Changeset 2906

Timestamp:

May 18, 2006, 11:45:48 AM (18 years ago)

Author:

linda

Message:

Made correction to the parallel report

Location:

inundation/parallel

Files:

• build_submesh.py (modified) (4 diffs)
• documentation/code/RunParallelAdvection.py (modified) (1 diff)
• documentation/code/RunParallelMerimbulaMetis.py (modified) (4 diffs)
• documentation/code/RunParallelSwMerimbulaMetis.py (modified) (3 diffs)
• documentation/figures/domain.eps (modified) (previous)
• documentation/figures/domain.fig (modified) (2 diffs)
• documentation/figures/subdomain.eps (modified) (previous)
• documentation/figures/subdomain.fig (modified) (2 diffs)
• documentation/figures/subdomainfinal.eps (modified) (previous)
• documentation/figures/subdomainfinal.fig (modified) (3 diffs)
• documentation/figures/subdomainghost.eps (modified) (previous)
• documentation/figures/subdomainghost.fig (modified) (2 diffs)
• documentation/parallel.tex (modified) (12 diffs)
• print_stats.py (modified) (1 diff)
• run_parallel_sw_merimbula_test.py (modified) (3 diffs)

inundation/parallel/build_submesh.py

@@ -13 +13 @@
 
 import sys
+import pypar    # The Python-MPI interface
 
 from Numeric import zeros, Float, Int, concatenate, \
@@ -18 +19 @@
 
 from mesh import Mesh
+
 
 
@@ -553 +555 @@
 #
 #########################################################
-def extract_hostmesh(submesh):
+def extract_hostmesh(submesh, triangles_per_proc):
 
     submesh_cell = {}
@@ -570 +572 @@
         submesh_cell["ghost_quan"][k] = submesh["ghost_quan"][k][0]
 
-    return submesh_cell
-
+    numprocs = pypar.size()
+    points, vertices, boundary, quantities, ghost_recv_dict, full_send_dict = \
+            build_local_mesh(submesh_cell, 0, triangles_per_proc[0], numprocs)
+    return  points, vertices, boundary, quantities, ghost_recv_dict, \
+           full_send_dict
+

inundation/parallel/documentation/code/RunParallelAdvection.py

@@ -58 +58 @@
 
 #######################
-# Partition the domain
+# Partition the mesh
 #######################
 

inundation/parallel/documentation/code/RunParallelMerimbulaMetis.py

@@ -89 +89 @@
     filename = 'merimbula_10785.tsh'
 
-    domain_full = pmesh_to_domain_instance(filename, Advection_Domain)
-    domain_full.set_quantity('stage', Set_Stage(756000.0,756500.0,4.0))
+    mesh_full = pmesh_to_domain_instance(filename, Advection_Domain)
+    mesh_full.set_quantity('stage', Set_Stage(756000.0,756500.0,4.0))
 
     # Define the domain boundaries for visualisation
    
-    rect = array(domain_full.xy_extent, Float)
+    rect = array(mesh_full.xy_extent, Float)
 
     # Subdivide the mesh
 
     nodes, triangles, boundary, triangles_per_proc, quantities  =\
-            pmesh_divide_metis(domain_full, numprocs)
+            pmesh_divide_metis(mesh_full, numprocs)
 
     # Build the mesh that should be assigned to each processor,
@@ -114 +114 @@
     # Build the local mesh for processor 0
 
-    hostmesh = extract_hostmesh(submesh)
-    points, vertices, boundary, quantities, ghost_recv_dict, full_send_dict = \
-             build_local_mesh(hostmesh, 0, triangles_per_proc[0], numprocs)
+     points, vertices, boundary, quantities, ghost_recv_dict, full_send_dict =\
+             extract_hostmesh(submesh, triangles_per_proc)
+
 
 else:
@@ -145 +145 @@
 try:
     domain.initialise_visualiser(rect=rect)
-    #domain.visualiser.coloring['stage'] = True
-    #domain.visualiser.scale_z['stage'] = 0.2
 except:
     print 'No visualiser'
@@ -153 +151 @@
 
 T = Transmissive_boundary(domain)
-#R = Reflective_boundary(domain)
 domain.set_boundary( {'outflow': T, 'inflow': T, 'inner':T, \
                       'exterior': T, 'open':T, 'ghost':None} )
 
 # Set the initial quantities
-
 
 domain.set_quantity('stage', quantities['stage'])

inundation/parallel/documentation/code/RunParallelSwMerimbulaMetis.py

@@ -75 +75 @@
 
 #######################
-# Partition the domain
+# Partition the mesh
 #######################
 
@@ -84 +84 @@
     filename = 'merimbula_10785_1.tsh'
 
-    # Build the whole domain
+    # Build the whole mesh
     
-    domain_full = pmesh_to_domain_instance(filename, Domain)
+    mesh_full = pmesh_to_domain_instance(filename, Domain)
 
     # Define the domain boundaries for visualisation
 
-    rect = array(domain_full.xy_extent, Float)
+    rect = array(mesh_full.xy_extent, Float)
 
     # Initialise the wave
 
-    domain_full.set_quantity('stage', Set_Stage(756000.0,756500.0,2.0))
+    mesh_full.set_quantity('stage', Set_Stage(756000.0,756500.0,2.0))
 
     # Subdivide the mesh
     
     nodes, triangles, boundary, triangles_per_proc, quantities = \
-         pmesh_divide_metis(domain_full, numprocs)
+         pmesh_divide_metis(mesh_full, numprocs)
 
