added pbsjob.py

wetb/utils/cluster_tools/pbsjob.py

+'''
+Created on 04/12/2015
+
+@author: mmpe
+'''
+
+#import x
+import time
+from wetb.utils.cluster_tools.ssh_client import SSHClient
+import os
+import paramiko
+import subprocess
+
+
+
+NOT_SUBMITTED = "Job not submitted"
+PENDING = "Pending"
+RUNNING = "Running"
+DONE = "Done"
+class PBSJob(object):
+    _status = NOT_SUBMITTED
+    nodeid = None
+    def __init__(self, host, username, password):
+        self.client = SSHClient(host, username, password, port=22)
+
+
+    def execute(self, cmd, cwd="./"):
+        proc = subprocess.Popen(cmd, stdout=subprocess.PIPE, stderr=subprocess.PIPE, shell=True, cwd=cwd)
+        stdout, stderr = proc.communicate()
+        errorcode = proc.returncode
+        return errorcode, stdout.decode(), stderr.decode()
+
+    def submit(self, job, cwd, pbs_out_file):
+        self.cwd = cwd
+        self.pbs_out_file = os.path.relpath(cwd + pbs_out_file).replace("\\", "/")
+        self.nodeid = None
+        try:
+            os.remove (self.pbs_out_file)
+        except FileNotFoundError:
+            pass
+        _, out, _ = self.execute("qsub %s" % job, cwd)
+        self.jobid = out.split(".")[0]
+        self._status = PENDING
+
+    @property
+    def status(self):
+        if self._status in [NOT_SUBMITTED, DONE]:
+            return self._status
+
+        if self.nodeid is None:
+            self.nodeid = self.get_nodeid()
+            if self.nodeid is not None:
+                self._status = RUNNING
+
+        if self.in_queue() and self.nodeid is None:
+            self._status = PENDING
+        elif os.path.isfile(self.pbs_out_file):
+            self._status = DONE
+        return self._status
+
+    def get_nodeid(self):
+            errorcode, out, err = self.execute("qstat -f %s | grep exec_host" % self.jobid)
+            if errorcode == 0:
+                return out.strip().replace("exec_host = ", "").split(".")[0]
+            elif errorcode == 1 and out == "":
+                return None
+            elif errorcode == 153 and 'qstat: Unknown Job Id' in err:
+                return None
+            else:
+                raise Exception(str(errorcode) + out + err)
+
+    def stop(self):
+        try:
+            self.execute("qdel %s" % self.jobid)
+        except Warning as e:
+            if 'qdel: Unknown Job Id' in str(e):
+                return
+            raise e
+
+
+    def in_queue(self):
+        errorcode, out, err = self.execute("qstat %s" % self.jobid)
+        if errorcode == 0:
+            return True
+        elif 'qstat: Unknown Job Id' in str(err):
+            return False
+        else:
+            raise Exception(str(errorcode) + out + err)
+