def test_boruvka_sequential_4elt(self):
# get MST from Boruvka algorithm
graph = load_graph_for_boruvka(path_4elt)
dest, weight, firstedge, outdegree = graph
n_edges = dest.size
n_vertices = firstedge.size
t1 = Timer()
t1.tic()
mst, n_mst = boruvka_minho_seq(dest, weight, firstedge, outdegree)
t1.tac()
if n_mst < mst.size:
mst = mst[:n_mst]
# print 'graph nodes: ', n_edges
# print 'MST edges: ', n_mst
# get MST from scipy library
graph_csr = load_sparse_csr(path_4elt)
scipy_mst = minimum_spanning_tree(graph_csr)
true_mst_size = scipy_mst.size
assert_msg = 'MST number of edges mismatch'
self.assertEqual(n_mst, true_mst_size, assert_msg)
assert_msg = 'MST total weight mismatch'
self.assertEqual(weight[mst].sum(), scipy_mst.sum(), assert_msg)
def sl_mst_lifetime_seq(dest, weight, fe, od, disconnect_weight=None):
if disconnect_weight is None:
disconnect_weight = weight.max()
mst, n_edges = boruvka_minho_seq(dest, weight, fe, od)
# Get array with only the considered weights in the MST
# and remove those edges in the MST edge list
mst_weights = weight[mst[:n_edges]]
# Sort the MST weights. There are no repeated edges at this
# point since the output MST is like a directed graph.
sortedWeightArgs = mst_weights.argsort()
mst_weights = mst_weights[sortedWeightArgs]
mst = mst[sortedWeightArgs]
# Allocate array for the lifetimes.
lifetimes = mst_weights[1:] - mst_weights[:-1]
arg_max_lt = lifetimes.argmax()
max_lt = lifetimes[arg_max_lt]
# this is the lifetime between edges with no connection and the weakest link
#lt_threshold = disconnect_weight - max_lt
lt_threshold = disconnect_weight - mst_weights[-1]
# if the maximum lifetime if higher or equal than the lifetime threshold
# cut the tree
if max_lt >= lt_threshold:
# from arg_max_lt onward all edges are discarded
n_discarded = lifetimes.size - arg_max_lt + 1
# remove edges
mst = mst[:-n_discarded]
del lifetimes, mst_weights
ndest = np.empty(mst.size * 2, dtype=dest.dtype)
nweight = np.empty(mst.size * 2, dtype=weight.dtype)
nfe = np.empty_like(fe)
nod = np.zeros_like(od)
# build graph from mst
getGraphFromEdges_seq(dest, weight, fe, od, mst, nod, nfe, ndest, nweight)
labels = connected_comps_seq(ndest, nweight, nfe, nod)
del ndest, nweight, nfe, nod
return labels
def test_seq_gpu(self):
print "HOST VS DEVICE"
same_sol = list()
same_cost = list()
for r in range(20):
sp_mat = load_sparse_csr(path_4elt)
dest = sp_mat.indices
weight = sp_mat.data
firstedge = sp_mat.indptr[:-1] # last element is the total number
outdegree = np.empty_like(firstedge)
outdegree_from_firstedge(firstedge, outdegree, dest.size)
n_edges = dest.size
n_vertices = firstedge.size
t1, t2 = Timer(), Timer()
t1.tic()
mst1, n_edges1 = boruvka_minho_seq(dest, weight,
firstedge, outdegree)
t1.tac()
if n_edges1 < mst1.size:
mst1 = mst1[:n_edges1]
mst1.sort()
assert_msg = '4elt dataset MST not fully connected in sequential'
self.assertEqual(mst1.size, n_vertices-1, assert_msg)
t2.tic()
mst2, n_edges2 = boruvka_minho_gpu(dest, weight, firstedge,
outdegree, MAX_TPB=256)
t2.tac()
if n_edges2 < mst2.size:
mst2 = mst2[:n_edges2]
mst2.sort()
assert_msg = '4elt dataset MST not fully connected in gpu'
self.assertEqual(mst2.size, n_vertices-1, assert_msg)
# how many edges are common to both solutions
# same_sol.append(np.in1d(mst1, mst2).sum())
# check MST cost
cost1 = weight[mst1].sum()
