anuga 1.3.5__zip

Users/steve/Miniconda/envs/anuga/Lib/site-packages/anuga/parallel/distribute_mesh.py

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+#########################################################
+#
+#
+#  Read in a data file and subdivide the triangle list
+#
+#
+#  The final routine, pmesh_divide_metis, does automatic
+# grid partitioning. Once testing has finished on this
+# routine the others should be removed.
+#
+#  Authors: Linda Stals and Matthew Hardy, June 2005
+#  Modified: Linda Stals, Nov 2005
+#            Jack Kelly, Nov 2005
+#            Steve Roberts, Aug 2009 (updating to numpy)
+#
+#
+#########################################################
+
+
+import sys
+from os import sep
+from sys import path
+from math import floor
+
+import numpy as num
+import numpy.lib.arraysetops as numset
+
+from anuga.abstract_2d_finite_volumes.neighbour_mesh import Mesh
+from anuga import indent
+
+try:
+    import local_config as config
+except:
+    import config as config
+
+
+verbose = False
+
+#########################################################
+#
+# If the triangles list is reordered, the quantities
+# assigned to the triangles must also be reorded.
+#
+# *) quantities contain the quantites in the old ordering
+# *) proc_sum[i] contains the number of triangles in
+# processor i
+# *) tri_index is a map from the old triangle ordering to
+# the new ordering, where the new number for triangle
+# i is proc_sum[tri_index[i][0]]+tri_index[i][1]
+#
+# -------------------------------------------------------
+#
+# *) The quantaties are returned in the new ordering
+#
+#########################################################
+
+def reorder(quantities, tri_index, proc_sum):
+
+    # Find the number triangles
+
+    N = len(tri_index)
+
+    # Temporary storage area
+
+    index = num.zeros(N, num.int)
+    q_reord = {}
+
+    # Find the new ordering of the triangles
+
+    for i in xrange(N):
+        bin = tri_index[i][0]
+        bin_off_set = tri_index[i][1]
+        index[i] = proc_sum[bin]+bin_off_set
+
+    # Reorder each quantity according to the new ordering
+
+    for k in quantities:
+        q_reord[k] = num.zeros((N, 3), num.float)
+        for i in range(N):
+            q_reord[k][index[i]]=quantities[k].vertex_values[i]
+    del index
+
+    return q_reord
+
+
+def reorder_new(quantities, epart_order, proc_sum):
+
+    # Find the number triangles
+
+    N = len(epart_order)
+
+    # Temporary storage area
+
+
+    q_reord = {}
+
+    # Reorder each quantity according to the new ordering
+
+    for k in quantities:
+        q_reord[k] = num.zeros((N, 3), num.float)
+        q_reord[k][:] = quantities[k].vertex_values[epart_order]
+        
+
+    return q_reord
+
+
+#########################################################
+#
+# Divide the mesh using a call to metis, through pymetis.
+#
+# -------------------------------------------------------
+#
+# *)  The nodes, triangles, boundary, and quantities are
+# returned. triangles_per_proc defines the subdivision.
+# The first triangles_per_proc[0] triangles are assigned
+# to processor 0, the next triangles_per_proc[1] are
+# assigned to processor 1 etc. The boundary and quantites
+# are ordered the same way as the triangles
+#
+#########################################################
+
+#path.append('..' + sep + 'pymetis')
+
+try:
+    from anuga.pymetis.metis_ext import partMeshNodal
+except ImportError:
+    print "***************************************************"
+    print "         Metis is probably not compiled."
+    print "         Read anuga.pymetis README"
+    print "***************************************************"
+    raise ImportError
+
+def pmesh_divide_metis(domain, n_procs):
+    # Wrapper for old pmesh_divide_metis which does not return tri_index or r_tri_index
+    nodes, ttriangles, boundary, triangles_per_proc, quantities, tri_index, r_tri_index = pmesh_divide_metis_helper(domain, n_procs)
+
+    return nodes, ttriangles, boundary, triangles_per_proc, quantities
+
+def pmesh_divide_metis_with_map(domain, n_procs):
+
+    return pmesh_divide_metis_helper(domain, n_procs)
+
+def pmesh_divide_metis_helper(domain, n_procs):
+    
+    # Initialise the lists
+    # List, indexed by processor of # triangles.
+    
+    #triangles_per_proc = []
+    
+    # List of lists, indexed by processor of vertex numbers
+    
+    #tri_list = []
+
+    # Serial to Parallel and Parallel to Serial Triangle index maps
+    tri_index = {}
+    r_tri_index = {} # reverse tri index, parallel to serial triangle index mapping
+    
+
+    # Prepare variables for the metis call
+    
+    n_tri = len(domain.triangles)
+    if n_procs != 1: #Because metis chokes on it...
+        n_vert = domain.get_number_of_nodes()
+        t_list = domain.triangles.copy()
+        t_list = num.reshape(t_list, (-1,))
+    
+        # The 1 here is for triangular mesh elements.
+        # FIXME: Should update to Metis 5
+        edgecut, epart, npart = partMeshNodal(n_tri, n_vert, t_list, 1, n_procs)
+        # print edgecut
+        # print npart
+        #print epart
+        del edgecut
+        del npart
+
+        # Sometimes (usu. on x86_64), partMeshNodal returns an array of zero
+        # dimensional arrays. Correct this.
+        if type(epart[0]) == num.ndarray:
+            epart_new = num.zeros(len(epart), num.int)
+            epart_new[:] = epart[:][0]
+#            for i in xrange(len(epart)):
+#                epart_new[i] = epart[i][0]
+            epart = epart_new
+            del epart_new
+
+
+        triangles_per_proc = num.bincount(epart)
+
+        msg =  "Metis created a partition where at least one submesh has no triangles. "
+        msg += "Try using a smaller number of mpi processes."
+        assert num.all(triangles_per_proc>0), msg
+
+        proc_sum = num.zeros(n_procs+1,num.int)
+        proc_sum[1:] = num.cumsum(triangles_per_proc)
+
+
+
+        epart_order = num.argsort(epart, kind='mergesort')
+        new_triangles = domain.triangles[epart_order]
+
+        #new_r_tri_index_flat = num.zeros((n_tri,3), num.int)
+        new_tri_index = num.zeros((n_tri,2), num.int)
+        for i in xrange(n_procs):
+            ids = num.arange(proc_sum[i],proc_sum[i+1])
+            eids = epart_order[ids]
+            nrange = num.reshape(num.arange(triangles_per_proc[i]), (-1,1))
+            nones = num.ones_like(nrange)
+            #print ids.shape
+            #print nrange.shape
+            new_tri_index[eids] = num.concatenate((i*nones, nrange), axis = 1)
+            #new_r_tri_index_flat[ids] = num.concatenate((i*nones, nrange, num.reshape(eids, (-1,1))), axis = 1)
+
+
+        if verbose:
+            from pprint import pprint
+            print 'epart'
+            pprint(epart)
+            print 'new_tri_index'
+            pprint(new_tri_index)
+
+        #print 50*'='
+        
+        new_boundary = {}
+        for b in domain.boundary:
+            t =  new_tri_index[b[0]]
+            #print t
+            new_boundary[proc_sum[t[0]]+t[1], b[1]] = domain.boundary[b]
+
+        #quantities = reorder(domain.quantities, tri_index, proc_sum)
+        new_quantities = reorder_new(domain.quantities, epart_order, proc_sum)
+
+    else:
+        new_boundary = domain.boundary.copy()
+        triangles_per_proc = [n_tri]
+        new_triangles = domain.triangles.copy()
+        new_tri_index = []
+        epart_order = []
+        
+        # This is essentially the same as a chunk of code from reorder.
