Merge branch 'SSCHAcode:master' into master

Author: diegomartinez2

Modules/Cluster.py

@@ -319,7 +319,7 @@ def __setattr__(self, name, value):
 
 
 
-    def ExecuteCMD(self, cmd, raise_error = True, return_output = False, on_cluster = False):
+    def ExecuteCMD(self, cmd, raise_error = False, return_output = False, on_cluster = False):
         """
         EXECUTE THE CMD ON THE CLUSTER
         ==============================
@@ -797,7 +797,7 @@ def submit(self, script_location):
         #cmd = self.sshcmd + " %s '%s %s/%s.sh'" % (self.hostname, self.submit_command, 
         #                                           self.workdir, label+ "_" + str(indices[0]))
 
-        return self.ExecuteCMD(cmd, True, return_output=True)
+        return self.ExecuteCMD(cmd, False, return_output=True)
 
     def get_output_path(self, label):
         """
@@ -996,7 +996,15 @@ def check_job_finished(self, job_id, verbose = True):
         lines = output.split("\n")
         if len(lines):
             for l in lines:
-                data = l.strip().split()
+                l = l.strip()
+                if not l:
+                    if verbose:
+                        now = datetime.datetime.now()
+                        sys.stderr.write("{}/{}/{} - {}:{}:{} | job {}: No response from the server \n".format(now.year, now.month, now.day, now.hour, now.minute, now.second, job_id))
+                        sys.stderr.flush()
+                    return False
+                    
+                data = l.split()
                 if len(data) == 0:
                     if verbose:
                         now = datetime.datetime.now()
@@ -1367,7 +1375,7 @@ def setup_workdir(self, verbose = True):
         sshcmd = self.sshcmd + " %s 'mkdir -p %s'" % (self.hostname, 
                                                       workdir)
 
-        self.ExecuteCMD(sshcmd)
+        self.ExecuteCMD(sshcmd, raise_error= True)
 #        
 #        retval = os.system(sshcmd)
 #        if retval != 0:
@@ -1415,7 +1423,7 @@ def parse_string(self, string):
 
         #print(cmd)
 
-        status, output = self.ExecuteCMD(cmd, return_output = True)
+        status, output = self.ExecuteCMD(cmd, return_output = True, raise_error= True)
 #        
 #        p = subprocess.Popen(cmd, stdout=subprocess.PIPE, shell=True)
 #        output, err = p.communicate()