Merge pull request #19 from pyiron/gent

Gent minimal changes

pysqa/basic.py

@@ -58,6 +58,9 @@ def __init__(self, config, directory="~/.queues"):
         elif self._config["queue_type"] == "MOAB":
             class_name = "MoabCommands"
             module_name = "pysqa.wrapper.moab"
+        elif self._config["queue_type"] == "GENT":
+            class_name = "GentCommands"
+            module_name = "pysqa.wrapper.gent"
         else:
             raise ValueError()
         self._commands = getattr(importlib.import_module(module_name), class_name)()

pysqa/modular.py

@@ -7,7 +7,6 @@
 
 class ModularQueueAdapter(BasisQueueAdapter):
     def __init__(self, config, directory="~/.queues"):
-        config["queue_type"] = "SLURM"
         super(ModularQueueAdapter, self).__init__(config=config, directory=directory)
         self._queue_to_cluster_dict = {
             k: v["cluster"] for k, v in self._config["queues"].items()

pysqa/wrapper/gent.py

@@ -0,0 +1,44 @@
+# coding: utf-8
+# Copyright (c) Max-Planck-Institut für Eisenforschung GmbH - Computational Materials Design (CM) Department
+# Distributed under the terms of "New BSD License", see the LICENSE file.
+
+import pandas
+from pysqa.wrapper.slurm import SlurmCommands
+
+
+__author__ = "Jan Janssen"
+__copyright__ = (
+    "Copyright 2019, Max-Planck-Institut für Eisenforschung GmbH - "
+    "Computational Materials Design (CM) Department"
+)
+__version__ = "1.0"
+__maintainer__ = "Jan Janssen"
+__email__ = "janssen@mpie.de"
+__status__ = "development"
+__date__ = "Feb 9, 2019"
+
+
+class GentCommands(SlurmCommands):
+    @staticmethod
+    def get_job_id_from_output(queue_submit_output):
+          return int(queue_submit_output.splitlines()[-1].rstrip().lstrip().split(';')[0])
+
+    @staticmethod
+    def get_queue_from_output(queue_submit_output):
+          return str(queue_submit_output.splitlines()[-1].rstrip().lstrip().split(';')[1])
+
+    @staticmethod
+    def convert_queue_status(queue_status_output):
+        qstat = queue_status_output.splitlines()
+        queue = qstat[0].split(':')[1].strip()
+        if len(qstat) <= 1: # first row contains cluster name, check if there are jobs
+            return None
+
+        line_split_lst = [line.split('|') for line in qstat[1:]]
+        job_id_lst, user_lst, status_lst, job_name_lst, queue_lst = zip(*[(int(jobid), user, status.lower(), jobname, queue)
+                                                               for jobid, user, status, jobname in line_split_lst])
+        return pandas.DataFrame({'cluster': queue_lst,
+                                 'jobid': job_id_lst,
+                                 'user': user_lst,
+                                 'jobname': job_name_lst,
+                                 'status': status_lst})