+        
+        new_quantities = {}
+        for k in domain.quantities:
+            new_quantities[k] = num.zeros((n_tri, 3), num.float)
+            for i in range(n_tri):
+                new_quantities[k][i] = domain.quantities[k].vertex_values[i]
+        
+    # Extract the node list
+    new_nodes = domain.get_nodes().copy()
+    
+
+    return new_nodes, new_triangles, new_boundary, triangles_per_proc, new_quantities, new_tri_index, epart_order
+
+#########################################################
+#
+# Subdivide the domain. This module is primarily
+# responsible for building the ghost layer and
+# communication pattern
+#
+#
+#  Author: Linda Stals, June 2005
+#  Modified: Linda Stals, Nov 2005 (optimise python code)
+#            Steve Roberts, Aug 2009 (convert to numpy)
+#
+#
+#########################################################
+
+
+
+#########################################################
+#
+# Subdivide the triangles into non-overlapping domains.
+#
+#  *)  The subdivision is controlled by triangles_per_proc.
+# The first triangles_per_proc[0] triangles are assigned
+# to the first processor, the second triangles_per_proc[1]
+# are assigned to the second processor etc.
+#
+#  *) nodes, triangles and boundary contains all of the
+# nodes, triangles and boundary tag information for the
+# whole domain. The triangles should be orientated in the
+# correct way and the nodes number consecutively from 0.
+#
+# -------------------------------------------------------
+#
+#  *) A dictionary containing the full_nodes, full_triangles
+# and full_boundary information for each processor is
+# returned. The node information consists of
+# [global_id, x_coord, y_coord].
+#
+#########################################################
+
+def submesh_full(mesh, triangles_per_proc):
+
+    # Initialise
+
+
+    #print triangles_per_proc
+    
+    nodes = mesh.nodes
+    triangles = mesh.triangles
+    boundary = mesh.boundary
+
+    tlower = 0
+    nproc = len(triangles_per_proc)
+    nnodes = len(nodes)
+    node_list = []
+    triangle_list = []
+    boundary_list = []
+    submesh = {}
+
+#    node_range = num.reshape(num.arange(nnodes),(nnodes,1))
+#
+#    #print node_range
+#    tsubnodes = num.concatenate((node_range, nodes), 1)
+
+    #print node_range
+    #print nodes
+    # Loop over processors
+
+    for p in xrange(nproc):
+
+        # Find triangles on processor p
+
+        tupper = triangles_per_proc[p]+tlower
+        subtriangles = triangles[tlower:tupper]
+        triangle_list.append(subtriangles)
+
+        # Find the boundary edges on processor p
+
+        subboundary = {}
+        for k in boundary:
+            if (k[0] >=tlower and k[0] < tupper):
+                subboundary[k]=boundary[k]
+        boundary_list.append(subboundary)
+
+        # Find nodes in processor p
+
+#        nodemap = num.zeros(nnodes, 'i')
+#        for t in subtriangles:
+#            nodemap[t[0]]=1
+#            nodemap[t[1]]=1
+#            nodemap[t[2]]=1
+#
+#        y = tsubnodes.take(num.flatnonzero(nodemap),axis=0)
+
+        #node_list.append(y)
+
+        ids = num.unique(subtriangles.flat)
+
+            
+        lnodes = nodes[ids]
+#       print nodes.shape
+#       print ids.shape
+#       print lnodes.shape
+        x = num.concatenate((num.reshape(ids, (-1,1)),lnodes ), 1)
+#       print x
+#       print y
+        node_list.append(x)
+
+            
+        # Move to the next processor
+
+        tlower = tupper
+
+    # Put the results in a dictionary
+
+    submesh["full_nodes"] = node_list
+    submesh["full_triangles"] = triangle_list
+    submesh["full_boundary"] = boundary_list
+
+    # Clean up before exiting
+
+    #del (nodemap)
+
+    return submesh
+
+
+#########################################################
+#
+# Build the ghost layer of triangles
+#
+#  *) Given the triangle subpartion for the processor
+# build a ghost layer of triangles. The ghost layer
+# consists of two layers of neighbouring triangles.
+#
+#  *) The vertices in the ghost triangles must also
+# be added to the node list for the current processor
+#
+#
+# -------------------------------------------------------
+#
+#  *) The extra triangles and nodes are returned.
+#
+#  *)  The node information consists of
+# [global_id, x_coord, y_coord].
+#
+#  *) The triangle information consists of
+# [triangle number, t], where t = [v1, v2, v3].
