added hawc2/hawc2_pbsjob.py

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)
+
+        logfilename = htcfile.simulation.logfile[0]
+        self.loginterpreter = LogInterpreter(htcfile.simulation.time_stop[0])
+        print (self.loginterpreter.filename)
+        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.loginterpreter.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))

wetb/hawc2/log_file.py

@@ -70,7 +70,7 @@ class LogInterpreter(object):
             if self.status == UNKNOWN or self.status == MISSING:
                 self.status = PENDING
             txt = new_lines
-            self.txt += txt
+            sself.txt += txt
             if self.status == PENDING and self.position > 0:
                 self.status = INITIALIZATION