     # Build the mesh that should be assigned to each processor,
@@ -113 +113 @@
 
     # Build the local mesh for processor 0
-
-    hostmesh = extract_hostmesh(submesh)
+    
     points, vertices, boundary, quantities, ghost_recv_dict, full_send_dict = \
-             build_local_mesh(hostmesh, 0, triangles_per_proc[0], numprocs)
+              extract_hostmesh(submesh, triangles_per_proc)
 
 else:

inundation/parallel/documentation/figures/domain.fig

@@ -11 +11 @@
 2 2 0 2 0 7 50 -1 -1 0.000 0 0 -1 0 0 5
          7110 3870 8955 3870 8955 4500 7110 4500 7110 3870
-4 0 0 50 -1 0 16 0.0000 4 180 1290 7380 4140 Build Local\001
-4 0 0 50 -1 0 16 0.0000 4 180 600 7380 4410 Mesh\001
+4 0 0 50 -1 0 16 0.0000 4 195 1275 7380 4140 Build Local\001
+4 0 0 50 -1 0 16 0.0000 4 195 615 7380 4410 Mesh\001
 -6
 6 8010 2745 8145 3420
-4 0 0 50 -1 0 24 0.0000 4 45 105 8010 2790 .\001
-4 0 0 50 -1 0 24 0.0000 4 45 105 8010 2970 .\001
-4 0 0 50 -1 0 24 0.0000 4 45 105 8010 3195 .\001
-4 0 0 50 -1 0 24 0.0000 4 45 105 8010 3420 .\001
+4 0 0 50 -1 0 24 0.0000 4 30 90 8010 2790 .\001
+4 0 0 50 -1 0 24 0.0000 4 30 90 8010 2970 .\001
+4 0 0 50 -1 0 24 0.0000 4 30 90 8010 3195 .\001
+4 0 0 50 -1 0 24 0.0000 4 30 90 8010 3420 .\001
 -6
 6 7065 1755 9000 2475
 2 2 0 2 0 7 50 -1 -1 0.000 0 0 -1 0 0 5
          7110 1800 8955 1800 8955 2430 7110 2430 7110 1800
-4 0 0 50 -1 0 16 0.0000 4 180 1290 7380 2070 Build Local\001
-4 0 0 50 -1 0 16 0.0000 4 180 600 7380 2340 Mesh\001
+4 0 0 50 -1 0 16 0.0000 4 195 1275 7380 2070 Build Local\001
+4 0 0 50 -1 0 16 0.0000 4 195 615 7380 2340 Mesh\001
 -6
 6 9585 2700 9720 3375
-4 0 0 50 -1 0 24 0.0000 4 45 105 9585 2745 .\001
-4 0 0 50 -1 0 24 0.0000 4 45 105 9585 2925 .\001
-4 0 0 50 -1 0 24 0.0000 4 45 105 9585 3150 .\001
-4 0 0 50 -1 0 24 0.0000 4 45 105 9585 3375 .\001
+4 0 0 50 -1 0 24 0.0000 4 30 90 9585 2745 .\001
+4 0 0 50 -1 0 24 0.0000 4 30 90 9585 2925 .\001
+4 0 0 50 -1 0 24 0.0000 4 30 90 9585 3150 .\001
+4 0 0 50 -1 0 24 0.0000 4 30 90 9585 3375 .\001
 -6
 2 2 0 2 0 7 50 -1 -1 0.000 0 0 -1 0 0 5
@@ -45 +45 @@
         1 1 3.00 120.00 120.00
          4950 3150 7065 4185
-4 0 0 50 -1 0 16 0.0000 4 180 1755 2925 3105 Build Commun.\001
-4 0 9 50 -1 0 16 0.0000 4 180 1260 3240 3870 Processor 0\001
-4 0 0 50 -1 0 16 0.0000 4 240 630 2925 3330 Layer\001
-4 0 9 50 -1 0 16 0.0000 4 180 1260 900 3870 Processor 0\001
-4 0 0 50 -1 0 16 0.0000 4 180 870 990 3375 Domain\001
-4 0 0 50 -1 0 16 0.0000 4 180 1095 990 3105 Subdivide\001
-4 0 9 50 -1 0 16 0.0000 4 180 1260 9135 4230 Processor 0\001
-4 0 12 50 -1 0 16 0.0000 4 180 1230 5670 3375 Subdomain\001
-4 0 12 50 -1 0 16 0.0000 4 180 540 5670 3060 Send\001
-4 0 9 50 -1 0 16 0.0000 4 240 1260 9135 2160 Processor p\001
+4 0 0 50 -1 0 16 0.0000 4 195 1770 2925 3105 Build Commun.\001
+4 0 9 50 -1 0 16 0.0000 4 195 1275 3240 3870 Processor 0\001
+4 0 0 50 -1 0 16 0.0000 4 255 630 2925 3330 Layer\001
+4 0 9 50 -1 0 16 0.0000 4 195 1275 900 3870 Processor 0\001
+4 0 9 50 -1 0 16 0.0000 4 195 1275 9135 4230 Processor 0\001
+4 0 12 50 -1 0 16 0.0000 4 195 555 5670 3060 Send\001
+4 0 9 50 -1 0 16 0.0000 4 255 1275 9135 2160 Processor p\001
+4 0 0 50 -1 0 16 0.0000 4 195 1095 990 3105 Subdivide\001
+4 0 0 50 -1 0 16 0.0000 4 195 615 990 3375 Mesh\001
+4 0 12 50 -1 0 16 0.0000 4 195 1020 5670 3375 Submesh\001

