def collect_pieces(skel):
global _rank
global _size
# Gather minimal info for element polygons (to display Skeleton at #0)
# Only the #0 will store the gathered information.
# no. of nodes & no. of elements
nnodes = mpitools.Allgather_Int(skel.nnodes())
#RCL: Use maxnnodes as base offset for the indices of non-corner mesh nodes
skel.maxnnodes = max(nnodes)
nelems = mpitools.Allgather_Int(skel.nelements())
myCoords = list(
reduce(
lambda x,y: x+y, [(skel.nodePosition(nd)[0],
skel.nodePosition(nd)[1])
for nd in skel.node_iterator()]
))
coordSizes = [i*2 for i in nnodes]
allCoords = mpitools.Allgather_DoubleVec(myCoords,
size_known=coordSizes)
# allCoords = [[(x0,y0),(x1,y1), ...], [...], ...]
allCoords = [ [(allCoords[i][2*j],allCoords[i][2*j+1])
for j in range(nnodes[i])]
for i in range(_size) ]
# element connectivity signature
myEConSigs = [el.nnodes() for el in skel.element_iterator()]
allEConSigs = mpitools.Allgather_IntVec(myEConSigs, size_known=nelems)
# element connectivity
myECons = [ [skel.node_index_dict[nd.getIndex()] for nd in el.nodes]
for el in skel.element_iterator()]
myECons = reduce(lambda x,y: x+y, myECons)
conSizes = [reduce(lambda x,y: x+y, aECS) for aECS in allEConSigs]
temp = mpitools.Allgather_IntVec(myECons, size_known=conSizes)
def listrize(list, signature):
nsig = len(signature)
count = 0
output = [[] for i in range(nsig)]
for i in range(nsig):
for j in range(signature[i]):
output[i].append(list[count])
count += 1
return output
allECons = [listrize(temp[i], allEConSigs[i]) for i in range(_size)]
if _rank == 0:
skel.all_skeletons = {"nodes": allCoords,
"elements": allECons}
def createWorkOrder(self, activeNodes):
global _rank
global _size
# First the data collection
nnodes = mpitools.Allgather_Int(len(activeNodes))
allnodes = mpitools.Allgather_IntVec(
[n.getIndex() for n in activeNodes], size_known=nnodes)
allsignatures = mpitools.Allgather_IntVec(
[n.nshared() for n in activeNodes], size_known=nnodes)
nshared = [reduce(lambda x, y: x + y, s) for s in allsignatures]
myshared = [n.sharedWith() for n in activeNodes]
myshared = reduce(lambda x, y: x + y, myshared)
allshared = mpitools.Allgather_IntVec(myshared, size_known=nshared)
def listrize(list, signature):
nsig = len(signature)
count = 0
output = [[] for i in range(nsig)]
for i in range(nsig):
for j in range(signature[i]):
output[i].append(list[count])
count += 1
return output
for i in range(len(allshared)):
allshared[i] = listrize(allshared[i], allsignatures[i])
scheduler = Scheduler(nnodes, allnodes, allshared, self)
self.mywork = scheduler(_rank)
def collect_pieces(femesh):
# Build dictionary (instead of using the mesh assigned indices (via index() or get_index())
# which are unique but may have gaps)
nodedict = {}
i = 0
for node in femesh.node_iterator():
nodedict[node.index()] = i
i += 1
global _rank
global _size
# Gather minimal info for element polygons (to display mesh Skeleton at #0)
# Only the #0 will store the reconstituted information.
#RCL: Collect number of nodes from each process into an array.
# One gets this for nnodes: [nnodes0, nnodes1, ...]
nnodes = mpitools.Allgather_Int(femesh.nnodes())
#RCL: Same for the elements.
# One gets this for nelems: [nelems0, nelems1, ...]
nelems = mpitools.Allgather_Int(femesh.nelements())
myCoords = reduce(lambda x, y: x + y,
[[nd.position().x, nd.position().y]
for nd in femesh.node_iterator()])
coordSizes = [i * 2 for i in nnodes]
#RCL: Collect (x,y) coordinates of nodes from each process
# coordSizes contains the array of number of coordinates (counting x and y separately) from each process
# The return value is a 2-D array, indexed first by the process number(?)
# One gets this for allCoords: [[x0,y0,x1,y1,...], [x0',y0',x1',y1',...], ...]
allCoords = mpitools.Allgather_DoubleVec(myCoords, size_known=coordSizes)
#RCL: One gets the following format after the list comprehension operations
# allCoords = [[(x0,y0),(x1,y1), ...], [...], ...]
allCoords = [[(allCoords[i][2 * j], allCoords[i][2 * j + 1])
for j in range(nnodes[i])] for i in range(_size)]
# element connectivity signature
myEConSigs = [len(el.perimeter()) for el in femesh.element_iterator()]
#RCL: One gets this for allEConSigs: [[elnnodes0,elnnodes1,...],[elnnodes0',elnnodes1',...],...]
allEConSigs = mpitools.Allgather_IntVec(myEConSigs, size_known=nelems)
# element connectivity
#RCL: nodedict must be a map to the 0-based indices of the nodes
myECons = [[nodedict[nd.index()] for nd in el.node_iterator()]
for el in femesh.element_iterator()]
myECons = reduce(lambda x, y: x + y, myECons)
#RCL: conSizes looks like [[elnnodes0+elnnodes1+...],[elnnodes0'+elnnodes1'+...],...]
conSizes = [reduce(lambda x, y: x + y, aECS) for aECS in allEConSigs]
#RCL: temp looks like
# [[el0_nodeindex1,el0_nodeindex2,...el1_nodeindex1,el1_nodeindex2,...],[el0'_nodeindex1,el0'_nodeindex2,...,el1'_nodeindex1,el1'_nodeindex2,...],...]
temp = mpitools.Allgather_IntVec(myECons, size_known=conSizes)
#RCL: The connectivity information could still be shrunk, but its hard...