+#
+#########################################################
+
+def ghost_layer_old(submesh, mesh, p, tupper, tlower, parameters = None):
+
+    ncoord = mesh.number_of_nodes
+    ntriangles = mesh.number_of_triangles
+
+    if parameters is None:
+        layer_width  = 2
+    else:
+        layer_width = parameters['ghost_layer_width']
+
+
+    trianglemap = num.zeros(ntriangles, num.int)
+
+    # Find the first layer of boundary triangles
+    for t in xrange(tlower, tupper):
+        
+        n = mesh.neighbours[t, 0]
+        if n >= 0:
+            if n < tlower or n >= tupper:
+                trianglemap[n] = 1
+
+        n = mesh.neighbours[t, 1]
+        if n >= 0:
+            if n < tlower or n >= tupper:
+                trianglemap[n] = 1
+
+        n = mesh.neighbours[t, 2]
+        if n >= 0:
+            if n < tlower or n >= tupper:
+                trianglemap[n] = 1
+
+
+    # Find the subsequent layers of ghost triangles
+    for i in range(layer_width-1):
+
+        for t in xrange(ntriangles):
+            if trianglemap[t]==i+1:
+
+                n = mesh.neighbours[t, 0]
+                if n >= 0:
+                    if (n < tlower or n >= tupper) and trianglemap[n] == 0:
+                        trianglemap[n] = i+2
+
+                n = mesh.neighbours[t, 1]
+                if n >= 0:
+                    if (n < tlower or n >= tupper) and trianglemap[n] == 0:
+                        trianglemap[n] = i+2
+
+                n = mesh.neighbours[t, 2]
+                if n >= 0:
+                    if (n < tlower or n >= tupper) and trianglemap[n] == 0:
+                        trianglemap[n] = i+2
+
+    # Build the triangle list and make note of the vertices
+
+
+    nodemap = num.zeros(ncoord, num.int)
+    fullnodes = submesh["full_nodes"][p]
+
+    subtriangles = []
+    for i in xrange(ntriangles):
+        if trianglemap[i] != 0:
+            t = list(mesh.triangles[i])
+            nodemap[t[0]] = 1
+            nodemap[t[1]] = 1
+            nodemap[t[2]] = 1
+
+    trilist = num.reshape(num.arange(ntriangles),(ntriangles,1))
+    tsubtriangles = num.concatenate((trilist, mesh.triangles), 1)
+    subtriangles = tsubtriangles.take(num.flatnonzero(trianglemap),axis=0)
+
+    
+    # Keep a record of the triangle vertices, if they are not already there
+
+    for n in fullnodes:
+        nodemap[int(n[0])] = 0
+
+    nodelist = num.reshape(num.arange(ncoord),(ncoord,1))
+    tsubnodes = num.concatenate((nodelist, mesh.get_nodes()), 1)
+    subnodes = tsubnodes.take(num.flatnonzero(nodemap),axis=0)
+
+    # Clean up before exiting
+
+    del (nodelist)
+    del (trilist)
+    del (tsubnodes)
+    del (nodemap)
+    del (trianglemap)
+
+    # Return the triangles and vertices sitting on the boundary layer
+
+    return subnodes, subtriangles, layer_width
+
+
+
+def ghost_layer(submesh, mesh, p, tupper, tlower, parameters = None):
+
+    ncoord = mesh.number_of_nodes
+    ntriangles = mesh.number_of_triangles
+
+    if parameters is None:
+        layer_width  = 2
+    else:
+        layer_width = parameters['ghost_layer_width']
+
+
+    full_ids = num.arange(tlower, tupper)
+
+    n0 = mesh.neighbours[full_ids, :]
+    n0 = num.unique(n0.flat)
+    n0 = num.extract(n0>=0,n0)
+    n0 = num.extract(num.logical_or(n0<tlower, tupper<= n0), n0)
+
+    layer_cells = {}
+    layer_cells[0] = n0
+
+
+    # Find the subsequent layers of ghost triangles
+    for i in range(layer_width-1):
+
+        # use previous layer as a start
+        n0 = mesh.neighbours[n0, :]
+        n0 = num.unique(n0.flat)
+        n0 = num.extract(n0>=0,n0)
+        n0 = num.extract(num.logical_or(n0<tlower, tupper<= n0), n0)
+
+        for j in xrange(i+1):
+            n0 = numset.setdiff1d(n0,layer_cells[j])
+
+        layer_cells[i+1] = n0
+
+
+    # Build the triangle list and make note of the vertices
+    new_trianglemap = layer_cells[0]
+    for i in range(layer_width-1):
+        new_trianglemap = numset.union1d(new_trianglemap,layer_cells[i+1])
+
+    new_subtriangles = num.concatenate((num.reshape(new_trianglemap, (-1,1)), mesh.triangles[new_trianglemap]), 1)
+
+
+
+
+    fullnodes = submesh["full_nodes"][p]
+    full_nodes_ids = num.array(fullnodes[:,0],num.int)
+
+    new_nodes = num.unique(mesh.triangles[new_trianglemap].flat)
+    new_nodes = numset.setdiff1d(new_nodes,full_nodes_ids)
+
+    new_subnodes = num.concatenate((num.reshape(new_nodes, (-1,1)), mesh.nodes[new_nodes]), 1)
+
+    # Clean up before exiting
+
+    del (new_nodes)
+    del (layer_cells)
+    del (n0)
+    del (new_trianglemap)
+
+    # Return the triangles and vertices sitting on the boundary layer
+
+    return new_subnodes, new_subtriangles, layer_width
+
+#########################################################
+#
+# Find the edges of the ghost trianlges that do not
+# have a neighbour in the current cell. These are
+# treated as a special type of boundary edge.
+#
+#  *) Given the ghost triangles in a particular
+# triangle, use the mesh to find its neigbours. If
+# the neighbour is not in the processor set it to
+# be a boundary edge
+#
+#  *) The vertices in the ghost triangles must also
+# be added to the node list for the current processor
+#
+#  *) The boundary edges for the ghost triangles are
+# ignored.
+#
+# -------------------------------------------------------
+#
+#  *) The type assigned to the ghost boundary edges is 'ghost'
+#
+#  *)  The boundary information is returned as a directorier
+# with the key = (triangle id, edge no) and the values
+# assigned to the key is 'ghost'
+#
+#
+#########################################################
+def is_in_processor(ghost_list, tlower, tupper, n):
+
+    return num.equal(ghost_list,n).any() or (tlower <= n and tupper > n)
+
+
+def ghost_bnd_layer_old(ghosttri, tlower, tupper, mesh, p):
+
+
+    boundary = mesh.boundary
+
+    ghost_list = []
+    subboundary = {}
+
+
+    # FIXME SR: For larger layers need to pass through the correct
+    # boundary tag!
