hawc2_pbsjob included in cluster_simulation

wetb/hawc2/hawc2_pbsjob.py

-
-
-from wetb.hawc2.htc_file import HTCFile
-from wetb.utils.cluster_tools.pbsjob import PBSJob
-from wetb.hawc2.log_file import LogInterpreter
-import os
-import time
-from wetb.utils.cluster_tools import pbsjob
-class HAWC2PBSJob(PBSJob):
-
-    def __init__(self, host, username, password):
-        PBSJob.__init__(self, host, username, password)
-
-
-    def submit(self, job, cwd, pbs_out_file):
-        with open (cwd + job) as fid:
-            htcfilename = [l for l in fid if l.startswith('wine')][0].rsplit(" ", 1)[1].strip()
-        print (htcfilename)
-        htcfile = HTCFile(cwd + htcfilename)
-
-        self.log_filename = htcfile.simulation.logfile[0]
-        self.loginterpreter = LogInterpreter(htcfile.simulation.time_stop[0])
-        PBSJob.submit(self, job, cwd, pbs_out_file)
-
-    def status_monitor(self, update=5):
-        i = 0
-        self.loglinenumber = 0
-        while self.in_queue():
-            i += 1
-            print (i, self.status, self.get_nodeid())
-            if self.status is pbsjob.RUNNING:
-                #self.test()
-                scratch_log_filename = "/scratch/%s/%s.g-000.risoe.dk/%s" % (self.client.username, self.jobid, self.log_filename)
-                try:
-                    n, out, err = self.client.execute('tail --lines=+%d %s' % (self.loglinenumber, scratch_log_filename))
-                    self.loginterpreter.update_status(out)
-                    print (self.loginterpreter.status, self.loginterpreter.pct, self.loginterpreter.remaining_time, self.loginterpreter.lastline)
-                    with open("status" + self.jobid, 'w') as fid:
-                        fid.write(";".join([self.loginterpreter.status, str(self.loginterpreter.pct), str(self.loginterpreter.remaining_time), self.loginterpreter.lastline]))
-                    #print (out)
-                    self.loglinenumber += out.count ("\n")
-                    #print (err)
-
-                except Warning as e:
-                    if not "tail: cannot open" in str(e):
-                        print (str(e))
-
-            time.sleep(update)
-        print (i, self.status, self.get_nodeid())
-
-    def test(self):
-        self.log_filename = "logfiles/short.log"
-        scratch_log_filename = "/scratch/%s/%s.g-000.risoe.dk/%s" % (self.client.username, self.jobid, self.log_filename)
-        print (scratch_log_filename)
-        try:
-            n, out, err = self.client.execute('tail --lines=+%d %s' % (self.loglinenumber, scratch_log_filename))
-            print (n)
-            print (out)
-            self.loglinenumber += out.count ("\n")
-            print (err)
-
-        except Warning as e:
-            print (str(e))