cost2 = weight[mst2].sum()
self.assertEqual(cost1, cost2, 'MSTs have diferent costs')
def mst_cal():
sp_cal = load_csr_graph(home + "QCThesis/datasets/graphs/USA-road-d.CAL.csr")
dest, weight, firstEdge, outDegree = get_boruvka_format(sp_cal)
del sp_cal
print "# edges: ", dest.size
print "# vertices: ", firstEdge.size
print "size of graph (MB): ", (dest.size + weight.size + firstEdge.size + outDegree.size) * 4.0 / 1024 / 1024
times_cpu = list()
times_gpu = list()
equal_mst = list()
equal_cost = list()
t1, t2 = Timer(), Timer()
for r in range(10):
print "cpu round ", r
t1.tic()
mst1, n_edges1 = boruvka_minho_seq(dest, weight, firstEdge, outDegree)
t1.tac()
print "finished in ", t1.elapsed
if n_edges1 < mst1.size:
mst1 = mst1[:n_edges1]
print "gpu round ", r
t2.tic()
mst2, n_edges2 = boruvka_minho_gpu(dest, weight, firstEdge, outDegree, MAX_TPB=512)
t2.tac()
print "finished in ", t2.elapsed
print ""
if n_edges2 < mst2.size:
mst2 = mst2[:n_edges2]
equal_mst.append(np.in1d(mst1,mst2).all())
equal_cost.append(weight[mst1].sum() == weight[mst2].sum())
if r > 0:
times_cpu.append(t1.elapsed)
times_gpu.append(t2.elapsed)
print equal_mst
print equal_cost
print "average time cpu: ", np.mean(times_cpu)
print "average time gpu: ", np.mean(times_gpu)
def host_vs_device():
print "HOST VS DEVICE"
same_sol = list()
same_cost = list()
for r in range(20):
dest, weight, firstEdge, outDegree = load_graph("4elt")
t1, t2 = Timer(), Timer()
t1.tic()
mst1, n_edges1 = boruvka_minho_seq(dest, weight, firstEdge, outDegree)
t1.tac()
if n_edges1 < mst1.size:
mst1 = mst1[:n_edges1]
mst1.sort()
t2.tic()
mst2, n_edges2 = boruvka_minho_gpu(dest, weight, firstEdge, outDegree, MAX_TPB=256)
t2.tac()
if n_edges2 < mst2.size:
mst2 = mst2[:n_edges2]
mst2.sort()
same_sol.append(np.in1d(mst1,mst2).sum())
same_cost.append(weight[mst1].sum() == weight[mst2].sum())
#same_sol.append((mst1==mst2).all())
print "no. edges: ", weight.size
print "no. nodes: ", firstEdge.size
print "Same solution: ", same_sol
print "Same cost:", np.all(same_cost)
print "Solution CPU cost: ", weight[mst1].sum()
print "Solution GPU cost: ", weight[mst2].sum()
print "Host time elapsed: ", t1.elapsed
print "Device time elapsed: ", t2.elapsed
def host_boruvka():
print "HOST CPU BORUVKA"
dest, weight, firstEdge, outDegree = load_graph("4elt")
t1 = Timer()
t1.tic()
mst, n_edges = boruvka_minho_seq(dest, weight, firstEdge, outDegree)
t1.tac()
print "mst size", mst.size
if n_edges < mst.size:
mst = mst[:n_edges]
print "time elapsed: ", t1.elapsed
mst.sort() # mst has to be sorted for comparison with device mst because different threads might be able to write first
print mst
print n_edges
def analyze_graph_from_h5(filename, verbose=False):
def v_print(vstr):
if verbose:
print vstr
csr_mat = load_h5_to_csr(filename)
dest, weight, firstEdge, outDegree = get_boruvka_format(csr_mat)
del csr_mat
n_e = dest.size
n_v = firstEdge.size
mem = (dest.size*dest.itemsize + weight.size*weight.itemsize + firstEdge.size*firstEdge.itemsize + outDegree.size*outDegree.itemsize)/ (1024.0**2)
print "# edges: ", n_e
print "# vertices: ", n_v
print "size of graph (MB): ", mem
times_cpu = list()
times_gpu = list()
equal_mst = list()
equal_cost = list()
mst_costs = {'cpu':list(), 'gpu':list()}