+
+    for t in ghosttri:
+        ghost_list.append(t[0])
+    
+    for t in ghosttri:
+
+        n = mesh.neighbours[t[0], 0]
+        if not is_in_processor(ghost_list, tlower, tupper, n):
+            if boundary.has_key( (t[0], 0) ):
+                subboundary[t[0], 0] = boundary[t[0],0]
+            else:
+                subboundary[t[0], 0] = 'ghost'
+
+
+        n = mesh.neighbours[t[0], 1]
+        if not is_in_processor(ghost_list, tlower, tupper, n):
+            if boundary.has_key( (t[0], 1) ):
+                subboundary[t[0], 1] = boundary[t[0],1]
+            else:
+                subboundary[t[0], 1] = 'ghost'
+
+
+        n = mesh.neighbours[t[0], 2]
+        if not is_in_processor(ghost_list, tlower, tupper, n):
+            if boundary.has_key( (t[0], 2) ):
+                subboundary[t[0], 2] = boundary[t[0],2]
+            else:
+                subboundary[t[0], 2] = 'ghost'
+            
+    return subboundary
+
+
+def ghost_bnd_layer(ghosttri, tlower, tupper, mesh, p):
+
+
+    boundary = mesh.boundary
+
+    ghost_list = []
+    subboundary = {}
+
+
+    new_ghost_list = ghosttri[:,0]
+
+    #print new_ghost_list
+
+    # 0 edge boundaries
+    nghb0 = mesh.neighbours[new_ghost_list,0]
+    gl0 = num.extract(num.logical_or(nghb0 < tlower, nghb0 >= tupper), new_ghost_list)
+    nghb0 = mesh.neighbours[gl0,0]
+    flag = numset.in1d(nghb0,new_ghost_list)
+    gl0 = num.extract(num.logical_not(flag),gl0)
+    edge0 = 0*num.ones_like(gl0)
+    n0 = len(edge0)
+    values0 = ['ghost']*n0
+
+    # 1 edge boundary
+    nghb1 = mesh.neighbours[new_ghost_list,1]
+    gl1 = num.extract(num.logical_or(nghb1 < tlower, nghb1 >= tupper), new_ghost_list)
+    nghb1 = mesh.neighbours[gl1,1]
+    flag = numset.in1d(nghb1,new_ghost_list)
+    gl1 = num.extract(num.logical_not(flag),gl1)
+    edge1 = 1*num.ones_like(gl1)
+    n1 = len(edge1)
+    values1 = ['ghost']*n1
+
+    # 2 edge boundary
+    nghb2 = mesh.neighbours[new_ghost_list,2]
+    gl2 = num.extract(num.logical_or(nghb2 < tlower, nghb2 >= tupper), new_ghost_list)
+    nghb2 = mesh.neighbours[gl2,2]
+    flag = numset.in1d(nghb2,new_ghost_list)
+    gl2 = num.extract(num.logical_not(flag),gl2)
+    edge2 = 2*num.ones_like(gl2)
+    n2 = len(edge2)
+    values2 = ['ghost']*n2
+
+
+    gl = num.concatenate((gl0,gl1,gl2))
+    edge = num.concatenate((edge0,edge1,edge2))
+    values = values0 + values1 + values2
+#    print gl
+#    print edge
+#    print values
+
+    subboundary = dict(zip(zip(gl,edge),values))
+    #intersect with boundary 
+
+    # FIXME SR: these keys should be viewkeys but need python 2.7
+    subboundary.update( (k,boundary[k]) for k in set(subboundary.keys()) & set(boundary.keys()) )
+
+    #print subboundary
+
+
+    return subboundary
+
+#########################################################
+#
+# The ghost triangles on the current processor will need
+# to get updated information from the neighbouring
+# processor containing the corresponding full triangles.
+#
+#  *) The tri_per_proc is used to determine which
+# processor contains the full node copy.
+#
+# -------------------------------------------------------
+#
+#  *) The ghost communication pattern consists of
+# [global node number, neighbour processor number].
+#
+#########################################################
+
+def ghost_commun_pattern_old(subtri, p, tri_per_proc):
+
+    # Loop over the ghost triangles
+
+    ghost_commun = num.zeros((len(subtri), 2), num.int)
+
+    for i in xrange(len(subtri)):
+        global_no = subtri[i][0]
+
+        # Find which processor contains the full triangle
+
+        nproc = len(tri_per_proc)
+        neigh = nproc-1
+        sum = 0
+        for q in xrange(nproc-1):
+            if (global_no < sum+tri_per_proc[q]):
+                neigh = q
+                break
+            sum = sum+tri_per_proc[q]
+
+        # Keep a copy of the neighbour processor number
+
+        ghost_commun[i] = [global_no, neigh]
+
+    return ghost_commun
+
+
+
+def ghost_commun_pattern_old_2(subtri, p, tri_per_proc_range):
+
+    # Loop over the ghost triangles
+
+    ghost_commun = num.zeros((len(subtri), 2), num.int)
+
+    #print tri_per_proc_range
+    #print tri_per_proc
+    
+    for i in xrange(len(subtri)):
+        global_no = subtri[i][0]
+
+        # Find which processor contains the full triangle
+        new_neigh = num.searchsorted(tri_per_proc_range, global_no)
+
+        ghost_commun[i] = [global_no, new_neigh]
+
+    return ghost_commun
+
+
+def ghost_commun_pattern(subtri, p, tri_per_proc_range):
+
+
+    global_no = num.reshape(subtri[:,0],(-1,1))
+    neigh = num.reshape(num.searchsorted(tri_per_proc_range, global_no), (-1,1))
+
+    ghost_commun = num.concatenate((global_no, neigh), axis=1)
+
+
+    return ghost_commun
+
+#########################################################
+#
+# The full triangles in this processor must communicate
+# updated information to neighbouring processor that
+# contain ghost triangles
+#
+#  *) The ghost communication pattern for all of the
+# processor must be built before calling this processor.
+#
+#  *) The full communication pattern is found by looping
+# through the ghost communication pattern for all of the
+# processors. Recall that this information is stored in
+# the form [global node number, neighbour processor number].
+# The full communication for the neighbour processor is
+# then updated.
+#
+# -------------------------------------------------------
+#
+#  *) The full communication pattern consists of
+# [global id, [p1, p2, ...]], where p1, p2 etc contain
+# a ghost node copy of the triangle global id.
+#
+#########################################################
+
+def full_commun_pattern(submesh, tri_per_proc):
+    tlower = 0
+    nproc = len(tri_per_proc)
+    full_commun = []
+
+    # Loop over the processor
+
+    for p in xrange(nproc):
+
+        # Loop over the full triangles in the current processor
+        # and build an empty dictionary
+
+        fcommun = {}
+        tupper = tri_per_proc[p]+tlower
+        for i in xrange(tlower, tupper):
+            fcommun[i] = []
+        full_commun.append(fcommun)
+        tlower = tupper
+
+    # Loop over the processor again
+
+    for p in xrange(nproc):
+
+        # Loop over the ghost triangles in the current processor,
+        # find which processor contains the corresponding full copy
+        # and note that the processor must send updates to this
+        # processor
+
+        for g in submesh["ghost_commun"][p]:
+            neigh = g[1]
+            full_commun[neigh][g[0]].append(p)
+
+    return full_commun
+
+
+#########################################################
+#
+# Given the non-overlapping grid partition, an extra layer
+# of triangles are included to help with the computations.
+# The triangles in this extra layer are not updated by
+# the processor, their updated values must be sent by the
+# processor containing the original, full, copy of the
+# triangle. The communication pattern that controls these
+# updates must also be built.