inundation/parallel/documentation/figures/subdomain.fig

@@ -8 +8 @@
 -2
 1200 2
-6 1575 1845 4725 4095
-2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 4
-         1980 2340 2880 3060 1575 3060 1980 2340
-2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 4
-         1980 2340 3150 2070 2880 3015 2880 3060
-2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 3
-         2880 3060 3285 4095 3960 2835
-2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 3
-         3150 2070 4725 1845 3960 2880
-2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 3
-         3960 2880 4545 4095 4725 1845
-2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
-         3285 4095 4545 4095
-2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 3
-         3150 2115 3960 2880 2880 3060
-4 0 0 50 -1 0 16 0.0000 4 180 135 3870 2295 4\001
-4 0 0 50 -1 0 16 0.0000 4 195 135 3915 3690 6\001
-4 0 0 50 -1 0 16 0.0000 4 180 135 4365 2970 7\001
-4 0 0 50 -1 0 16 0.0000 4 180 135 3330 3375 5\001
-4 0 0 50 -1 0 16 0.0000 4 180 135 3375 2745 3\001
-4 0 0 50 -1 0 16 0.0000 4 180 135 2655 2520 2\001
-4 0 0 50 -1 0 16 0.0000 4 180 135 2025 2835 1\001
--6
 2 1 0 2 0 7 50 -1 -1 0.000 0 0 -1 1 0 2
         1 1 2.00 90.00 120.00
@@ -55 +32 @@
 2 1 0 1 4 7 50 -1 -1 0.000 0 0 -1 0 0 2
          4500 7785 5760 7785
-4 0 1 50 -1 0 16 0.0000 4 180 135 1080 6345 1\001
-4 0 1 50 -1 0 16 0.0000 4 180 135 1710 6030 2\001
-4 0 1 50 -1 0 16 0.0000 4 180 135 2430 6255 3\001
-4 0 1 50 -1 0 16 0.0000 4 180 135 2385 6885 5\001
-4 0 4 50 -1 0 16 0.0000 4 180 135 5085 5985 4\001
-4 0 4 50 -1 0 16 0.0000 4 180 135 5580 6660 7\001
-4 0 4 50 -1 0 16 0.0000 4 195 135 5130 7380 6\001
-4 0 0 50 -1 0 16 0.0000 4 180 1440 1035 8235 Subdomain 0\001
-4 0 0 50 -1 0 16 0.0000 4 180 1440 4500 8235 Subdomain 1\001
+2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 4
+         1980 2340 2880 3060 1575 3060 1980 2340
+2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 4
+         1980 2340 3150 2070 2880 3015 2880 3060
+2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 3
+         2880 3060 3285 4095 3960 2835
+2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 3
+         3150 2070 4725 1845 3960 2880
+2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 3
+         3960 2880 4545 4095 4725 1845
+2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
+         3285 4095 4545 4095
+2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 3
+         3150 2115 3960 2880 2880 3060
+4 0 0 50 -1 0 16 0.0000 4 195 135 2025 2835 0\001
+4 0 0 50 -1 0 16 0.0000 4 195 135 2655 2520 1\001
+4 0 0 50 -1 0 16 0.0000 4 195 135 3375 2745 2\001
+4 0 0 50 -1 0 16 0.0000 4 195 135 3870 2295 3\001
+4 0 0 50 -1 0 16 0.0000 4 195 135 3330 3375 4\001
+4 0 0 50 -1 0 16 0.0000 4 195 135 3915 3690 5\001
+4 0 0 50 -1 0 16 0.0000 4 195 135 4365 2970 6\001
+4 0 1 50 -1 0 16 0.0000 4 195 135 1080 6345 0\001
+4 0 1 50 -1 0 16 0.0000 4 195 135 1710 6030 1\001
+4 0 1 50 -1 0 16 0.0000 4 195 135 2430 6255 2\001
+4 0 1 50 -1 0 16 0.0000 4 195 135 2385 6885 4\001
+4 0 4 50 -1 0 16 0.0000 4 195 135 5085 5985 3\001
+4 0 4 50 -1 0 16 0.0000 4 195 135 5580 6660 6\001
+4 0 4 50 -1 0 16 0.0000 4 195 135 5130 7380 5\001
+4 0 0 50 -1 0 16 0.0000 4 195 1215 1035 8235 Submesh 0\001
+4 0 0 50 -1 0 16 0.0000 4 195 1215 4500 8235 Submesh 1\001

