class SwissFelCluster:
def __init__(self, cores=8, memory="24 GB", workers=5):
self.cluster = SLURMCluster(cores=cores, memory=memory)
self.client = Client(self.cluster)
self.ip = socket.gethostbyname(socket.gethostname())
self.dashboard_port_scheduler = self.client._scheduler_identity.get(
"services")["dashboard"]
self.username = getpass.getuser()
def _repr_html_(self):
return self.client._repr_html_()
def scale_workers(self, N_workers):
self.cluster.scale(N_workers)
def create_dashboard_tunnel(self, ssh_host="ra"):
print(
"type following commant in a terminal, if port is taken, change first number in command."
)
print(" ".join([
f"jupdbport={self.dashboard_port_scheduler}",
"&&",
"ssh",
"-f",
"-L",
f"$jupdbport:{self.ip}:{self.dashboard_port_scheduler}",
f"{self.username}@{ssh_host}",
"sleep 10",
"&&",
"firefox",
"http://localhost:$jupdbport",
]))
if __name__ == '__main__':
ex_path = sys.argv[1]
tf_path = sys.argv[2]
net_out_path = sys.argv[3]
meta_out_path = sys.argv[4]
start_time = time.time()
expression_matrix = pd.read_csv(ex_path, sep='\t')
tf_names = load_tf_names(tf_path)
gene_names = expression_matrix.columns
client = Client(LocalCluster())
print(client._repr_html_())
network_graph, meta_graph = create_graph(
expression_matrix.as_matrix(),
gene_names,
tf_names,
"GBM",
SGBM_KWARGS,
client=client, # broadcast!
early_stop_window_length=25,
include_meta=True)
# Good!
a, b = client.persist([network_graph, meta_graph])
network_df = a.compute(sync=True)
meta_df = b.compute(sync=True)