+#
+#  *) Assumes that full triangles, nodes etc have already
+# been found and stored in submesh
+#
+#  *) See the documentation for ghost_layer,
+# ghost_commun_pattern and full_commun_pattern
+#
+# -------------------------------------------------------
+#
+#  *) The additional information is added to the submesh
+# dictionary. See the documentation for ghost_layer,
+# ghost_commun_pattern and full_commun_pattern
+#
+#  *) The ghost_triangles, ghost_nodes, ghost_boundary,
+# ghost_commun and full_commun is added to submesh
+#########################################################
+
+def submesh_ghost(submesh, mesh, triangles_per_proc, parameters = None):
+
+    nproc = len(triangles_per_proc)
+    tlower = 0
+    ghost_triangles = []
+    ghost_nodes = []
+    ghost_commun = []
+    ghost_bnd = []
+    ghost_layer_width = []
+
+    # Loop over the processors
+    triangles_per_proc_ranges = num.cumsum(triangles_per_proc) - 1
+    
+    for p in xrange(nproc):
+
+        # Find the full triangles in this processor
+
+        tupper = triangles_per_proc[p]+tlower
+
+        # Build the ghost boundary layer
+
+        [subnodes, subtri, layer_width] = \
+                   ghost_layer(submesh, mesh, p, tupper, tlower, parameters)
+        ghost_layer_width.append(layer_width)
+        ghost_triangles.append(subtri)
+        ghost_nodes.append(subnodes)
+
+
+        # Find the new boundary formed by the ghost triangles
+        
+        subbnd = ghost_bnd_layer(subtri, tlower, tupper, mesh, p)
+        ghost_bnd.append(subbnd)
+        
+        # Build the communication pattern for the ghost nodes
+        gcommun = \
+                ghost_commun_pattern(subtri, p, triangles_per_proc_ranges)
+        ghost_commun.append(gcommun)
+
+        # Move to the next processor
+
+        tlower = tupper
+
+
+    # Record the ghost layer and communication pattern
+    submesh["ghost_layer_width"] = ghost_layer_width
+    submesh["ghost_nodes"] = ghost_nodes
+    submesh["ghost_triangles"] = ghost_triangles
+    submesh["ghost_commun"] = ghost_commun
+    submesh["ghost_boundary"] = ghost_bnd
+    
+    # Build the communication pattern for the full triangles
+
+    full_commun = full_commun_pattern(submesh, triangles_per_proc)
+    submesh["full_commun"] = full_commun
+
+    # Return the submesh
+
+    return submesh
+
+
+#########################################################
+#
+# Certain quantities may be assigned to the triangles,
+# these quantities must be subdivided in the same way
+# as the triangles
+#
+#  *) The quantities are ordered in the same way as the
+# triangles
+#
+# -------------------------------------------------------
+#
+#  *) The quantites attached to the full triangles are
+# stored in full_quan
+#
+#  *) The quantities attached to the ghost triangles are
+# stored in ghost_quan
+#########################################################
+
+def submesh_quantities(submesh, quantities, triangles_per_proc):
+
+    nproc = len(triangles_per_proc)
+
+    lower = 0
+
+    # Build an empty dictionary to hold the quantites
+
+    submesh["full_quan"] = {}
+    submesh["ghost_quan"] = {}
+    for k in quantities:
+        submesh["full_quan"][k] = []
+        submesh["ghost_quan"][k] = []
+
+    # Loop trough the subdomains
+
+    for p in xrange(nproc):
+        upper =   lower+triangles_per_proc[p]
+
+        # Find the global ID of the ghost triangles
+
+        global_id = []
+        M = len(submesh["ghost_triangles"][p])
+        for j in xrange(M):
+            global_id.append(submesh["ghost_triangles"][p][j][0])
+
+        # Use the global ID to extract the quantites information from
+        # the full domain
+
+        for k in quantities:
+            submesh["full_quan"][k].append(quantities[k][lower:upper])
+            submesh["ghost_quan"][k].append(num.zeros( (M,3) , num.float))
+            for j in range(M):
+                submesh["ghost_quan"][k][p][j] = \
+                                               quantities[k][global_id[j]]
+
+        lower = upper
+
+    return submesh
+
+#########################################################
+#
+# Build the grid partition on the host.
+#
+#  *) See the documentation for submesh_ghost and
+# submesh_full
+#
+# -------------------------------------------------------
+#
+#  *) A dictionary containing the full_triangles,
+# full_nodes, full_boundary, ghost_triangles, ghost_nodes,
+# ghost_boundary, ghost_commun and full_commun and true boundary polygon is returned.
+#
+#########################################################
+
+def build_submesh(nodes, triangles, boundary, quantities,
+                  triangles_per_proc, parameters = None):
+
+    # Temporarily build the mesh to find the neighbouring
+    # triangles and true boundary polygon\
+
+    mesh = Mesh(nodes, triangles, boundary)
+    boundary_polygon = mesh.get_boundary_polygon()
+    
+
+    # Subdivide into non-overlapping partitions
+
+    submeshf = submesh_full(mesh, triangles_per_proc)
+    
+    # Add any extra ghost boundary layer information
+
+    submeshg = submesh_ghost(submeshf, mesh, triangles_per_proc, parameters)
+
+    # Order the quantities information to be the same as the triangle
+    # information
+
+    submesh = submesh_quantities(submeshg, quantities, \
+                                 triangles_per_proc)
+
+    submesh["boundary_polygon"] = boundary_polygon
+    return submesh
+
+#########################################################
+#
+#  Given the subdivision of the grid assigned to the
+# current processor convert it into a form that is
+# appropriate for the GA datastructure.
+#
+#  The main function of these modules is to change the
+# node numbering. The GA datastructure assumes they
+# are numbered consecutively from 0.
+#
+#  The module also changes the communication pattern
+# datastructure into a form needed by parallel_advection
+#
+#  Authors: Linda Stals and Matthew Hardy, June 2005
+#  Modified: Linda Stals, Nov 2005 (optimise python code)
+#            Steve Roberts, Aug 2009 (updating to numpy)
+#
+#
+#########################################################
+
+ 
+#########################################################
+# Convert the format of the data to that used by ANUGA
+#
+#
+# *) Change the nodes global ID's to an integer value,
+#starting from 0.
+#
+# *) The triangles and boundary edges must also be
+# updated accordingly.
+#
+# -------------------------------------------------------
+#
+# *) The nodes, triangles and boundary edges defined by
+# the new numbering scheme are returned
+#
+#########################################################
+
+def build_local_GA(nodes, triangles, boundaries, tri_map):
+
+    Nnodes =len(nodes)
+    Ntriangles = len(triangles)
+    
+    # Extract the nodes (using the local ID)
+    
+    GAnodes = num.take(nodes, (1, 2), 1)
+
+    # Build a global ID to local ID mapping
+
+    NGlobal = 0
+    for i in xrange(Nnodes):
+        if nodes[i][0] > NGlobal:
+            NGlobal = nodes[i][0]
+
+    node_map = -1*num.ones(int(NGlobal)+1, num.int)
+
+    num.put(node_map, num.take(nodes, (0,), 1).astype(num.int), \
+        num.arange(Nnodes))
+        
+    # Change the global IDs in the triangles to the local IDs
+
+    GAtriangles = num.zeros((Ntriangles, 3), num.int)
+    GAtriangles[:,0] = num.take(node_map, triangles[:,0])
+    GAtriangles[:,1] = num.take(node_map, triangles[:,1])
+    GAtriangles[:,2] = num.take(node_map, triangles[:,2])
+
+    # Change the triangle numbering in the boundaries
+
+    GAboundaries = {}
+    for b in boundaries:
+        GAboundaries[tri_map[b[0]], b[1]] = boundaries[b]
+        
+    
+    return GAnodes, GAtriangles, GAboundaries, node_map
+
+
+#########################################################
+# Change the communication format to that needed by the
+# parallel advection file.