# If we store the nodes for each element, duplicate nodes results. Storage becomes ~4*(number of (double x and double y))
def listrize(list, signature):
#RCL: nsig is the number of elements if allEConsigs[i] is passed as signature
nsig = len(signature)
count = 0
output = [[] for i in range(nsig)]
for i in range(nsig):
for j in range(signature[i]):
output[i].append(list[count])
count += 1
return output
#RCL: allECons looks like [[[nodeindex1,nodeindex2,...],[nodeindex1',nodeindex2',...],...], [], ...]
allECons = [listrize(temp[i], allEConSigs[i]) for i in range(_size)]
if _rank == 0:
femesh.all_meshskeletons = {"nodes": allCoords, "elements": allECons}
def _refinement(self, skeleton, newSkeleton, context):
global _rank
if _rank == 0:
pBar = progressbar.getProgress()
markedEdges = refine.EdgeMarkings()
self.newEdgeNodes = {} # allows sharing of new edge nodes
# Primary marking
self.targets(skeleton, context, self.degree.divisions, markedEdges,
self.criterion)
# Additional marking -- only for (conservative) bisection at this point.
self.degree.markExtras(skeleton, markedEdges)
# Now, share the marking information on the boundary
shareMarkings(markedEdges, skeleton)
# Refine elements and segments
segmentdict = {} # which segments have been handled already.
elements = skeleton.elements
# At this point, to properly update progress bar, every process has
# loop over the same range(maxn).
# TODO: Is progress bar not supposed to work within IPC call?
n = len(elements)
alln = mpitools.Allgather_Int(n)
maxn = max(alln)
nelem = 0
ntotal = reduce(lambda x, y: x + y, alln)
for ii in range(maxn):
try:
oldElement = elements[ii]
count = 1
oldnnodes = oldElement.nnodes()
# Get list of number of subdivisions on each edge ("marks")
marks = markedEdges.getMarks(oldElement)
# Find the canonical order for the marks. (The order is
# ambiguous due to the arbitrary choice of the starting
# edge. Finding the canonical order allows the refinement
# rule to be found in the rule table.) rotation is the
# offset into the elements node list required to match the
# refinement rule to the element's marked edges.
# signature is the canonical ordering of the marks.
rotation, signature = refine.findSignature(marks)
# Create new nodes along the subdivided element edges
edgenodes = [
self.getNewEdgeNodes(oldElement.nodes[i],
oldElement.nodes[(i + 1) % oldnnodes],
marks[i], newSkeleton, skeleton)
for i in range(oldnnodes)
]
# Create new elements
newElements = self.rules[signature].apply(oldElement, rotation,
edgenodes, newSkeleton,
self.alpha)
# If the old element's homogeneity is "1", it's safe to say that
# new elements' homogeneities are "1".
if oldElement.homogeneity(skeleton.MS) == 1.:
for el in newElements:
el.copyHomogeneity(oldElement)
# The calls to Skeleton.newElement() made by the
# refinement rules have created new SkeletonSegments in
# newSkeleton, but have not set the parentage of those
# segments. We have to fix that here.
for newElement in newElements:
for segment in newElement.getSegments(newSkeleton):
# Only look at each segment once.
if not segmentdict.has_key(segment):
segmentdict[segment] = 1
pseg = refine.findParentSegment(
skeleton, newElement, segment, edgenodes)
if pseg:
pseg.add_child(segment)
segment.add_parent(pseg)
except IndexError:
count = 0
# No. of elements done.
nelem_step = mpitools.Allgather_Int(count)
nelem += reduce(lambda x, y: x + y, nelem_step)
if _rank == 0:
if pBar.query_stop():
pBar.set_failure()
pBar.set_message("Failed")
mpitools.Isend_Bool(False, range(1, _size))
return None
else:
pBar.set_progress(1.0 * (nelem) / ntotal)
pBar.set_message("refining skeleton: %d/%d" % (nelem, ntotal))
mpitools.Isend_Bool(True, range(1, _size))
else:
if not mpitools.Recv_Bool(0):
return
# New nodes that are created from the segments that are shared,
# have to be informed bertween sharers.
shareCommonNodes(self, markedEdges, skeleton, newSkeleton)
# Collecting Skeletons
skeletonIPC.collect_pieces(newSkeleton)
newSkeleton.cleanUp()
## report_skeleton(newSkeleton)
## if _rank == 0:
## debug.fmsg(newSkeleton.all_skeletons)
return newSkeleton