t1, t2 = Timer(), Timer()
for r in range(10):
v_print('------ Round {} -------'.format(r))
t1.reset()
t1.tic()
mst1, n_edges1 = boruvka_minho_seq(dest, weight, firstEdge, outDegree)
t1.tac()
v_print('CPU finished in {} s'.format(t1.elapsed))
if n_edges1 < mst1.size:
mst1 = mst1[:n_edges1]
t2.reset()
t2.tic()
mst2, n_edges2 = boruvka_minho_gpu(dest, weight, firstEdge, outDegree, MAX_TPB=512)
t2.tac()
v_print('GPU finished in {} s'.format(t2.elapsed))
if n_edges2 < mst2.size:
mst2 = mst2[:n_edges2]
mst_costs['cpu'].append(weight[mst1].sum())
mst_costs['gpu'].append(weight[mst2].sum())
equal_mst.append(np.in1d(mst1,mst2).all())
equal_cost.append(weight[mst1].sum() == weight[mst2].sum())
if r > 0:
times_cpu.append(t1.elapsed)
times_gpu.append(t2.elapsed)
max_cost = max((max(mst_costs['cpu']), max(mst_costs['gpu'])))
cost_error = map(lambda x: abs(x[0]-x[1]), zip(*mst_costs.values()))
cost_error = map(lambda x: x/max_cost, cost_error)
error_threshold = 1e-5
cpu_str = ''
for t in times_cpu:
cpu_str += str(t) + ','
gpu_str = ''
for t in times_gpu:
gpu_str += str(t) + ','
cpu_costs = ''
for c in mst_costs['cpu']:
cpu_costs += str(c) + ','
gpu_costs = ''
for c in mst_costs['gpu']:
gpu_costs += str(c) + ','
print 'dataset: {}'.format(os.path.basename(filename))
print 'CPU times,{},{},{},{}'.format(n_e,n_v,mem,cpu_str[:-1])
print 'GPU times,{},{},{},{}'.format(n_e,n_v,mem,gpu_str[:-1])
print 'CPU costs,{},{},{},{}'.format(n_e,n_v,mem,cpu_costs[:-1])
print 'GPU costs,{},{},{},{}'.format(n_e,n_v,mem,gpu_costs[:-1])
print ''
print 'All equal MSTs: {}'.format(np.all(np.array(equal_mst) == equal_mst[0]))
print 'All equal costs: {}'.format(np.all(equal_cost))
print 'All cost errors <= {}: {}'.format(error_threshold, np.all(map(lambda x:x<error_threshold, cost_error)))
print 'Max normalized error: {}'.format(max(cost_error))
speedup = np.array(times_cpu) / np.array(times_gpu)
print 'Times(s)\tMean\tStd\tMax\tMin'
print 'CPU \t{:.5F}\t{:.5F}\t{:.5F}\t{:.5F}'.format(np.mean(times_cpu), np.std(times_cpu), np.max(times_cpu), np.min(times_cpu))
print 'GPU \t{:.5F}\t{:.5F}\t{:.5F}\t{:.5F}'.format(np.mean(times_gpu), np.std(times_gpu), np.max(times_gpu), np.min(times_gpu))
print 'SpeedUp \t{:.5F}\t{:.5F}\t{:.5F}\t{:.5F}'.format(np.mean(speedup), np.std(speedup), np.max(speedup), np.min(speedup))
print 'Error \t{:.5F}\t{:.5F}\t{:.5F}\t{:.5F}'.format(np.mean(cost_error), np.std(cost_error), np.max(cost_error), np.min(cost_error))
def mst_cluster_coassoc():
t1,t2 = Timer(), Timer()
#foldername = "/home/courses/aac2015/diogoaos/QCThesis/datasets/gaussmix1e4/"
foldername = home + "QCThesis/datasets/gaussmix1e4/"
print "Loading datasets"
t1.tic()
# dest = np.genfromtxt(foldername + "prot_dest.csr", dtype = np.int32, delimiter=",")
# weight = np.genfromtxt(foldername + "prot_weight.csr", dtype = np.float32, delimiter=",")
# fe = np.genfromtxt(foldername + "prot_fe.csr", dtype = np.int32, delimiter=",")
dest = np.genfromtxt(foldername + "full_dest.csr", dtype = np.int32, delimiter=",")
weight = np.genfromtxt(foldername + "full_weight.csr", dtype = np.float32, delimiter=",")
fe = np.genfromtxt(foldername + "full_fe.csr", dtype = np.int32, delimiter=",")
t1.tac()
print "loading elapsed time : ", t1.elapsed
fe = fe[:-1]
od = np.empty_like(fe)
outdegree_from_firstedge(fe, od, dest.size)