inundation/parallel/documentation/figures/subdomainfinal.fig

@@ -8 +8 @@
 -2
 1200 2
-6 1575 1845 4725 4095
-2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 4
-         1980 2340 2880 3060 1575 3060 1980 2340
-2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 4
-         1980 2340 3150 2070 2880 3015 2880 3060
-2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 3
-         2880 3060 3285 4095 3960 2835
-2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 3
-         3150 2070 4725 1845 3960 2880
-2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 3
-         3960 2880 4545 4095 4725 1845
-2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
-         3285 4095 4545 4095
-2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 3
-         3150 2115 3960 2880 2880 3060
-4 0 0 50 -1 0 16 0.0000 4 180 135 3870 2295 4\001
-4 0 0 50 -1 0 16 0.0000 4 195 135 3915 3690 6\001
-4 0 0 50 -1 0 16 0.0000 4 180 135 4365 2970 7\001
-4 0 0 50 -1 0 16 0.0000 4 180 135 3330 3375 5\001
-4 0 0 50 -1 0 16 0.0000 4 180 135 3375 2745 3\001
-4 0 0 50 -1 0 16 0.0000 4 180 135 2655 2520 2\001
-4 0 0 50 -1 0 16 0.0000 4 180 135 2025 2835 1\001
--6
 2 1 0 2 0 7 50 -1 -1 0.000 0 0 -1 1 0 2
         1 1 2.00 90.00 120.00
@@ -57 +34 @@
 2 1 0 1 4 7 50 -1 -1 0.000 0 0 -1 0 0 3
          1894 5605 3469 5380 2704 6415
-2 1 0 1 4 7 50 -1 -1 0.000 0 0 -1 0 0 3
-         2682 6392 3267 7607 3447 5357
 2 1 0 1 4 7 50 -1 -1 0.000 0 0 -1 0 0 2
          2025 7650 3285 7650
@@ -67 +42 @@
 2 1 0 1 1 7 50 -1 -1 0.000 0 0 -1 0 0 2
          4455 6705 4905 7740
-4 0 0 50 -1 0 16 0.0000 4 180 1260 1035 8235 Processor 0\001
-4 0 0 50 -1 0 16 0.0000 4 180 1260 4860 8190 Processor 1\001
-4 0 1 50 -1 0 16 0.0000 4 180 135 4860 7020 5\001
-4 0 1 50 -1 0 16 0.0000 4 180 135 765 6390 1\001
-4 0 1 50 -1 0 16 0.0000 4 180 135 1395 6075 2\001
-4 0 1 50 -1 0 16 0.0000 4 180 135 2115 6300 3\001
-4 0 4 50 -1 0 16 0.0000 4 180 135 3060 6615 7\001
-4 0 4 50 -1 0 16 0.0000 4 195 135 2655 7245 6\001
-4 0 1 50 -1 0 16 0.0000 4 180 135 2070 6930 4\001
-4 0 4 50 -1 0 16 0.0000 4 180 135 2520 5895 5\001
-4 0 4 50 -1 0 16 0.0000 4 180 135 5445 5940 1\001
-4 0 4 50 -1 0 16 0.0000 4 180 135 5940 6615 2\001
-4 0 4 50 -1 0 16 0.0000 4 180 135 5490 7335 3\001
-4 0 1 50 -1 0 16 0.0000 4 180 135 4815 6390 4\001
+2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 4
+         1980 2340 2880 3060 1575 3060 1980 2340
+2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 4
+         1980 2340 3150 2070 2880 3015 2880 3060
+2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 3
+         2880 3060 3285 4095 3960 2835
+2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 3
+         3150 2070 4725 1845 3960 2880
+2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 3
+         3960 2880 4545 4095 4725 1845
+2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
+         3285 4095 4545 4095
+2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 3
+         3150 2115 3960 2880 2880 3060
+2 1 0 1 4 7 50 -1 -1 0.000 0 0 -1 0 0 2
+         2700 6435 3285 7650
+4 0 0 50 -1 0 16 0.0000 4 195 1275 1035 8235 Processor 0\001
+4 0 0 50 -1 0 16 0.0000 4 195 1275 4860 8190 Processor 1\001
+4 0 0 50 -1 0 16 0.0000 4 195 135 2025 2835 0\001
+4 0 0 50 -1 0 16 0.0000 4 195 135 2655 2520 1\001
+4 0 0 50 -1 0 16 0.0000 4 195 135 3375 2745 2\001
+4 0 0 50 -1 0 16 0.0000 4 195 135 3870 2295 3\001
+4 0 0 50 -1 0 16 0.0000 4 195 135 3330 3375 4\001
+4 0 0 50 -1 0 16 0.0000 4 195 135 3915 3690 5\001
+4 0 0 50 -1 0 16 0.0000 4 195 135 4365 2970 6\001
+4 0 1 50 -1 0 16 0.0000 4 195 135 765 6390 0\001
+4 0 1 50 -1 0 16 0.0000 4 195 135 1395 6075 1\001
+4 0 1 50 -1 0 16 0.0000 4 195 135 2115 6300 2\001
+4 0 1 50 -1 0 16 0.0000 4 195 135 2070 6930 3\001
+4 0 4 50 -1 0 16 0.0000 4 195 135 2520 5895 4\001
+4 0 4 50 -1 0 16 0.0000 4 195 135 2655 7245 5\001
+4 0 4 50 -1 0 16 0.0000 4 195 135 5445 5940 0\001
+4 0 4 50 -1 0 16 0.0000 4 195 135 5940 6615 1\001
+4 0 4 50 -1 0 16 0.0000 4 195 135 5490 7335 2\001
+4 0 1 50 -1 0 16 0.0000 4 195 135 4815 6390 3\001
+4 0 1 50 -1 0 16 0.0000 4 195 135 4860 7020 4\001

