def sample_loop(self):
while True:
#try:
conn = mddb_utils.get_dbconn(self.param_dict['dbname'],
self.param_dict['dbuser'],
self.param_dict['dbhost'],
self.param_dict['dbpass'])
res = mddb_utils.execute_query(conn,
"select param_value from ControlParams where param_name = 'sampleloop'")
print datetime.datetime.now()
try:
nt = mddb_utils.execute_query(conn, "select resample_blocking(E'{gmdhost}:{gmdport}')".format(**self.param_dict))
except Exception as e:
m = "Error {0}".format(str(e))
print m
try:
mddb_utils.execute_query(conn, "insert into ErrorMessages values (statement_timestamp(),{0},{1})".format("sample_loop", m.encode("utf-8")))
except:
pass
nt = 0
time.sleep(2)
continue
if int(nt) > 0:
time.sleep(0.05)
else:
time.sleep(2)
print res
if res == 'quitting':
mddb_utils.execute_query(conn,
"select controlparams_upsert('sampleloop', 'notrunning')")
mddb_utils.execute_query(conn,
"update ExpJobs set active = False;")
conn.close()
break
cur = conn.cursor()
cur.execute('select S.subspace_id from subspaces S, expjobs E where S.subspace_id = E.subspace_id group by S.subspace_id having bool_or(active)')
num_active_subspaces = cur.rowcount
if num_active_subspaces == 0:
cur = conn.cursor(cursor_factory=psycopg2.extras.RealDictCursor)
cur.execute('select * from mdq_pop()')
if cur.rowcount > 0:
ss_dict = cur.fetchone()
if any(ss_dict.values()):
ss_dict['protein_seq'] = "".join(ss_dict['expanded_terms'])
mddb_utils.subspace_init(dict(self.param_dict.items() + ss_dict.items()))
cur.close()
conn.commit()
conn.close()
def load_trj(self,d):
print d
d2 = copy.deepcopy(self.param_dict)
d2.update(d)
d = d2
print d
pdbid = d['pdb_id']
query = "SELECT SS.subspace_id, SS.seqid FROM seq_pdb SP, seq_subspace SS WHERE SP.pdb_id = %s AND SP.seqid = SS.seqid"
conn = mddb_utils.get_dbconn(d['dbname'],
d['dbuser'],
d['dbhost'],
d['dbpass'])
cur = conn.cursor()
cur.execute(query,(pdbid,))
rows = cur.fetchall()
ss_id = None
seq_id = None
if (len(rows) == 0):
print "Creating New Subspace:"
query = "SELECT seqid from seq_pdb where pdb_id = %s"
cur = conn.cursor()
cur.execute(query,(pdbid,))
seqid = cur.fetchall()[0][0]
cur.close()
self.update_dict(d,pdbid)
self.config_ss()
ss_id = mddb_utils.subspace_init(d)
else:
ss_id = rows[0][0]
seqid = rows[0][1]
self.update_dict(d,pdbid)
mddb_utils.load_trajectories(conn,ss_id,d)
cur.close()
cur = conn.cursor()
query = "INSERT INTO seq_subspace (seqid,subspace_id) VALUES (%s, %s)"
print query
cur.execute(query, (seqid, ss_id))
conn.commit()
print cur.fetchone()[0]
cur.close()
conn.close()
print "Successfuly Loaded Trajectory"
def __init__(self):
self.param_dict = dict(self.param_dict.items() + self.mddb_param_dict.items())
self.add_parser_options(self.param_dict)
self.param_dict = self.parse_param_dict()
if self.param_dict['mode'] == 'initdb':
self.quit_everything()
self.init_database(self.schema_files)
self.load_stored_procedures(self.sp_files)
self.load_configs()
sys.exit(0)
if self.param_dict['mode'] == 'initss':
mddb_utils.subspace_init(self.param_dict)
sys.exit(0)
if self.param_dict['mode'] == 'trjs':
conn = mddb_utils.get_dbconn(self.param_dict['dbname'],
self.param_dict['dbuser'],
self.param_dict['dbhost'],
self.param_dict['dbpass'])
mddb_utils.add_trajectories(conn, self.param_dict)
conn.close()
sys.exit(0)
if self.param_dict['mode'] == 'loop':
self.sample_loop()
sys.exit(0)
if self.param_dict['mode'] == 'setup':
self.quit_everything()
#self.clear_jobqueue()
#self.init_database(self.schema_files)
#self.load_stored_procedures(self.sp_files)
#self.load_configs()
l = []
l.append({'hostname':'stampede', 'sequentialism': '1', 'res_config_name': 'gpu'})
self.setup_workers(l)
#self.start_sampleloop()
sys.exit(0)
if self.param_dict['mode'] == 'qjobs':
#trj_id_list = ['137']
#trj_len = 1000
#num_points = 1
#l = map(lambda x: getStartingPoints(x, trj_len, num_points), trj_id_list)
#l = list(itertools.chain(*l))
l = []
timestamps = [(3294, 555, 50), (3264, 5, 50), (3264, 929, 100)]
for ts in timestamps:
l = l + MDDBController.get_prev_timestamps(*ts)
l = map(lambda (trj_id,t): {'trj_id': "{0:03d}".format(trj_id), 't': t}, l)
l = l[99:]
default_params = {'nstep_simulation': 50000000,
'trj_save_freq': 50000,
'source': 'deshaw',
'generator': 'amber',
'template_dir': 'amber_min',
'dbname': self.param_dict['dbname'],
'dbuser': self.param_dict['dbuser'],
'dbhost': self.param_dict['dbhost'],
'dbpass': self.param_dict['dbpass'],
}
conn = mddb_utils.get_dbconn(self.param_dict['dbname'],
self.param_dict['dbuser'],
self.param_dict['dbhost'],
self.param_dict['dbpass'])
cur = conn.cursor()
cur.execute('truncate table jobqueue')
for d in l:
d.update(default_params)
print d
data = 'ARRAY' + str([json.dumps(d)])
cur.execute('select jobqueue_insert({0})'.format(data))
cur.close()
conn.commit()
conn.close()
if self.param_dict['mode'] == 'cmd':
mc = mddb_cmd()
mc.init_conn(self.param_dict)
mc.cmdloop()
sys.exit(0)
