| 1 | |
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| 2 | """Run parallel shallow water domain. |
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| 3 | |
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| 4 | run using command like: |
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| 5 | |
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| 6 | mpirun -np m python run_parallel_sw_merimbula.py |
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| 7 | |
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| 8 | where m is the number of processors to be used. |
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| 9 | |
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| 10 | Will produce sww files with names domain_Pn_m.sww where m is number of processors and |
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| 11 | n in [0, m-1] refers to specific processor that owned this part of the partitioned mesh. |
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| 12 | """ |
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| 13 | |
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| 14 | #------------------------------------------------------------------------------ |
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| 15 | # Import necessary modules |
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| 16 | #------------------------------------------------------------------------------ |
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| 17 | |
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| 18 | import os |
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| 19 | import sys |
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| 20 | import time |
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| 21 | import pypar |
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| 22 | import numpy as num |
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| 23 | import unittest |
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| 24 | import tempfile |
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| 25 | from struct import pack, unpack |
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| 26 | from Scientific.IO.NetCDF import NetCDFFile |
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| 27 | import copy |
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| 28 | |
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| 29 | #------------------------ |
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| 30 | # ANUGA Modules |
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| 31 | #------------------------ |
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| 32 | from anuga.utilities.numerical_tools import ensure_numeric |
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| 33 | from anuga.utilities.util_ext import double_precision |
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| 34 | from anuga.utilities.norms import l1_norm, l2_norm, linf_norm |
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| 35 | |
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| 36 | from anuga import Domain |
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| 37 | from anuga import Reflective_boundary |
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| 38 | from anuga import Dirichlet_boundary |
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| 39 | from anuga import Time_boundary |
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| 40 | from anuga import Transmissive_boundary |
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| 41 | from anuga import File_boundary |
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| 42 | |
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| 43 | from mux import WAVEHEIGHT_MUX2_LABEL, EAST_VELOCITY_MUX2_LABEL, \ |
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| 44 | NORTH_VELOCITY_MUX2_LABEL |
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| 45 | from mux import read_mux2_py |
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| 46 | from anuga.file_conversion.urs2sts import urs2sts |
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| 47 | from anuga.file.urs import Read_urs |
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| 48 | from anuga.file.sts import create_sts_boundary |
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| 49 | |
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| 50 | from anuga.utilities.numerical_tools import ensure_numeric |
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| 51 | from anuga.coordinate_transforms.redfearn import redfearn |
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| 52 | from anuga.coordinate_transforms.geo_reference import Geo_reference |
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| 53 | |
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| 54 | from anuga import rectangular_cross_domain |
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| 55 | from anuga.pmesh.mesh_interface import create_mesh_from_regions |
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| 56 | from anuga import create_domain_from_file |
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| 57 | |
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| 58 | from anuga_parallel import distribute, myid, numprocs, send, receive, barrier, finalize |
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| 59 | |
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| 60 | from anuga.file.test_mux import Test_Mux |
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| 61 | |
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| 62 | class Test_urs2sts_parallel(Test_Mux): |
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| 63 | """ A suite of tests to test urs2sts file conversion functions. |
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| 64 | These tests are quite coarse-grained: converting a file |
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| 65 | and checking that its headers and some of its contents |
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| 66 | are correct. |
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| 67 | """ |
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| 68 | |
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| 69 | def sequential_test_time_varying_file_boundary_sts(self): |
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| 70 | """sequential_ltest_time_varying_file_boundary_sts_sequential(self): |
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| 71 | Read correct points from ordering file and apply sts to boundary. The boundary is time varying. FIXME add to test_urs2sts. |
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| 72 | """ |
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| 73 | lat_long_points=[[6.01,97.0],[6.02,97.0],[6.05,96.9],[6.0,97.0]] |
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| 74 | bounding_polygon=[[6.0,97.0],[6.01,97.0],[6.02,97.0], |
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| 75 | [6.02,97.02],[6.00,97.02]] |
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| 76 | tide = 3.0 |
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| 77 | time_step_count = 65 |
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| 78 | time_step = 2. |
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| 79 | n=len(lat_long_points) |
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| 80 | first_tstep=num.ones(n,num.int) |
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| 81 | last_tstep=(time_step_count)*num.ones(n,num.int) |
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| 82 | finaltime=num.float(time_step*(time_step_count-1)) |
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| 83 | yieldstep=num.float(time_step) |
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| 84 | gauge_depth=20*num.ones(n,num.float) |
