def node_cluster_stat(index, parameter_list):
"""
08-14-05
"""
index = int(index) #08-14-05 convert it to integer form, cause it's transferred as a string
from cluster_stat import cluster_stat
hostname, dbname, schema, source_table, output, gene_table, \
gene_table_commit, OffsetLimitList, debug = parameter_list
target_table = 'cluster_stat'
offset, limit = OffsetLimitList[index]
output = '%s.%s'%(output, index)
uniformity = 0
min_node_size = 0
min_node_depth = 5
bonferroni = 0
commit = 0
report = 0
log = 0
wu = 1
if debug:
sys.stderr.write("Index: %s; Offset: %s; Limit: %s\n"%(index, offset, limit))
instance = cluster_stat(hostname, dbname, schema, source_table, target_table, \
offset, limit, output, bonferroni, report, log, wu, commit, uniformity, \
min_node_size, min_node_depth)
instance.run()
del instance
depth_cut_off = 5
dir_files = output
leave_one_out = 1
wu = 1
report = 0
commit = gene_table_commit
subgraph_cut_off = 0
debug = 0
new_table = 0
recurrence_gap_size = 2
connectivity_gap_size = 2
instance = gene_stat(hostname, dbname, schema, target_table, source_table, \
leave_one_out, wu, report, depth_cut_off, dir_files, commit, gene_table, \
subgraph_cut_off, debug, new_table, recurrence_gap_size, connectivity_gap_size)
instance.run()
del instance
return output
def run(self):
"""
08-14-05
"""
communicator = MPI.world.duplicate()
fake_no_of_nodes = int((communicator.size-1)*times_nodes) #NOTICE: fake_no_of_nodes is used to enlarge(or shrink) the actual number of nodes,
#to balance the amount of work on each node
OffsetLimitList = Numeric.zeros((fake_no_of_nodes,2), Numeric.Int)
if communicator.rank == 0:
(conn, curs) = db_connect(self.hostname, self.dbname, self.schema)
OffsetLimitList = self.createOffsetLimitList(curs, self.source_table, fake_no_of_nodes)
OffsetLimitList = Numeric.array(OffsetLimitList, Numeric.Int) #transform it into Numeric array to broadcast()
if self.commit: #08-14-05 create the gene_table
instance = gene_stat()
instance.createGeneTable(curs, self.gene_table)
curs.execute('end')
if self.debug:
sys.stderr.write("OffsetLimitList: %s"%repr(OffsetLimitList))
del conn, curs
communicator.broadcast(OffsetLimitList, 0) #share the OffsetLimitList
mpi_synchronize(communicator)
job_list = range(len(OffsetLimitList)) #corresponding to the indices in the OffsetLimitList
parameter_list =[self.hostname, self.dbname, self.schema, self.source_table, self.output, \
self.gene_table, self.commit, OffsetLimitList, self.debug]
if self.debug:
sys.stderr.write("The common parameter_list is %s.\n"%repr(parameter_list))
of_name_list = mpi_schedule_jobs(communicator, job_list, node_cluster_stat, parameter_list, self.debug)
mpi_synchronize(communicator)
#collecting 08-14-05 not really necessary, but just to make the number of files small
if communicator.rank==0:
netmine_wrapper_instance = netmine_wrapper()
netmine_wrapper_instance.collect_and_merge_output(of_name_list, self.output)
def run(self):
"""
09-05-05
10-23-05
create views from old schema
result goes to the new schema's p_gene_table
(input_node)
--db_connect()
--form_schema_tables()
--form_schema_tables()
--get_gene_no2go_no_set()
--get_go_no2depth()
(pass data to computing_node)
(computing_node)
(take data from other nodes, 0 and size-1)
(judge_node)
--gene_stat()
--db_connect()
--gene_p_map_redundancy()
(output_node)
--db_connect()
--form_schema_tables()
--form_schema_tables()
--MpiPredictionFilter()
--MpiPredictionFilter_instance.createGeneTable()
--get_go_no2edge_counter_list()(if necessary)
(pass go_no2edge_counter_list to computing_node)
(input_node)
--fetch_cluster_block()
(computing_node)
--get_no_of_unknown_genes()
--node_fire_handler()
--cleanup_handler()
--judge_node()
--gene_stat_instance.(match functions)
--output_node()
--output_node_handler()
--MpiPredictionFilter_instance.submit_to_p_gene_table()
"""
communicator = MPI.world.duplicate()
node_rank = communicator.rank
if node_rank == 0:
(conn, curs) = db_connect(self.hostname, self.dbname, self.schema)
"""
#01-02-06
old_schema_instance = form_schema_tables(self.input_fname)
new_schema_instance = form_schema_tables(self.jnput_fname)
"""
gene_no2go_no = get_gene_no2go_no_set(curs)
gene_no2go_no_pickle = cPickle.dumps(gene_no2go_no, -1) #-1 means use the highest protocol
go_no2depth = get_go_no2depth(curs)
go_no2depth_pickle = cPickle.dumps(go_no2depth, -1)
go_no2gene_no_set = get_go_no2gene_no_set(curs)
go_no2gene_no_set_pickle = cPickle.dumps(go_no2gene_no_set, -1)
for node in range(1, communicator.size-2): #send it to the computing_node
communicator.send(gene_no2go_no_pickle, node, 0)
communicator.send(go_no2depth_pickle, node, 0)
communicator.send(go_no2gene_no_set_pickle, node, 0)
elif node_rank<=communicator.size-3: #WATCH: last 2 nodes are not here.
