def __init__(self, input_nodes, hidden_layers_nodes, config={}):
"""
Deep Auto Encoder Cox Class Constructor.
Parameters
----------
input_nodes: int
The number of input nodes. It's also equal to the number of features.
hidden_layers_nodes: list
Number of nodes in hidden layers of neural network.
config: dict
Some configurations or hyper-parameters of neural network.
"""
#super(DAECox, self).__init__()
# neural nodes
self.input_nodes = input_nodes
self.hidden_layers_nodes = hidden_layers_nodes
# network hyper-parameters
_check_config(config)
self.config = config
# reset computational graph
tf.compat.v1.reset_default_graph()
# graph level random seed
tf.compat.v1.set_random_seed(config["seed"])
# some gobal settings
self.global_step = tf.compat.v1.get_variable('global_step', initializer=tf.constant(0), trainable=False)
self.keep_prob = tf.compat.v1.placeholder(tf.float32)
# It's the best way to use `tf.placeholder` instead of `tf.data.Dataset`.
# Since style of `batch` is not appropriate in survival analysis.
self.X = tf.compat.v1.placeholder(tf.float32, [None, input_nodes], name='X-Input')
self.Y = tf.compat.v1.placeholder(tf.float32, [None, 1], name='Y-Input')
def disable_nfs3():
prot = '4'
if (config.nfs_srv != 'native'):
prot = '3,4'
#print (config.nfs_srv, prot)
_check_config("/etc/ganesha/ganesha.conf", "NFS_Core_Param", " ",
'{NFS_Protocols = %s;}' % (prot), 1)
def __init_redisconf(self, path, hostname):
src = os.path.join(self.config.home, "etc/redis.conf.tpl")
dist = os.path.join(path, "redis.conf")
cmd = "cp " + src + " " + dist
os.system(cmd)
cmd = "mkdir -p " + self.workdir + "/data"
os.system(cmd)
#cmd = "chmod a+w " + self.workdir + "/data"
#os.system(cmd)
_check_config(dist, "port", " ", self.port, True)
_check_config(dist, "dir", " ", self.workdir + "/data", True)
_check_config(dist, "pidfile", " ", self.workdir + "/run/redis-server.pid", True)
_check_config(dist, "logfile", " ", self.workdir + "/redis.log", True)
_check_config(dist, "bind", " ", hostname, True)
return True
def __init__(self, hidden_layers_nodes, input_samples, input_nodes, config={}):
"""
Deep Global Balancing Cox regression (DGBCox) Class Constructor.
Parameters
----------
hidden_layers_nodes: list
Number of nodes in hidden layers of deep auto-encoder neural network.
input_samples: int
The number of input samples.
input_nodes: int
The number of input nodes (i.e. features/genes).
config: dict
Some configurations or hyper-parameters of DGBCox.
"""
# super(DGBCox, self).__init__()
# nodes
self.input_nodes = input_nodes
# samples
self.input_samples = input_samples
# neural nodes
self.hidden_layers_nodes = hidden_layers_nodes
# hyper-parameters
_check_config(config)
self.config = config
# reset default computational graph before tf.Session()
tf.compat.v1.reset_default_graph()
# graph level random seed
tf.compat.v1.set_random_seed(config["seed"])
# some gobal settings
self.global_step = tf.compat.v1.get_variable('global_step', initializer=tf.constant(0), trainable=False)
self.keep_prob = self.config['dropout_keep_prob']
# It's the best way to use `tf.placeholder` instead of `tf.data.Dataset`.
# Since style of `batch` is not appropriate in survival analysis.
self.X = tf.compat.v1.placeholder(tf.float32, [None, input_nodes], name='X-Input')
self.Y = tf.compat.v1.placeholder(tf.float32, [None, 1], name='Y-Input')
def etcd_set_config(cls, init_cluster, state, proxy):
config = Config()
ip = socket.gethostbyname(config.hostname)
os.system("echo > /etc/etcd/etcd.conf")
_check_config("/etc/etcd/etcd.conf", "ETCD_NAME", "=", '"' + "%s" % (config.hostname) + '"', True)
_check_config("/etc/etcd/etcd.conf", "ETCD_DATA_DIR", "=", '"' + config.etcd_data_path + '"', True)
_check_config("/etc/etcd/etcd.conf", "ETCD_ADVERTISE_CLIENT_URLS", "=", '"' + "http://%s:2379" % (config.hostname) + '"', True)
_check_config("/etc/etcd/etcd.conf", "ETCD_LISTEN_CLIENT_URLS", "=", '"' + "http://%s:2379,http://127.0.0.1:2379" % (ip) + '"', True)
_check_config("/etc/etcd/etcd.conf", "ETCD_INITIAL_CLUSTER", "=", '"' + "%s" % (init_cluster) + '"', True)
if proxy:
# set etcd conf as proxy mode
_check_config("/etc/etcd/etcd.conf", "ETCD_PROXY", "=", '"' + "on" + '"', True)
else:
_check_config("/etc/etcd/etcd.conf", "ETCD_LISTEN_PEER_URLS", "=", '"' + "http://0.0.0.0:2380" + '"', True)
_check_config("/etc/etcd/etcd.conf", "ETCD_INITIAL_CLUSTER_STATE", "=", '"' + "%s" % (state) + '"', True)
_check_config("/etc/etcd/etcd.conf", "ETCD_INITIAL_ADVERTISE_PEER_URLS", "=", '"' + "http://%s:2380" % (config.hostname) + '"', True)
def add_raw_redis(self, idx, _uuid):
workdir = os.path.join(self.workdir, "redis", _uuid)
cmd = "mkdir -p " + workdir
os.system(cmd)
src = os.path.join(self.config.home, "etc/redis.conf.tpl")
dist = os.path.join(workdir, "redis.conf")
cmd = "cp " + src + " " + dist
os.system(cmd)
port = 16384 + idx
_check_config(dist, "port", " ", port, True)
_check_config(dist, "dir", " ", workdir, True)
_check_config(dist, "pidfile", " ", workdir + "/redis-server.pid",
True)
_check_config(dist, "logfile", " ", workdir + "/redis.log", True)
_check_config(dist, "bind", " ", socket.gethostname(), True)
_check_config(dist, "unixsocket", " ", workdir + "/redis.socket", True)
_check_config(dist, "unixsocketperm", " ", "770", True)