inundation/parallel/documentation/figures/subdomainghost.fig

@@ -8 +8 @@
 -2
 1200 2
-6 1575 1845 4725 4095
-2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 4
-         1980 2340 2880 3060 1575 3060 1980 2340
-2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 4
-         1980 2340 3150 2070 2880 3015 2880 3060
-2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 3
-         2880 3060 3285 4095 3960 2835
-2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 3
-         3150 2070 4725 1845 3960 2880
-2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 3
-         3960 2880 4545 4095 4725 1845
-2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
-         3285 4095 4545 4095
-2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 3
-         3150 2115 3960 2880 2880 3060
-4 0 0 50 -1 0 16 0.0000 4 180 135 3870 2295 4\001
-4 0 0 50 -1 0 16 0.0000 4 195 135 3915 3690 6\001
-4 0 0 50 -1 0 16 0.0000 4 180 135 4365 2970 7\001
-4 0 0 50 -1 0 16 0.0000 4 180 135 3330 3375 5\001
-4 0 0 50 -1 0 16 0.0000 4 180 135 3375 2745 3\001
-4 0 0 50 -1 0 16 0.0000 4 180 135 2655 2520 2\001
-4 0 0 50 -1 0 16 0.0000 4 180 135 2025 2835 1\001
--6
-6 315 5355 3510 7650
-6 1890 5355 3510 7650
-2 1 1 1 4 7 50 -1 -1 4.000 0 0 -1 0 0 3
-         1894 5605 3469 5380 2704 6415
-2 1 1 1 4 7 50 -1 -1 4.000 0 0 -1 0 0 3
-         2682 6392 3267 7607 3447 5357
--6
-2 1 0 1 1 7 50 -1 -1 0.000 0 0 -1 0 0 4
-         720 5895 1620 6615 315 6615 720 5895
-2 1 0 1 1 7 50 -1 -1 0.000 0 0 -1 0 0 4
-         720 5895 1890 5625 1620 6570 1620 6615
-2 1 0 1 1 7 50 -1 -1 0.000 0 0 -1 0 0 3
-         1890 5670 2700 6435 1620 6615
-2 1 0 1 1 7 50 -1 -1 0.000 0 0 -1 0 0 3
-         1620 6615 2025 7650 2700 6390
-2 1 1 1 4 7 50 -1 -1 4.000 0 0 -1 0 0 2
-         2025 7650 3285 7650
-4 0 1 50 -1 0 16 0.0000 4 180 135 765 6390 1\001
-4 0 1 50 -1 0 16 0.0000 4 180 135 1395 6075 2\001
-4 0 1 50 -1 0 16 0.0000 4 180 135 2115 6300 3\001
-4 0 1 50 -1 0 16 0.0000 4 180 135 2070 6930 5\001
-4 0 4 50 -1 0 16 0.0000 4 180 135 2520 5895 4\001
-4 0 4 50 -1 0 16 0.0000 4 180 135 3060 6615 7\001
-4 0 4 50 -1 0 16 0.0000 4 195 135 2655 7245 6\001
--6
 2 1 0 2 0 7 50 -1 -1 0.000 0 0 -1 1 0 2
         1 1 2.00 90.00 120.00
@@ -78 +30 @@
 2 1 1 1 1 7 50 -1 -1 4.000 0 0 -1 0 0 2
          4455 6705 4905 7740
-4 0 4 50 -1 0 16 0.0000 4 180 135 5445 5940 4\001
-4 0 4 50 -1 0 16 0.0000 4 180 135 5940 6615 7\001
-4 0 4 50 -1 0 16 0.0000 4 195 135 5490 7335 6\001
-4 0 1 50 -1 0 16 0.0000 4 180 135 4815 6390 3\001
-4 0 1 50 -1 0 16 0.0000 4 180 135 4860 7020 5\001
-4 0 0 50 -1 0 16 0.0000 4 180 1440 1035 8235 Subdomain 0\001
-4 0 0 50 -1 0 16 0.0000 4 180 1440 4860 8190 Subdomain 1\001
+2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 4
+         1980 2340 2880 3060 1575 3060 1980 2340
+2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 4
+         1980 2340 3150 2070 2880 3015 2880 3060
+2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 3
+         2880 3060 3285 4095 3960 2835
+2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 3
+         3150 2070 4725 1845 3960 2880
+2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 3
+         3960 2880 4545 4095 4725 1845
+2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 2
+         3285 4095 4545 4095
+2 1 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 3
+         3150 2115 3960 2880 2880 3060
+2 1 0 1 1 7 50 -1 -1 0.000 0 0 -1 0 0 4
+         720 5895 1620 6615 315 6615 720 5895
+2 1 0 1 1 7 50 -1 -1 0.000 0 0 -1 0 0 4
+         720 5895 1890 5625 1620 6570 1620 6615
+2 1 0 1 1 7 50 -1 -1 0.000 0 0 -1 0 0 3
+         1890 5670 2700 6435 1620 6615
+2 1 0 1 1 7 50 -1 -1 0.000 0 0 -1 0 0 3
+         1620 6615 2025 7650 2700 6390
+2 1 1 1 4 7 50 -1 -1 4.000 0 0 -1 0 0 2
+         2025 7650 3285 7650
+2 1 1 1 4 7 50 -1 -1 4.000 0 0 -1 0 0 3
+         1894 5605 3469 5380 2704 6415
+2 1 1 1 4 0 50 -1 -1 4.000 0 0 -1 0 0 2
+         2700 6435 3285 7650
+4 0 0 50 -1 0 16 0.0000 4 195 1215 4860 8190 Submesh 1\001
+4 0 0 50 -1 0 16 0.0000 4 195 135 2025 2835 0\001
+4 0 0 50 -1 0 16 0.0000 4 195 135 2655 2520 1\001
+4 0 0 50 -1 0 16 0.0000 4 195 135 3375 2745 2\001
+4 0 0 50 -1 0 16 0.0000 4 195 135 3870 2295 3\001
+4 0 0 50 -1 0 16 0.0000 4 195 135 3330 3375 4\001
+4 0 0 50 -1 0 16 0.0000 4 195 135 3915 3690 5\001
+4 0 0 50 -1 0 16 0.0000 4 195 135 4365 2970 6\001
+4 0 0 50 -1 0 16 0.0000 4 195 1215 1215 8235 Submesh 0\001
+4 0 1 50 -1 0 16 0.0000 4 195 135 1170 6120 1\001
+4 0 1 50 -1 0 16 0.0000 4 195 135 1935 6165 2\001
+4 0 4 50 -1 0 16 0.0000 4 195 135 2430 5850 3\001
+4 0 1 50 -1 0 16 0.0000 4 195 135 1980 6885 4\001
+4 0 1 50 -1 0 16 0.0000 4 195 135 4725 6390 2\001
+4 0 1 50 -1 0 16 0.0000 4 195 135 675 6435 0\001
+4 0 15 50 -1 0 16 0.0000 4 255 345 2655 7425 (5)\001
+4 0 24 50 -1 0 16 0.0000 4 255 345 5400 7515 (2)\001
+4 0 15 50 -1 0 16 0.0000 4 255 345 855 6525 (0)\001
+4 0 15 50 -1 0 16 0.0000 4 255 345 1350 6255 (1)\001
+4 0 15 50 -1 0 16 0.0000 4 255 345 2115 6390 (2)\001
+4 0 15 50 -1 0 16 0.0000 4 255 345 2565 6075 (4)\001
+4 0 15 50 -1 0 16 0.0000 4 255 345 1890 7200 (3)\001
+4 0 4 50 -1 0 16 0.0000 4 195 135 2520 7110 5\001
+4 0 24 50 -1 0 16 0.0000 4 255 345 4950 6480 (3)\001
+4 0 1 50 -1 0 16 0.0000 4 195 135 4815 7290 4\001
+4 0 24 50 -1 0 16 0.0000 4 255 345 4815 6930 (4)\001
+4 0 4 50 -1 0 16 0.0000 4 195 135 5895 6525 6\001
+4 0 24 50 -1 0 16 0.0000 4 255 345 5760 6885 (1)\001
+4 0 4 50 -1 0 16 0.0000 4 195 135 5445 7155 5\001
+4 0 24 50 -1 0 16 0.0000 4 255 345 5355 6210 (0)\001
+4 0 4 50 -1 0 16 0.0000 4 195 135 5490 5895 3\001