data, source, tag = communicator.receiveString(0, 0)
gene_no2go_no = cPickle.loads(data) #take the data
data, source, tag = communicator.receiveString(0, 0)
go_no2depth = cPickle.loads(data)
data, source, tag = communicator.receiveString(0, 0)
go_no2gene_no_set = cPickle.loads(data)
data, source, tag = communicator.receiveString(communicator.size-1, 0) #from the last node
go_no2edge_counter_list = cPickle.loads(data)
#choose a functor for recurrence_array
functor_dict = {0: None,
1: lambda x: int(x>=self.recurrence_x),
2: lambda x: math.pow(x, self.recurrence_x)}
functor = functor_dict[self.recurrence_x_type]
elif node_rank == communicator.size-2: #judge node
gene_stat_instance = gene_stat(depth_cut_off=self.depth)
(conn, curs) = db_connect(self.hostname, self.dbname, self.schema)
gene_stat_instance.dstruc_loadin(curs)
from gene_p_map_redundancy import gene_p_map_redundancy
node_distance_class = gene_p_map_redundancy()
elif node_rank==communicator.size-1: #establish connection before pursuing
(conn, curs) = db_connect(self.hostname, self.dbname, self.schema)
"""
#01-02-06, input and output are all directed to files
old_schema_instance = form_schema_tables(self.input_fname)
new_schema_instance = form_schema_tables(self.jnput_fname)
MpiPredictionFilter_instance = MpiPredictionFilter()
MpiPredictionFilter_instance.view_from_table(curs, old_schema_instance.splat_table, new_schema_instance.splat_table)
MpiPredictionFilter_instance.view_from_table(curs, old_schema_instance.mcl_table, new_schema_instance.mcl_table)
MpiPredictionFilter_instance.view_from_table(curs, old_schema_instance.pattern_table, new_schema_instance.pattern_table)
if self.new_table:
MpiPredictionFilter_instance.createGeneTable(curs, new_schema_instance.p_gene_table)
"""
if self.go_no2edge_counter_list_fname:
go_no2edge_counter_list = cPickle.load(open(self.go_no2edge_counter_list_fname,'r'))
else:
if self.eg_d_type==2:
go_no2edge_counter_list = None
else:
gene_no2go_no = get_gene_no2go_no_set(curs)
go_no2edge_counter_list = get_go_no2edge_counter_list(curs, gene_no2go_no, self.edge_type2index)
go_no2edge_counter_list_pickle = cPickle.dumps(go_no2edge_counter_list, -1)
for node in range(1, communicator.size-2): #send it to the computing_node
communicator.send(go_no2edge_counter_list_pickle, node, 0)
mpi_synchronize(communicator)
free_computing_nodes = range(1,communicator.size-2) #exclude the last node
if node_rank == 0:
"""
curs.execute("DECLARE crs CURSOR FOR SELECT id, vertex_set, edge_set, no_of_edges,\
connectivity, unknown_gene_ratio, recurrence_array, d_matrix from %s"%(old_schema_instance.pattern_table))
"""
self.counter = 0 #01-02-06 counter is used as id
reader = csv.reader(open(self.input_fname, 'r'), delimiter='\t')
parameter_list = [reader]
input_node(communicator, parameter_list, free_computing_nodes, self.message_size, \
self.report, input_handler=self.input_handler)
del reader
elif node_rank in free_computing_nodes:
no_of_unknown_genes = get_no_of_unknown_genes(gene_no2go_no)
GradientScorePrediction_instance = GradientScorePrediction(gene_no2go_no, go_no2gene_no_set, go_no2depth, \
go_no2edge_counter_list, no_of_unknown_genes, self.depth, self.min_layer1_associated_genes, \
self.min_layer1_ratio, self.min_layer2_associated_genes, self.min_layer2_ratio, self.exponent, \
self.score_list, self.max_layer, self.norm_exp, self.eg_d_type, self.debug)
parameter_list = [GradientScorePrediction_instance, functor]
computing_node(communicator, parameter_list, self.node_fire_handler, self.cleanup_handler, self.report)
elif node_rank == communicator.size-2:
self.judge_node(communicator, curs, gene_stat_instance, node_distance_class)
elif node_rank==communicator.size-1:
#01-02-06 output goes to plain file, not database
writer = csv.writer(open(self.jnput_fname, 'w'), delimiter='\t')
parameter_list = [writer]
output_node(communicator, free_computing_nodes, parameter_list, self.output_node_handler, self.report)
del writer