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| 85 | ha=2*num.ones((n,time_step_count),num.float) |
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| 86 | ua=10*num.ones((n,time_step_count),num.float) |
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| 87 | va=-10*num.ones((n,time_step_count),num.float) |
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| 88 | |
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| 89 | times=num.arange(0., num.float(time_step_count*time_step), time_step) |
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| 90 | for i in range(n): |
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| 91 | #ha[i]+=num.sin(times) |
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| 92 | ha[i]+=times/finaltime |
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| 93 | |
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| 94 | |
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| 95 | |
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| 96 | sts_file="test" |
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| 97 | if myid==0: |
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| 98 | base_name, files = self.write_mux2(lat_long_points, |
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| 99 | time_step_count, |
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| 100 | time_step, |
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| 101 | first_tstep, |
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| 102 | last_tstep, |
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| 103 | depth=gauge_depth, |
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| 104 | ha=ha, |
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| 105 | ua=ua, |
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| 106 | va=va) |
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| 107 | # base name will not exist, but 3 other files are created |
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| 108 | |
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| 109 | # Write order file |
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| 110 | file_handle, order_base_name = tempfile.mkstemp("") |
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| 111 | os.close(file_handle) |
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| 112 | os.remove(order_base_name) |
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| 113 | d="," |
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| 114 | order_file=order_base_name+'order.txt' |
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| 115 | fid=open(order_file,'w') |
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| 116 | |
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| 117 | # Write Header |
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| 118 | header='index, longitude, latitude\n' |
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| 119 | fid.write(header) |
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| 120 | indices=[3,0,1] |
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| 121 | for i in indices: |
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| 122 | line=str(i)+d+str(lat_long_points[i][1])+d+\ |
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| 123 | str(lat_long_points[i][0])+"\n" |
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| 124 | fid.write(line) |
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| 125 | fid.close() |
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| 126 | |
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| 127 | urs2sts(base_name, |
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| 128 | basename_out=sts_file, |
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| 129 | ordering_filename=order_file, |
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| 130 | mean_stage=tide, |
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| 131 | verbose=False) |
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| 132 | self.delete_mux(files) |
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| 133 | |
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| 134 | assert(os.access(sts_file+'.sts', os.F_OK)) |
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| 135 | |
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| 136 | os.remove(order_file) |
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| 137 | |
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| 138 | barrier() |
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| 139 | boundary_polygon = create_sts_boundary(sts_file) |
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| 140 | |
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| 141 | # Append the remaining part of the boundary polygon to be defined by |
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| 142 | # the user |
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| 143 | bounding_polygon_utm=[] |
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| 144 | for point in bounding_polygon: |
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| 145 | zone,easting,northing=redfearn(point[0],point[1]) |
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| 146 | bounding_polygon_utm.append([easting,northing]) |
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| 147 | |
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| 148 | boundary_polygon.append(bounding_polygon_utm[3]) |
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| 149 | boundary_polygon.append(bounding_polygon_utm[4]) |
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| 150 | |
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| 151 | assert num.allclose(bounding_polygon_utm,boundary_polygon) |
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| 152 | |
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| 153 | |
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| 154 | extent_res=1000000 |
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| 155 | meshname = 'urs_test_mesh' + '.tsh' |
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| 156 | interior_regions=None |
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| 157 | boundary_tags={'ocean': [0,1], 'otherocean': [2,3,4]} |
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| 158 | |
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| 159 | # have to change boundary tags from last example because now bounding |
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| 160 | # polygon starts in different place. |
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| 161 | if myid==0: |
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| 162 | create_mesh_from_regions(boundary_polygon, |
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| 163 | boundary_tags=boundary_tags, |
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| 164 | maximum_triangle_area=extent_res, |
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| 165 | filename=meshname, |
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| 166 | interior_regions=interior_regions, |
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| 167 | verbose=True) |
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| 168 | |
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| 169 | barrier() |
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| 170 | |
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| 171 | domain_fbound = Domain(meshname) |
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| 172 | domain_fbound.set_quantities_to_be_stored(None) |
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| 173 | domain_fbound.set_quantity('stage', tide) |
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| 174 | if verbose: print "Creating file boundary condition" |