# fix weights to dissimilarity
weight = 100 - weight
print "# edges : ", dest.size
print "# vertices : ", fe.size
print "edges/vertices ratio : ", dest.size * 1.0 / fe.size
t1.tic()
mst, n_edges = boruvka_minho_seq(dest, weight, fe, od)
t1.tac()
print "seq: time elapsed : ", t1.elapsed
print "seq: mst size :", mst.size
print "seq: n_edges : ", n_edges
if n_edges < mst.size:
mst = mst[:n_edges]
mst.sort()
ev1,ev2 = cuda.event(), cuda.event()
ev1.record()
d_dest = cuda.to_device(dest)
d_weight = cuda.to_device(weight)
d_fe = cuda.to_device(fe)
d_od = cuda.to_device(od)
ev2.record()
send_graph_time = cuda.event_elapsed_time(ev1,ev2)
t2.tic()
mst2, n_edges2 = boruvka_minho_gpu(d_dest, d_weight, d_fe, d_od, MAX_TPB=512, returnDevAry = True)
t2.tac()
ev1.record()
mst2 = mst2.copy_to_host()
n_edges2 = n_edges2.getitem(0)
ev2.record()
recv_mst_time = cuda.event_elapsed_time(ev1,ev2)
print "gpu: send graph time : ", send_graph_time
print "gpu: time elapsed : ", t2.elapsed
print "gpu: rcv mst time : ", recv_mst_time
print "gpu: mst size :", mst2.size
print "seq: n_edges : ", n_edges2
if n_edges2 < mst2.size:
mst2 = mst2[:n_edges2]
mst2.sort()
if n_edges == n_edges2:
mst_is_equal = (mst == mst2).all()
else:
mst_is_equal = False
print "mst gpu == seq : ", mst_is_equal
def check_colors():
print "CHECK COLORS SEQ & CUDA"
#dest, weight, firstEdge, outDegree = load_graph("4elt")
sp_cal = load_csr_graph(home + "QCThesis/datasets/graphs/USA-road-d.CAL.csr")
dest, weight, firstEdge, outDegree = get_boruvka_format(sp_cal)
del sp_cal
print "# edges: ", dest.size
print "# vertices: ", firstEdge.size
print "size of graph (MB): ", (dest.size + weight.size + firstEdge.size + outDegree.size) * 4.0 / 1024 / 1024
print "# vertices: ", firstEdge.size
print "# edges: ", dest.size
print "seq: Computing MST"
t1 = Timer()
t1.tic()
mst, n_edges = boruvka_minho_seq(dest, weight, firstEdge, outDegree)
t1.tac()
print "seq: time elapsed: ", t1.elapsed
print "seq: mst size :", mst.size
print "seq: n_edges: ", n_edges
if n_edges < mst.size:
mst = mst[:n_edges]
mst.sort()
print "gpu: Computing MST"
t1.tic()
mst2, n_edges2 = boruvka_minho_gpu(dest, weight, firstEdge, outDegree, MAX_TPB=256)
t1.tac()
print "gpu: time elapsed: ", t1.elapsed
print "gpu: mst size :", mst2.size
print "seq: n_edges: ", n_edges2
if n_edges2 < mst2.size:
mst2 = mst2[:n_edges2]
mst2.sort()
print "mst gpu == seq: ", (mst == mst2).all()
# make two cuts
mst = mst[:-2]
print "seq: Generating MST graph"
nod = np.zeros(outDegree.size, dtype = outDegree.dtype)
nfe = np.empty(firstEdge.size, dtype = firstEdge.dtype)
ndest = np.empty(mst.size * 2, dtype = dest.dtype)
nweight = np.empty(mst.size * 2, dtype = weight.dtype)
t1.tic()
get_new_graph(dest, weight, firstEdge, outDegree, mst, nod, nfe, ndest, nweight)
t1.tac()
print "seq: time elapsed: ", t1.elapsed
print "seq: Computing labels"
t1.tic()
colors = getLabels_seq(ndest, nweight, nfe, nod)
t1.tac()
print "seq: time elapsed: ", t1.elapsed
print "seq: # colors: ", np.unique(colors).size
print "gpu: Computing labels"
t1.tic()
colors2 = getLabels_gpu(ndest, nweight, nfe, nod, MAX_TPB=256)
t1.tac()
print "gpu: time elapsed: ", t1.elapsed
print "gpu: # colors: ", np.unique(colors2).size
print "colors gpu == seq: ", (colors == colors2).all()