+#
+# *) The index contains [global triangle no,
+# local triangle no.]
+#
+# -------------------------------------------------------
+#
+# *) The ghost_recv and full_send dictionaries are
+# returned.
+#
+# *) ghost_recv dictionary is local id, global id, value
+#
+# *) full_recv dictionary is local id, global id, value
+#
+# *) The information is ordered by the global id. This
+# means that the communication order is predetermined and
+# local and global id do not need to be
+# compared when the information is sent/received.
+#
+#########################################################
+
+def build_local_commun(tri_map, ghostc, fullc, nproc):
+
+    # Initialise
+
+    full_send = {}
+    ghost_recv = {}
+
+    # Build the ghost_recv dictionary (sort the
+    # information by the global numbering)
+    
+    ghostc = num.sort(ghostc, 0)
+    
+    for c in xrange(nproc):
+        s = ghostc[:,0]
+        d = num.compress(num.equal(ghostc[:,1],c), s)
+        if len(d) > 0:
+            ghost_recv[c] = [0, 0]
+            ghost_recv[c][1] = d
+            ghost_recv[c][0] = num.take(tri_map, d)
+            
+    # Build a temporary copy of the full_send dictionary
+    # (this version allows the information to be stored
+    # by the global numbering)
+
+    tmp_send = {}
+    for global_id in fullc:
+        for i in xrange(len(fullc[global_id])):
+            neigh = fullc[global_id][i]
+            if not tmp_send.has_key(neigh):
+                tmp_send[neigh] = []
+            tmp_send[neigh].append([global_id, \
+                                    tri_map[global_id]])
+
+    # Extract the full send information and put it in the form
+    # required for the full_send dictionary
+
+    for neigh in tmp_send:
+        neigh_commun = num.sort(tmp_send[neigh], 0)
+        full_send[neigh] = [0, 0]
+        full_send[neigh][0] = neigh_commun[:,1]
+        full_send[neigh][1] = neigh_commun[:,0]
+
+    return ghost_recv, full_send
+
+
+#########################################################
+# Convert the format of the data to that used by ANUGA
+#
+#
+# *) Change the nodes global ID's to an integer value,
+# starting from 0. The node numbering in the triangles
+# must also be updated to take this into account.
+#
+# *) The triangle number will also change, which affects
+# the boundary tag information and the communication
+# pattern.
+#
+# -------------------------------------------------------
+#
+# *) The nodes, triangles, boundary edges and communication
+# pattern defined by the new numbering scheme are returned
+#
+#########################################################
+
+def build_local_mesh(submesh, lower_t, upper_t, nproc):
+
+    # Combine the full nodes and ghost nodes
+
+    nodes = num.concatenate((submesh["full_nodes"], \
+                         submesh["ghost_nodes"]))
+
+    ghost_layer_width = submesh["ghost_layer_width"]
+    
+    # Combine the full triangles and ghost triangles
+
+    gtri =  num.take(submesh["ghost_triangles"],(1, 2, 3),1)
+    triangles = num.concatenate((submesh["full_triangles"], gtri))
+
+    # Combine the full boundaries and ghost boundaries
+
+    boundaries = submesh["full_boundary"]
+    for b in submesh["ghost_boundary"]:
+        boundaries[b]=submesh["ghost_boundary"][b]
+
+    # Make note of the new triangle numbers, including the ghost
+    # triangles
+
+    NGlobal = upper_t
+    for i in xrange(len(submesh["ghost_triangles"])):
+        id = submesh["ghost_triangles"][i][0]
+        if id > NGlobal:
+            NGlobal = id
+    #index = num.zeros(int(NGlobal)+1, num.int)
+    tri_map = -1*num.ones(int(NGlobal)+1, num.int)
+    tri_map[lower_t:upper_t]=num.arange(upper_t-lower_t)
+    for i in xrange(len(submesh["ghost_triangles"])):
+        tri_map[submesh["ghost_triangles"][i][0]] = i+upper_t-lower_t
+    
+    # Change the node numbering (and update the numbering in the
+    # triangles)
+
+    [GAnodes, GAtriangles, GAboundary, node_map] = \
+    build_local_GA(nodes, triangles, boundaries, tri_map)
+
+    # Extract the local quantities
+    
+    quantities ={}
+    for k in submesh["full_quan"]:
+        Nf = len(submesh["full_quan"][k])
+        Ng = len(submesh["ghost_quan"][k])
+        quantities[k] = num.zeros((Nf+Ng, 3), num.float)
+        quantities[k][0:Nf] = submesh["full_quan"][k] 
+        quantities[k][Nf:Nf+Ng] = submesh["ghost_quan"][k]
+                             
+    # Change the communication pattern into a form needed by
+    # the parallel_adv
+
+    gcommun = submesh["ghost_commun"]
+    fcommun = submesh["full_commun"]
+    [ghost_rec, full_send] = \
+                build_local_commun(tri_map, gcommun, fcommun, nproc)
+
+
+
+    tri_l2g  = extract_l2g_map(tri_map)
+    node_l2g = extract_l2g_map(node_map)
+     
+    return GAnodes, GAtriangles, GAboundary, quantities, ghost_rec, \
+           full_send, tri_map, node_map, tri_l2g, node_l2g, ghost_layer_width
+
+
+#########################################################
+#
+# Handle the communication between the host machine
+# (processor 0) and the processors. The host machine is
+# responsible for the doing the initial grid partitioning.
+#
+# The routines given below should be moved to the
+# build_submesh.py and build_local.py file to allow
+# overlapping of  communication and computation.
+# This should be done after more debugging.
+#
+#
+#  Author: Linda Stals, June 2005
+#  Modified: Linda Stals, Nov 2005 (optimise python code)
+#            Steve Roberts, Aug 2009 (update to numpy)
+#
+#
+#########################################################
+
+
+#########################################################
+#
+# Send the submesh to processor p.
+#
+# *) The order and form is strongly coupled with
+# rec_submesh.
+#
+# -------------------------------------------------------
+#
+# *) All of the information has been sent to processor p.