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| 175 | Bf = File_boundary(sts_file+'.sts', |
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| 176 | domain_fbound, |
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| 177 | boundary_polygon=boundary_polygon) |
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| 178 | Br = Reflective_boundary(domain_fbound) |
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| 179 | |
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| 180 | domain_fbound.set_boundary({'ocean': Bf,'otherocean': Br}) |
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| 181 | |
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| 182 | temp_fbound=num.zeros(int(finaltime/yieldstep)+1,num.float) |
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| 183 | if verbose: print "Evolving domain with file boundary condition" |
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| 184 | for i, t in enumerate(domain_fbound.evolve(yieldstep=yieldstep, |
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| 185 | finaltime=finaltime, |
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| 186 | skip_initial_step = False)): |
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| 187 | temp_fbound[i]=domain_fbound.quantities['stage'].centroid_values[2] |
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| 188 | if verbose: domain_fbound.write_time() |
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| 189 | |
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| 190 | |
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| 191 | domain_drchlt = Domain(meshname) |
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| 192 | domain_drchlt.set_quantities_to_be_stored(None) |
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| 193 | domain_drchlt.set_starttime(time_step) |
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| 194 | domain_drchlt.set_quantity('stage', tide) |
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| 195 | Br = Reflective_boundary(domain_drchlt) |
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| 196 | #Bd = Dirichlet_boundary([2.0+tide,220+10*tide,-220-10*tide]) |
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| 197 | Bd = Time_boundary(domain=domain_drchlt, f=lambda t: [2.0+t/finaltime+tide,220.+10.*tide+10.*t/finaltime,-220.-10.*tide-10.*t/finaltime]) |
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| 198 | #Bd = Time_boundary(domain=domain_drchlt,f=lambda t: [2.0+num.sin(t)+tide,10.*(2+20.+num.sin(t)+tide),-10.*(2+20.+num.sin(t)+tide)]) |
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| 199 | domain_drchlt.set_boundary({'ocean': Bd,'otherocean': Br}) |
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| 200 | temp_drchlt=num.zeros(int(finaltime/yieldstep)+1,num.float) |
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| 201 | |
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| 202 | for i, t in enumerate(domain_drchlt.evolve(yieldstep=yieldstep, |
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| 203 | finaltime=finaltime, |
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| 204 | skip_initial_step = False)): |
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| 205 | temp_drchlt[i]=domain_drchlt.quantities['stage'].centroid_values[2] |
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| 206 | #domain_drchlt.write_time() |
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| 207 | |
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| 208 | #print domain_fbound.quantities['stage'].vertex_values |
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| 209 | #print domain_drchlt.quantities['stage'].vertex_values |
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| 210 | |
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| 211 | assert num.allclose(temp_fbound,temp_drchlt),temp_fbound-temp_drchlt |
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| 212 | |
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| 213 | |
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| 214 | assert num.allclose(domain_fbound.quantities['stage'].vertex_values, |
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| 215 | domain_drchlt.quantities['stage'].vertex_values) |
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| 216 | |
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| 217 | assert num.allclose(domain_fbound.quantities['xmomentum'].vertex_values, |
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| 218 | domain_drchlt.quantities['xmomentum'].vertex_values) |
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| 219 | |
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| 220 | assert num.allclose(domain_fbound.quantities['ymomentum'].vertex_values, |
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| 221 | domain_drchlt.quantities['ymomentum'].vertex_values) |
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| 222 | |
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| 223 | if not sys.platform == 'win32': |
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| 224 | if myid==0: os.remove(sts_file+'.sts') |
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| 225 | |
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| 226 | if myid==0: os.remove(meshname) |
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| 227 | |
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| 228 | def parallel_test_time_varying_file_boundary_sts(self): |
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| 229 | """ parallel_test_time_varying_file_boundary_sts_sequential(self): |
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| 230 | Read correct points from ordering file and apply sts to boundary. |
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| 231 | The boundary is time varying. Compares sequential result with |
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| 232 | distributed result found using anuga_parallel |
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| 233 | """ |
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| 234 | |
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| 235 | #------------------------------------------------------------ |
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| 236 | # Define test variables |
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| 237 | #------------------------------------------------------------ |
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| 238 | lat_long_points=[[6.01,97.0],[6.02,97.0],[6.05,96.9],[6.0,97.0]] |
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| 239 | bounding_polygon=[[6.0,97.0],[6.01,97.0],[6.02,97.0], |
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| 240 | [6.02,97.02],[6.00,97.02]] |
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| 241 | tide = 3.0 |
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| 242 | time_step_count = 65 |
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| 243 | time_step = 2 |
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| 244 | n=len(lat_long_points) |
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| 245 | first_tstep=num.ones(n,num.int) |
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| 246 | last_tstep=(time_step_count)*num.ones(n,num.int) |
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| 247 | finaltime=num.float(time_step*(time_step_count-1)) |
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| 248 | yieldstep=num.float(time_step) |
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| 249 | gauge_depth=20*num.ones(n,num.float) |
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| 250 | ha=2*num.ones((n,time_step_count),num.float) |
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| 251 | ua=10*num.ones((n,time_step_count),num.float) |