inundation/parallel/documentation/parallel.tex

@@ -27 +27 @@
 
 The first step in parallelising the code is to subdivide the mesh
-into, roughly, equally sized partitions. On a rectangular domain this may be
+into, roughly, equally sized partitions. On a rectangular mesh this may be
 done by a simple co-ordinate based dissection, but on a complicated
-domain such as the Merimbula grid shown in Figure \ref{fig:mergrid}
+domain such as the Merimbula mesh shown in Figure \ref{fig:mergrid}
 a more sophisticated approach must be used.  We use pymetis, a
 python wrapper around the Metis
@@ -40 +40 @@
 \begin{figure}[hbtp]
   \centerline{ \includegraphics[scale = 0.75]{figures/mermesh.eps}}
-  \caption{The Merimbula grid.}
+  \caption{The Merimbula mesh.}
  \label{fig:mergrid}
 \end{figure}
@@ -87 +87 @@
 setting up the communication pattern as well as assigning the local numbering scheme for the submeshes.
 
-Consider the example subpartitioning given in Figure \ref{fig:subdomain}. During the \code{evolve} calculations Triangle 3 in Submesh 0 will need to access its neighbour Triangle 4 stored in Submesh 1. The standard approach to this problem is to add an extra layer of triangles, which we call ghost triangles. The ghost triangles
+Consider the example subpartitioning given in Figure \ref{fig:subdomain}. During the \code{evolve} calculations Triangle 2 in Submesh 0 will need to access its neighbour Triangle 3 stored in Submesh 1. The standard approach to this problem is to add an extra layer of triangles, which we call ghost triangles. The ghost triangles
 are read-only, they should not be updated during the calculations, they are only there to hold any extra information that a processor may need to complete its calculations. The ghost triangle values are updated through communication calls. Figure \ref{fig:subdomaing} shows the submeshes with the extra layer of ghost triangles.
 
 \begin{figure}[hbtp]
   \centerline{ \includegraphics[scale = 0.6]{figures/subdomain.eps}}
-  \caption{An example subpartioning.}
+  \caption{An example subpartioning of a mesh.}
  \label{fig:subdomain}
 \end{figure}
@@ -99 +99 @@
 \begin{figure}[hbtp]
   \centerline{ \includegraphics[scale = 0.6]{figures/subdomainghost.eps}}
-  \caption{An example subpartioning with ghost triangles.}
+  \caption{An example subpartioning with ghost triangles. The numbers in brackets shows the local numbering scheme that is calculated and stored with the mesh, but not implemented until the local mesh is built. See Section \ref{sec:part4}. }
  \label{fig:subdomaing}
 \end{figure}
 
-When partitioning the mesh we introduce new, dummy, boundary edges. For example, Triangle 3 in Submesh 1, from Figure \ref{fig:subdomaing}, originally shared an edge with Triangle 2, but after partitioning that edge becomes a boundary edge. These new boundary edges are are tagged as \code{ghost} and should, in general, be assigned a type of \code{None}. The following piece of code taken from {\tt run_parallel_advection.py} shows an example.  
- 
+When partitioning the mesh we introduce new, dummy, boundary edges. For example, Triangle 2 in Submesh 1 from Figure \ref{fig:subdomaing} originally shared an edge with Triangle 1, but after partitioning that edge becomes a boundary edge. These new boundary edges are are tagged as \code{ghost} and should, in general, be assigned a type of \code{None}. The following piece of code taken from {\tt run_parallel_advection.py} shows an example.  
 {\small \begin{verbatim}  
 T = Transmissive_boundary(domain)
@@ -112 +111 @@
 \end{verbatim}}
 