+#
+#########################################################
+
+def send_submesh(submesh, triangles_per_proc, p, verbose=True):
+
+    import pypar
+    
+    myid = pypar.rank()
+    nprocs = pypar.size()
+    
+    if verbose: print 'P%d: Sending submesh to P%d' %(myid, p)
+    
+    # build and send the tagmap for the boundary conditions
+    
+    tagmap = {}
+    counter = 1
+    for b in submesh["full_boundary"][p]:
+        bkey = submesh["full_boundary"][p][b]
+        if not tagmap.has_key(bkey):
+            tagmap[bkey] = counter
+            counter = counter+1
+    for b in submesh["ghost_boundary"][p]:
+        bkey = submesh["ghost_boundary"][p][b]
+        if not tagmap.has_key(bkey):
+            tagmap[bkey] = counter
+            counter = counter+1
+
+
+    # send boundary tags
+    pypar.send(tagmap, p)
+
+    # send the quantities key information
+    pypar.send(submesh["full_quan"].keys(), p)
+
+    # compress full_commun
+    flat_full_commun = []
+
+    for c in submesh["full_commun"][p]:
+        for i in range(len(submesh["full_commun"][p][c])):
+            flat_full_commun.append([c,submesh["full_commun"][p][c][i]])
+
+    # send the array sizes so memory can be allocated
+
+    setup_array = num.zeros((9,),num.int)
+    setup_array[0] = len(submesh["full_nodes"][p])
+    setup_array[1] = len(submesh["ghost_nodes"][p])
+    setup_array[2] = len(submesh["full_triangles"][p])
+    setup_array[3] = len(submesh["ghost_triangles"][p])
+    setup_array[4] = len(submesh["full_boundary"][p])
+    setup_array[5] = len(submesh["ghost_boundary"][p])
+    setup_array[6] = len(submesh["ghost_commun"][p])
+    setup_array[7] = len(flat_full_commun)
+    setup_array[8] = len(submesh["full_quan"])
+
+    x = num.array(setup_array, num.int)
+    pypar.send(x, p, bypass=True)
+
+
+    # ghost layer width
+    x = num.array(submesh["ghost_layer_width"][p], num.int)
+    pypar.send(x, p, bypass=True)
+
+
+    # send the number of triangles per processor
+    x = num.array(triangles_per_proc)
+    pypar.send(x, p, bypass=True)
+
+    # send the nodes
+    x = num.array(submesh["full_nodes"][p], num.float)
+    pypar.send(x, p, bypass=True)
+
+    x = num.array(submesh["ghost_nodes"][p], num.float)
+    pypar.send(x, p, bypass=True)
+
+    # send the triangles
+    x = num.array(submesh["full_triangles"][p], num.int)
+    pypar.send(x, p, bypass=True)
+
+    # send ghost triangles
+    x = num.array(submesh["ghost_triangles"][p], num.int)
+    pypar.send(x, p, bypass=True)
+
+
+    # send the boundary
+    bc = []
+    for b in submesh["full_boundary"][p]:
+        bc.append([b[0], b[1], tagmap[submesh["full_boundary"][p][b]]])
+
+    x = num.array(bc, num.int)
+    pypar.send(x, p, bypass=True)
+
+
+    bc = []
+    for b in submesh["ghost_boundary"][p]:
+        bc.append([b[0], b[1], tagmap[submesh["ghost_boundary"][p][b]]])
+
+    x = num.array(bc, num.int)
+    pypar.send(x, p, bypass=True)
+
+
+
+    # send the communication pattern
+    x = submesh["ghost_commun"][p]
+    pypar.send(x, p, bypass=True)
+
+
+    x = num.array(flat_full_commun, num.int)
+    pypar.send(x, p, bypass=True)
+
+
+    # send the quantities
+    for k in submesh["full_quan"]:
+        x = num.array(submesh["full_quan"][k][p], num.float)
+        pypar.send(x, p, bypass=True)
+        
+    for k in submesh["ghost_quan"]:
+        x = num.array(submesh["ghost_quan"][k][p], num.float)
+        pypar.send(x,p, bypass=True)
+
+
+
+#########################################################
+#
+# Receive the submesh from processor p.
+#
+# *) The order and form is strongly coupled with
+# send_submesh.
+#
+# -------------------------------------------------------
+#
+# *) All of the information has been received by the
+# processor p and passed into build_local.
+#
+# *) The information is returned in a form needed by the
+# GA datastructure.
+#
+#########################################################
+
+def rec_submesh_flat(p, verbose=True):
+
+    import pypar
+    
+    numprocs = pypar.size()
+    myid = pypar.rank()
+
+    submesh_cell = {}
+    
+    if verbose: print indent+'P%d: Receiving submesh from P%d' %(myid, p)
+
+    # receive the tagmap for the boundary conditions
+    
+    tagmap = pypar.receive(p)
+
+    itagmap = {}
+    for t in tagmap:
+        itagmap[tagmap[t]]=t
+
+    # receive the quantities key information
+    qkeys = pypar.receive(p)
+
+    # recieve information about the array sizes
+    x = num.zeros((9,),num.int)
+    pypar.receive(p, buffer=x,  bypass=True)
+    setup_array = x
+
+    no_full_nodes      = setup_array[0]
+    no_ghost_nodes     = setup_array[1]
+    no_full_triangles  = setup_array[2]
+    no_ghost_triangles = setup_array[3]
+    no_full_boundary   = setup_array[4]
+    no_ghost_boundary  = setup_array[5]
+    no_ghost_commun    = setup_array[6]
+    no_full_commun     = setup_array[7]
+    no_quantities      = setup_array[8]
+
+    
+    # ghost layer width
+    x = num.zeros((1,),num.int)
+    pypar.receive(p, buffer=x,  bypass=True)
+    submesh_cell["ghost_layer_width"] = x[0]
+
+
+    # receive the number of triangles per processor
+    x = num.zeros((numprocs,),num.int)
+    pypar.receive(p, buffer=x,  bypass=True)
+    triangles_per_proc = x
+
+    # receive the full nodes
+    x = num.zeros((no_full_nodes,3),num.float)
+    pypar.receive(p, buffer=x,  bypass=True)
+    submesh_cell["full_nodes"] = x
+
+
+    # receive the ghost nodes
+    x = num.zeros((no_ghost_nodes,3),num.float)
+    pypar.receive(p, buffer=x,  bypass=True)
+    submesh_cell["ghost_nodes"] = x
+    
+    # receive the full triangles
+    x = num.zeros((no_full_triangles,3),num.int)
+    pypar.receive(p, buffer=x,  bypass=True)
+    submesh_cell["full_triangles"] = x
+
+    
+    # receive the ghost triangles
+    x = num.zeros((no_ghost_triangles,4),num.int)
+    pypar.receive(p, buffer=x,  bypass=True)