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| 252 | va=-10*num.ones((n,time_step_count),num.float) |
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| 253 | |
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| 254 | times=num.arange(0, time_step_count*time_step, time_step) |
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| 255 | for i in range(n): |
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| 256 | #ha[i]+=num.sin(times) |
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| 257 | ha[i]+=times/finaltime |
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| 258 | |
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| 259 | #------------------------------------------------------------ |
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| 260 | # Write mux data to file then convert to sts format |
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| 261 | #------------------------------------------------------------ |
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| 262 | sts_file="test" |
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| 263 | if myid==0: |
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| 264 | base_name, files = self.write_mux2(lat_long_points, |
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| 265 | time_step_count, |
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| 266 | time_step, |
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| 267 | first_tstep, |
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| 268 | last_tstep, |
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| 269 | depth=gauge_depth, |
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| 270 | ha=ha, |
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| 271 | ua=ua, |
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| 272 | va=va) |
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| 273 | # base name will not exist, but 3 other files are created |
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| 274 | |
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| 275 | # Write order file |
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| 276 | file_handle, order_base_name = tempfile.mkstemp("") |
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| 277 | os.close(file_handle) |
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| 278 | os.remove(order_base_name) |
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| 279 | d="," |
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| 280 | order_file=order_base_name+'order.txt' |
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| 281 | fid=open(order_file,'w') |
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| 282 | |
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| 283 | # Write Header |
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| 284 | header='index, longitude, latitude\n' |
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| 285 | fid.write(header) |
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| 286 | indices=[3,0,1] |
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| 287 | for i in indices: |
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| 288 | line=str(i)+d+str(lat_long_points[i][1])+d+\ |
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| 289 | str(lat_long_points[i][0])+"\n" |
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| 290 | fid.write(line) |
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| 291 | fid.close() |
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| 292 | |
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| 293 | urs2sts(base_name, |
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| 294 | basename_out=sts_file, |
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| 295 | ordering_filename=order_file, |
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| 296 | mean_stage=tide, |
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| 297 | verbose=False) |
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| 298 | self.delete_mux(files) |
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| 299 | |
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| 300 | assert(os.access(sts_file+'.sts', os.F_OK)) |
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| 301 | |
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| 302 | os.remove(order_file) |
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| 303 | |
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| 304 | barrier() |
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| 305 | #------------------------------------------------------------ |
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| 306 | # Define boundary_polygon on each processor. This polygon defines the |
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| 307 | # urs boundary and lies on a portion of the bounding_polygon |
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| 308 | #------------------------------------------------------------ |
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| 309 | boundary_polygon = create_sts_boundary(sts_file) |
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| 310 | |
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| 311 | # Append the remaining part of the boundary polygon to be defined by |
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| 312 | # the user |
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| 313 | bounding_polygon_utm=[] |
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| 314 | for point in bounding_polygon: |
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| 315 | zone,easting,northing=redfearn(point[0],point[1]) |
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| 316 | bounding_polygon_utm.append([easting,northing]) |
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| 317 | |
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| 318 | boundary_polygon.append(bounding_polygon_utm[3]) |
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| 319 | boundary_polygon.append(bounding_polygon_utm[4]) |
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| 320 | |
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| 321 | |
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| 322 | assert num.allclose(bounding_polygon_utm,boundary_polygon) |
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| 323 | |
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| 324 | extent_res=10000 |
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| 325 | meshname = 'urs_test_mesh' + '.tsh' |
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| 326 | interior_regions=None |
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| 327 | boundary_tags={'ocean': [0,1], 'otherocean': [2,3,4]} |
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| 328 | |
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| 329 | #------------------------------------------------------------ |
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| 330 | # Create mesh on the master processor and store in file. This file |
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| 331 | # is read in by each slave processor when needed |
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| 332 | #------------------------------------------------------------ |
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| 333 | if myid==0: |
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| 334 | create_mesh_from_regions(boundary_polygon, |
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| 335 | boundary_tags=boundary_tags, |
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| 336 | maximum_triangle_area=extent_res, |
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| 337 | filename=meshname, |
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| 338 | interior_regions=interior_regions, |
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| 339 | verbose=True) |
