantities, ghost_rec, full_send] = \ |
---|
| 1273 | build_local_mesh(submesh_cell, lower_t, upper_t, \ |
---|
| 1274 | numproc) |
---|
| 1275 | |
---|
| 1276 | return GAnodes, GAtriangles, boundary, quantities,\ |
---|
| 1277 | ghost_rec, full_send,\ |
---|
| 1278 | number_of_full_nodes, number_of_full_triangles |
---|
| 1279 | |
---|
| 1280 | |
---|
| 1281 | ######################################################### |
---|
| 1282 | # |
---|
| 1283 | # Extract the submesh that will belong to the |
---|
| 1284 | # "host processor" (i.e. processor zero) |
---|
| 1285 | # |
---|
| 1286 | # *) See the documentation for build_submesh |
---|
| 1287 | # |
---|
| 1288 | # ------------------------------------------------------- |
---|
| 1289 | # |
---|
| 1290 | # *) A dictionary containing the full_triangles, |
---|
| 1291 | # full_nodes, full_boundary, ghost_triangles, ghost_nodes, |
---|
| 1292 | # ghost_boundary, ghost_commun and full_commun belonging |
---|
| 1293 | # to processor zero are returned. |
---|
| 1294 | # |
---|
| 1295 | ######################################################### |
---|
| 1296 | def extract_hostmesh(submesh, triangles_per_proc): |
---|
| 1297 | |
---|
| 1298 | |
---|
| 1299 | submesh_cell = {} |
---|
| 1300 | submesh_cell["full_nodes"] = submesh["full_nodes"][0] |
---|
| 1301 | submesh_cell["ghost_nodes"] = submesh["ghost_nodes"][0] |
---|
| 1302 | submesh_cell["full_triangles"] = submesh["full_triangles"][0] |
---|
| 1303 | submesh_cell["ghost_triangles"] = submesh["ghost_triangles"][0] |
---|
| 1304 | submesh_cell["full_boundary"] = submesh["full_boundary"][0] |
---|
| 1305 | submesh_cell["ghost_boundary"] = submesh["ghost_boundary"][0] |
---|
| 1306 | submesh_cell["ghost_commun"] = submesh["ghost_commun"][0] |
---|
| 1307 | submesh_cell["full_commun"] = submesh["full_commun"][0] |
---|
| 1308 | submesh_cell["full_quan"] ={} |
---|
| 1309 | submesh_cell["ghost_quan"]={} |
---|
| 1310 | for k in submesh["full_quan"]: |
---|
| 1311 | submesh_cell["full_quan"][k] = submesh["full_quan"][k][0] |
---|
| 1312 | submesh_cell["ghost_quan"][k] = submesh["ghost_quan"][k][0] |
---|
| 1313 | |
---|
| 1314 | numprocs = len(triangles_per_proc) |
---|
| 1315 | points, vertices, boundary, quantities, ghost_recv_dict, full_send_dict = \ |
---|
| 1316 | build_local_mesh(submesh_cell, 0, triangles_per_proc[0], numprocs) |
---|
| 1317 | |
---|
| 1318 | |
---|
| 1319 | return points, vertices, boundary, quantities, ghost_recv_dict, \ |
---|
| 1320 | full_send_dict |
---|
| 1321 | |
---|
| 1322 | |
---|
| 1323 | |
---|
| 1324 | |
---|