-
-Looking at Figure \ref{fig:subdomaing} we see that after each \code{evolve} step Processor 0  will have to send the updated values for Triangle 3 and Triangle 5 to Processor 1, and similarly Processor 1 will have to send the updated values for triangles 4, 7 and 6 (recall that Submesh $p$ will be assigned to Processor $p$). The \code{build_submesh} function builds a dictionary that defines the communication pattern.
-
-Finally, the ANUGA code assumes that the triangles (and nodes etc.) are numbered consecutively starting from 1 (FIXME (Ole): Isn't it 0?). Consequently, if Submesh 1 in Figure \ref{fig:subdomaing} was passed into the \code{evolve} calculations it would crash due to the 'missing' triangles. The \code{build_submesh} function determines a local numbering scheme for each submesh, but it does not actually update the numbering, that is left to the function \code{build_local}.
+Looking at Figure \ref{fig:subdomaing} we see that after each \code{evolve} step Processor 0  will have to send the updated values for Triangle 2 and Triangle 4 to Processor 1, and similarly Processor 1 will have to send the updated values for Triangle 3 and Triangle 5 (recall that Submesh $p$ will be assigned to Processor $p$). The \code{build_submesh} function builds a dictionary that defines the communication pattern.
+
+Finally, the ANUGA code assumes that the triangles (and nodes etc.) are numbered consecutively starting from 0. Consequently, if Submesh 1 in Figure \ref{fig:subdomaing} was passed into the \code{evolve} calculations it would crash. The \code{build_submesh} function determines a local numbering scheme for each submesh, but it does not actually update the numbering, that is left to \code{build_local}.
+
 
 \subsection {Sending the Submeshes}\label{sec:part3}
@@ -121 +120 @@
 All of functions described so far must be run in serial on Processor 0. The next step is to start the parallel computation by spreading the submeshes over the processors. The communication is carried out by
 \code{send_submesh} and \code{rec_submesh} defined in {\tt build_commun.py}.
-The \code{send_submesh} function should be called on Processor 0 and sends the Submesh $p$ to Processor $p$, while \code{rec_submesh} should be called by Processor $p$ to receive Submesh $p$ from Processor 0. Note that the order of communication is very important, if any changes are made to the \code{send_submesh} function the corresponding change must be made to the \code{rec_submesh} function.
+The \code{send_submesh} function should be called on Processor 0 and sends the Submesh $p$ to Processor $p$, while \code{rec_submesh} should be called by Processor $p$ to receive Submesh $p$ from Processor 0. 
+
+As an aside, the order of communication is very important. If someone was to modify the \code{send_submesh} routine the corresponding change must be made to the \code{rec_submesh} routine.
 
 While it is possible to get Processor 0 to communicate it's submesh to itself, it is an expensive and unnecessary communication call. The {\tt build_commun.py} file also includes a function called \code{extract_hostmesh} that should be called on Processor 0 to extract Submesh 0.
 
 
-\subsection {Building the Local Mesh}
+\subsection {Building the Local Mesh}\label{sec:part4}
 After using \code{send_submesh} and \code{rec_submesh}, Processor $p$ should have its own local copy of Submesh $p$, however as stated previously the triangle numbering will be incorrect on all processors except number $0$. The \code{build_local_mesh} function from {\tt build_local.py} primarily focuses on renumbering the information stored with the submesh; including the nodes, vertices and quantities. Figure \ref{fig:subdomainf} shows what the mesh in each processor may look like.
 
@@ -147 +148 @@
 \begin{verbatim}
 #######################
-# Partition the domain
+# Partition the mesh
 #######################
 
@@ -157 +158 @@
 \end{verbatim}
 
-This rectangular mesh is artificial, and the approach to subpartitioning the mesh is different to the one described above, however this example may be of interest to those who want to measure the parallel efficiency of the code on their machine. A rectangular mesh should give a good load balance and is therefore an important first test problem.  
-
-
-A more \lq real life\rq\ mesh is the Merimbula mesh used in the code shown in Section \ref{sec:codeRPMM}. This example also solves the advection equation. In this case the techniques described in Section \ref{sec:part} must be used to partition the mesh. Figure \ref{fig:code} shows the part of the code that is responsible for spreading the domain over the processors. We now look at the code in detail.
+Most simulations will not be done on a rectangular mesh, and the approach to subpartitioning the mesh is different to the one described above, however this example may be of interest to those who want to measure the parallel efficiency of the code on their machine. A rectangular mesh should give a good load balance and is therefore an important first test problem.  
+
+
+A more \lq real life\rq\ mesh is the Merimbula mesh used in the code shown in Section \ref{sec:codeRPMM}. This example also solves the advection equation. In this case the techniques described in Section \ref{sec:part} must be used to partition the mesh. Figure \ref{fig:code} shows the part of the code that is responsible for spreading the mesh over the processors. We now look at the code in detail.
 
 \begin{figure}[htbp]
@@ -170 +171 @@
     filename = 'merimbula_10785.tsh'
 
-    domain_full = pmesh_to_domain_instance(filename, Advection_Domain)
-    domain_full.set_quantity('stage', Set_Stage(756000.0,756500.0,4.0))
-
-    # Define the domain boundaries for visualisation
-   
-    rect = array(domain_full.xy_extent, Float)
+    mesh_full = pmesh_to_domain_instance(filename, Advection_Domain)
+    mesh_full.set_quantity('stage', Set_Stage(756000.0,756500.0,4.0))
 
     # Subdivide the mesh
 
     nodes, triangles, boundary, triangles_per_proc, quantities  =\
-            pmesh_divide_metis(domain_full, numprocs)
+            pmesh_divide_metis(mesh_full, numprocs)
 