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| 340 | |
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| 341 | |
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| 342 | # barrier() |
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| 343 | domain_fbound = Domain(meshname) |
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| 344 | domain_fbound.set_quantities_to_be_stored(None) |
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| 345 | domain_fbound.set_quantity('stage', tide) |
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| 346 | # print domain_fbound.mesh.get_boundary_polygon() |
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| 347 | else: |
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| 348 | domain_fbound=None |
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| 349 | |
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| 350 | barrier() |
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| 351 | if ( verbose and myid == 0 ): |
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| 352 | print 'DISTRIBUTING PARALLEL DOMAIN' |
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| 353 | domain_fbound = distribute(domain_fbound) |
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| 354 | |
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| 355 | #-------------------------------------------------------------------- |
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| 356 | # Find which sub_domain in which the interpolation points are located |
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| 357 | # |
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| 358 | # Sometimes the interpolation points sit exactly |
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| 359 | # between two centroids, so in the parallel run we |
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| 360 | # reset the interpolation points to the centroids |
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| 361 | # found in the sequential run |
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| 362 | #-------------------------------------------------------------------- |
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| 363 | interpolation_points = [[279000,664000], [280250,664130], |
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| 364 | [279280,665400], [280500,665000]] |
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| 365 | |
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| 366 | interpolation_points=num.array(interpolation_points) |
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| 367 | |
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| 368 | #if myid==0: |
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| 369 | # import pylab as P |
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| 370 | # boundary_polygon=num.array(boundary_polygon) |
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| 371 | # P.plot(boundary_polygon[:,0],boundary_polygon[:,1]) |
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| 372 | # P.plot(interpolation_points[:,0],interpolation_points[:,1],'ko') |
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| 373 | # P.show() |
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| 374 | |
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| 375 | fbound_gauge_values = [] |
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| 376 | fbound_proc_tri_ids = [] |
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| 377 | for i, point in enumerate(interpolation_points): |
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| 378 | fbound_gauge_values.append([]) # Empty list for timeseries |
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| 379 | |
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| 380 | try: |
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| 381 | k = domain_fbound.get_triangle_containing_point(point) |
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| 382 | if domain_fbound.tri_full_flag[k] == 1: |
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| 383 | fbound_proc_tri_ids.append(k) |
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| 384 | else: |
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| 385 | fbound_proc_tri_ids.append(-1) |
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| 386 | except: |
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| 387 | fbound_proc_tri_ids.append(-2) |
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| 388 | |
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| 389 | |
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| 390 | if verbose: print 'P%d has points = %s' %(myid, fbound_proc_tri_ids) |
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| 391 | |
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| 392 | #------------------------------------------------------------ |
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| 393 | # Set boundary conditions |
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| 394 | #------------------------------------------------------------ |
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| 395 | Bf = File_boundary(sts_file+'.sts', |
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| 396 | domain_fbound, |
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| 397 | boundary_polygon=boundary_polygon) |
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| 398 | Br = Reflective_boundary(domain_fbound) |
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| 399 | |
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| 400 | domain_fbound.set_boundary({'ocean': Bf,'otherocean': Br}) |
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| 401 | |
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| 402 | #------------------------------------------------------------ |
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| 403 | # Evolve the domain on each processor |
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| 404 | #------------------------------------------------------------ |
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| 405 | for i, t in enumerate(domain_fbound.evolve(yieldstep=yieldstep, |
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| 406 | finaltime=finaltime, |
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| 407 | skip_initial_step = False)): |
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| 408 | |
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| 409 | stage = domain_fbound.get_quantity('stage') |
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| 410 | for i in range(4): |
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| 411 | if fbound_proc_tri_ids[i] > -1: |
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| 412 | fbound_gauge_values[i].append(stage.centroid_values[fbound_proc_tri_ids[i]]) |
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| 413 | |
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| 414 | #------------------------------------------------------------ |
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| 415 | # Create domain to be run sequntially on each processor |
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| 416 | #------------------------------------------------------------ |
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| 417 | domain_drchlt = Domain(meshname) |
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| 418 | domain_drchlt.set_quantities_to_be_stored(None) |
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| 419 | domain_drchlt.set_starttime(time_step) |
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| 420 | domain_drchlt.set_quantity('stage', tide) |
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| 421 | Br = Reflective_boundary(domain_drchlt) |