+    submesh_cell["ghost_triangles"] = x
+
+
+
+    # receive the full boundary
+    x = num.zeros((no_full_boundary,3),num.int)
+    pypar.receive(p, buffer=x,  bypass=True)
+    bnd_c = x
+
+    submesh_cell["full_boundary"] = {}
+    for b in bnd_c:
+        submesh_cell["full_boundary"][b[0],b[1]]=itagmap[b[2]]
+
+
+    # receive the ghost boundary
+    x = num.zeros((no_ghost_boundary,3),num.int)
+    pypar.receive(p, buffer=x,  bypass=True)
+    bnd_c = x
+
+    submesh_cell["ghost_boundary"] = {}
+    for b in bnd_c:
+        submesh_cell["ghost_boundary"][b[0],b[1]]=itagmap[b[2]]
+
+    # receive the ghost communication pattern
+    x = num.zeros((no_ghost_commun,2),num.int)
+    pypar.receive(p, buffer=x,  bypass=True)
+    submesh_cell["ghost_commun"] = x
+    
+    # receive the full communication pattern
+    x = num.zeros((no_full_commun,2),num.int)
+    pypar.receive(p, buffer=x,  bypass=True)
+    full_commun = x
+
+    submesh_cell["full_commun"] = {}
+    for c in full_commun:
+        submesh_cell["full_commun"][c[0]] = []
+    for c in full_commun:
+        submesh_cell["full_commun"][c[0]].append(c[1])
+
+    # receive the quantities
+
+    submesh_cell["full_quan"]={}
+    for i in range(no_quantities):
+        x = num.zeros((no_full_triangles,3), num.float)
+        pypar.receive(p, buffer=x, bypass=True)
+        submesh_cell["full_quan"][qkeys[i]]= x
+
+    submesh_cell["ghost_quan"]={}
+    for i in range(no_quantities):
+        x = num.zeros((no_ghost_triangles,3), num.float)
+        pypar.receive(p, buffer=x, bypass=True)
+        submesh_cell["ghost_quan"][qkeys[i]]= x
+    
+    return submesh_cell, triangles_per_proc,\
+           no_full_nodes, no_full_triangles
+
+
+
+#########################################################
+#
+# Receive the submesh from processor p.
+#
+# *) The order and form is strongly coupled with
+# send_submesh.
+#
+# -------------------------------------------------------
+#
+# *) All of the information has been received by the
+# processor p and passed into build_local.
+#
+# *) The information is returned in a form needed by the
+# GA datastructure.
+#
+#########################################################
+
+def rec_submesh(p, verbose=True):
+
+    import pypar
+    
+    numproc = pypar.size()
+    myid = pypar.rank()
+
+    [submesh_cell, triangles_per_proc,\
+     number_of_full_nodes, number_of_full_triangles] = rec_submesh_flat(p,verbose)
+    
+    # find the full triangles assigned to this processor
+
+    lower_t = 0
+    for i in range(myid):
+        lower_t = lower_t+triangles_per_proc[i]
+    upper_t = lower_t+triangles_per_proc[myid]
+
+    # convert the information into a form needed by the GA
+    # datastructure
+
+    [GAnodes, GAtriangles, boundary, quantities, \
+     ghost_rec, full_send, \
+     tri_map, node_map, tri_l2g, node_l2g, \
+     ghost_layer_width] = \
+     build_local_mesh(submesh_cell, lower_t, upper_t, numproc)
+    
+    return GAnodes, GAtriangles, boundary, quantities,\
+           ghost_rec, full_send,\
+           number_of_full_nodes, number_of_full_triangles, tri_map, node_map,\
+           tri_l2g, node_l2g, ghost_layer_width
+
+
+
+
+#########################################################
+#
+# Extract the submesh that will belong to the
+# processor 0 (i.e. processor zero)
+#
+#  *) See the documentation for build_submesh
+#
+# -------------------------------------------------------
+#
+#  *) A dictionary containing the full_triangles,
+# full_nodes, full_boundary, ghost_triangles, ghost_nodes,
+# ghost_boundary, ghost_commun and full_commun belonging
+# to processor zero are returned.
+#
+#########################################################
+def extract_submesh(submesh, triangles_per_proc, p2s_map=None, p=0):
+
+    
+    submesh_cell = {}
+    submesh_cell["ghost_layer_width"] = submesh["ghost_layer_width"][p]
+    submesh_cell["full_nodes"] = submesh["full_nodes"][p]
+    submesh_cell["ghost_nodes"] = submesh["ghost_nodes"][p]
+    submesh_cell["full_triangles"] = submesh["full_triangles"][p]
+    submesh_cell["ghost_triangles"] = submesh["ghost_triangles"][p]
+    submesh_cell["full_boundary"] = submesh["full_boundary"][p]
+    submesh_cell["ghost_boundary"] = submesh["ghost_boundary"][p]
+    submesh_cell["ghost_commun"] = submesh["ghost_commun"][p]
+    submesh_cell["full_commun"] = submesh["full_commun"][p]
+    submesh_cell["full_quan"] ={}
+    submesh_cell["ghost_quan"]={}
+    for k in submesh["full_quan"]:
+        submesh_cell["full_quan"][k] = submesh["full_quan"][k][p]
+        submesh_cell["ghost_quan"][k] = submesh["ghost_quan"][k][p]
+
+
+    # FIXME SR: I think there is already a structure with this info in the mesh
+    lower_t = 0
+    for i in range(p):
+        lower_t = lower_t+triangles_per_proc[i]
+    upper_t = lower_t+triangles_per_proc[p]
+
+    numprocs = len(triangles_per_proc)
+    points, vertices, boundary, quantities, ghost_recv_dict, \
+            full_send_dict, tri_map, node_map, tri_l2g, node_l2g, \
+            ghost_layer_width = \
+            build_local_mesh(submesh_cell, lower_t, upper_t, numprocs)
+
+
+    if p2s_map is None:
+        pass
+    else:
+        try:
+            tri_l2g = p2s_map[tri_l2g]
+        except:
+            tri_l2g = p2s_map
+
+    return  points, vertices, boundary, quantities, ghost_recv_dict, \
+           full_send_dict, tri_map, node_map, tri_l2g, node_l2g, ghost_layer_width
+           
+
+
+def extract_l2g_map(map):
+    # Extract l2g data  from corresponding map
+    # Maps
+
+    import numpy as num
+
+    b = num.arange(len(map))
+
+    l_ids = num.extract(map>-1,map)
+    g_ids = num.extract(map>-1,b)
+
+
+#    print len(g_ids)
+#    print len(l_ids)
+#    print l_ids
+#    print g_ids
+
+    l2g = num.zeros_like(g_ids)
+    l2g[l_ids] = g_ids
+
+    return l2g
+
+
+
+
+