     # Build the mesh that should be assigned to each processor.
@@ -195 +192 @@
     # Build the local mesh for processor 0
 
-    hostmesh = extract_hostmesh(submesh)
-    points, vertices, boundary, quantities, ghost_recv_dict, full_send_dict = \
-             build_local_mesh(hostmesh, 0, triangles_per_proc[0], numprocs)
+     points, vertices, boundary, quantities, ghost_recv_dict, full_send_dict =\
+              extract_hostmesh(submesh, triangles_per_proc)
 
 else:
@@ -213 +209 @@
 \begin{itemize}
 \item 
-These first few lines of code read in and define the (global) mesh.
+These first few lines of code read in and define the (global) mesh. The \code{Set_Stage} function sets the initial conditions. See the code in \ref{sec:codeRPMM} for the definition of \code{Set_Stage}.
 \begin{verbatim}
     filename = 'merimbula_10785.tsh'
-    domain_full = pmesh_to_domain_instance(filename, Advection_Domain)
-    domain_full.set_quantity('stage', Set_Stage(756000.0,756500.0,4.0))
-\end{verbatim}
-
-\item
-The \code{rect} array is used by the visualiser and records the domain size.
+    mesh_full = pmesh_to_domain_instance(filename, Advection_Domain)
+    mesh_full.set_quantity('stage', Set_Stage(756000.0,756500.0,4.0))
+\end{verbatim}
+
 \item \code{pmesh_divide_metis} divides the mesh into a set of non-overlapping subdomains as described in Section \ref{sec:part1}.
 \begin{verbatim}
     nodes, triangles, boundary, triangles_per_proc, quantities  =\
-            pmesh_divide_metis(domain_full, numprocs)
-\end{verbatim}
-
-\item The next step is to build a boundary layer of ghost triangles and define the communication pattern. This step is implemented by \code{build_submesh} as discussed in Section \ref{sec:part2}. 
+            pmesh_divide_metis(mesh_full, numprocs)
+\end{verbatim}
+
+\item The next step is to build a boundary layer of ghost triangles and define the communication pattern. This step is implemented by \code{build_submesh} as discussed in Section \ref{sec:part2}. The \code{submesh} variable contains a copy of the submesh for each processor. 
 \begin{verbatim}        
     submesh = build_submesh(nodes, triangles, boundary, quantities, \
@@ -240 +234 @@
 \end{verbatim}
 
-The processors receive a given subpartition by calling \code{rec_submesh}. The \code{rec_submesh} routine also calls \code{build_local_mesh}. The \code{build_local_mesh} routine described in Section \ref{sec:part4} ensures that the information is stored in a way that is compatible with the Domain datastructure. This means, for example, that the triangles and nodes must be numbered consecutively starting from 1 (FIXME (Ole): or is it 0?).
-\begin{verbatim}
-    points, vertices, boundary, quantities, ghost_recv_dict, full_send_dict = \
+
+The processors receives a given subpartition by calling \code{rec_submesh}. The \code{rec_submesh} routine also calls \code{build_local_mesh}. The \code{build_local_mesh} routine described in Section \ref{sec:part4} ensures that the information is stored in a way that is compatible with the Domain datastructure. This means, for example, that the triangles and nodes must be numbered consecutively starting from 0.
+
+\begin{verbatim}
+    points, vertices, boundary, quantities, ghost_recv_dict, full_send_dict=\
              rec_submesh(0)
 \end{verbatim}
 
-Note that the submesh is not received by, or sent to, Processor 0. Rather     \code{hostmesh = extract_hostmesh(submesh)} extracts the appropriate information. This saves the cost of an unnecessary communication call. It is described further in Section \ref{sec:part3}.
-\begin{verbatim}
-    hostmesh = extract_hostmesh(submesh)
-    points, vertices, boundary, quantities, ghost_recv_dict, full_send_dict = \
-             build_local_mesh(hostmesh, 0, triangles_per_proc[0], numprocs)
+Note that the submesh is not received by, or sent to, Processor 0. Rather     \code{hostmesh = extract_hostmesh(submesh)} simply extracts the mesh that has been assigned to Processor 0. Recall \code{submesh} contains the list of submeshes to be assigned to each processor. This is described further in Section \ref{sec:part3}. The \code{build_local_mesh} renumbers the nodes
+\begin{verbatim}
+    points, vertices, boundary, quantities, ghost_recv_dict, full_send_dict)=\
+              extract_hostmesh(submesh, triangles_per_proc)
 \end{verbatim}
 

inundation/parallel/print_stats.py

@@ -6 +6 @@
 #
 #
-#  The routine defined here are intended for debugging
+#  The routines defined here are intended for debugging
 # use. They print the norms of the quantities in the
 # domain. As opposed to the definitions given

inundation/parallel/run_parallel_sw_merimbula_test.py

@@ -102 +102 @@
     # Read in the test files
 
-#    filename = 'test-100.tsh'
-    filename = 'merimbula_10785_1.tsh'
+    filename = 'test-100.tsh'
+#    filename = 'merimbula_10785_1.tsh'
 
     # Build the whole domain
@@ -117 +117 @@
     # Initialise the wave
 
-#    domain_full.set_quantity('stage', Set_Stage(200.0,300.0,1.0))
-    domain_full.set_quantity('stage', Set_Stage(756000.0,756500.0,2.0))
+    domain_full.set_quantity('stage', Set_Stage(200.0,300.0,1.0))
+#    domain_full.set_quantity('stage', Set_Stage(756000.0,756500.0,2.0))
 #    domain_full.set_quantity('stage', Set_Stage(756000.0,756500.0,0.0))
 
@@ -211 +211 @@
 print 'Processor %d on %s: No of elements %d'%(domain.processor,processor_name,domain.number_of_elements)
 yieldstep = 0.05
-finaltime = 500.0
+finaltime = 5.0
 
 yieldstep = 1