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| 422 | #Bd = Dirichlet_boundary([2.0+tide,220+10*tide,-220-10*tide]) |
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| 423 | Bd = Time_boundary(domain=domain_drchlt, function=lambda t: [2.0+t/finaltime+tide,220.+10.*tide+10.*t/finaltime,-220.-10.*tide-10.*t/finaltime]) |
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| 424 | #Bd = Time_boundary(domain=domain_drchlt,function=lambda t: [2.0+num.sin(t)+tide,10.*(2+20.+num.sin(t)+tide),-10.*(2+20.+num.sin(t)+tide)]) |
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| 425 | domain_drchlt.set_boundary({'ocean': Bd,'otherocean': Br}) |
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| 426 | |
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| 427 | drchlt_gauge_values = [] |
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| 428 | drchlt_proc_tri_ids = [] |
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| 429 | for i, point in enumerate(interpolation_points): |
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| 430 | drchlt_gauge_values.append([]) # Empty list for timeseries |
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| 431 | |
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| 432 | try: |
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| 433 | k = domain_drchlt.get_triangle_containing_point(point) |
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| 434 | if domain_drchlt.tri_full_flag[k] == 1: |
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| 435 | drchlt_proc_tri_ids.append(k) |
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| 436 | else: |
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| 437 | drchlt_proc_tri_ids.append(-1) |
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| 438 | except: |
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| 439 | drchlt_proc_tri_ids.append(-2) |
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| 440 | |
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| 441 | |
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| 442 | if verbose: print 'P%d has points = %s' %(myid, drchlt_proc_tri_ids) |
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| 443 | |
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| 444 | #------------------------------------------------------------ |
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| 445 | # Evolve entire domain on each processor |
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| 446 | #------------------------------------------------------------ |
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| 447 | for i, t in enumerate(domain_drchlt.evolve(yieldstep=yieldstep, |
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| 448 | finaltime=finaltime, |
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| 449 | skip_initial_step = False)): |
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| 450 | |
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| 451 | stage = domain_drchlt.get_quantity('stage') |
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| 452 | for i in range(4): |
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| 453 | drchlt_gauge_values[i].append(stage.centroid_values[drchlt_proc_tri_ids[i]]) |
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| 454 | |
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| 455 | #------------------------------------------------------------ |
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| 456 | # Compare sequential values with parallel values |
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| 457 | #------------------------------------------------------------ |
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| 458 | barrier() |
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| 459 | success = True |
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| 460 | for i in range(4): |
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| 461 | if fbound_proc_tri_ids[i] > -1: |
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| 462 | fbound_gauge_values[i]=num.array(fbound_gauge_values[i]) |
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| 463 | drchlt_gauge_values[i]=num.array(drchlt_gauge_values[i]) |
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| 464 | #print i,fbound_gauge_values[i][4] |
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| 465 | #print i,drchlt_gauge_values[i][4] |
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| 466 | success = success and num.allclose(fbound_gauge_values[i], drchlt_gauge_values[i]) |
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| 467 | assert success#, (fbound_gauge_values[i]-drchlt_gauge_values[i]) |
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| 468 | |
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| 469 | #assert_(success) |
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| 470 | |
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| 471 | if not sys.platform == 'win32': |
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| 472 | if myid==0: os.remove(sts_file+'.sts') |
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| 473 | |
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| 474 | if myid==0: os.remove(meshname) |
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| 475 | |
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| 476 | # Because we are doing assertions outside of the TestCase class |
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| 477 | # the PyUnit defined assert_ function can't be used. |
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| 478 | def assert_(condition, msg="Assertion Failed"): |
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| 479 | if condition == False: |
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| 480 | #pypar.finalize() |
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| 481 | raise AssertionError, msg |
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| 482 | |
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| 483 | |
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| 484 | # Test an nprocs-way run of the shallow water equations |
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| 485 | # against the sequential code. |
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| 486 | |
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| 487 | if __name__=="__main__": |
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| 488 | verbose=True |
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| 489 | if myid ==0 and verbose: |
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| 490 | print 'PARALLEL START' |
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| 491 | suite = unittest.makeSuite(Test_urs2sts_parallel,'parallel_test') |
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| 492 | #suite = unittest.makeSuite(Test_urs2sts_parallel,'sequential_test') |
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| 493 | runner = unittest.TextTestRunner() |
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| 494 | runner.run(suite) |
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| 495 | |
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| 496 | #------------------------------------------ |
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| 497 | # Run the code code and compare sequential |
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| 498 | # results at 4 gauge stations |
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| 499 | #------------------------------------------ |
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| 500 | |
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| 501 | |
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| 502 | finalize() |
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