Fix timers for jobs

config.py

@@ -2,8 +2,10 @@
 import os
 import yaml
 import logging
+
 from jobs import tools
-from pathlib import Path
+from pathlib import Path 
+from datetime import datetime
 
 
 class Config():
@@ -391,6 +393,17 @@ def format_duration(self, duration):
         formatted_duration = f"{int(days)}d {int(hours)}h {int(minutes)}m {int(seconds)}s"
         return formatted_duration
 
+    def init_time_logging(self, job):
+        launch_time = datetime.now()
+        self.log_job_status(job, 'START', launch_time)
+
+        return launch_time
+
+    def finish_time_logging(self, job, launch_time):
+        end_time = datetime.now()
+        duration = end_time - launch_time
+        self.log_job_status(job, 'FINISH', end_time, duration)
+
     def get_dep_ids(self, job_name, add_dep=None):
         """Get dependency job ids for `job_name`"""
 

jobs/geosp.py

@@ -15,6 +15,7 @@ def main(cfg):
     Add GEOSP
     """
     prepare_data.set_cfg_variables(cfg)
+    launch_time = cfg.init_time_logging("geosp")
 
     #-----------------------------------------------------
     # Add GEOSP to all meteo files
@@ -58,3 +59,5 @@ def main(cfg):
             logging.info("Added GEOSP to file {}".format(merged_file))
             # Rename file to get original file name
             tools.rename_file(merged_file, src_file)
+
+    cfg.finish_time_logging("geosp", launch_time)

jobs/icon.py

@@ -33,6 +33,7 @@ def main(cfg):
         Object holding all user-configuration parameters as attributes.
     """
     prepare_data.set_cfg_variables(cfg)
+    launch_time = cfg.init_time_logging("icon")
 
     logfile = cfg.log_working_dir / "icon"
     logfile_finish = cfg.log_finished_dir / "icon"
@@ -81,3 +82,5 @@ def main(cfg):
     #
     #     if exitcode != 0:
     #        raise RuntimeError("sbatch returned exitcode {}".format(exitcode))
+
+    cfg.finish_time_logging("icon", launch_time)

jobs/prepare_data.py

@@ -102,6 +102,7 @@ def main(cfg):
         If any subprocess returns a non-zero exit code during execution.
     """
     set_cfg_variables(cfg)
+    launch_time = cfg.init_time_logging("prepare_data")
 
     if cfg.workflow_name.startswith('icon'):
         logging.info('ICON input data (IC/BC)')
@@ -525,3 +526,5 @@ def main(cfg):
                                         output_log=True)
 
                         logging.info("OK")
+
+    cfg.finish_time_logging("prepare_data", launch_time)

run_chain.py

@@ -235,20 +235,11 @@ def run_chunk(cfg, force, resume):
                 logfile = cfg.log_working_dir / job
                 logfile_finish = cfg.log_finished_dir / job
                 tools.change_logfile(logfile)
-                job_launch_time = datetime.now()
-                cfg.log_job_status(job, 'START', job_launch_time)
 
                 # Submit the job
                 script = cfg.create_sbatch_script(job, logfile)
                 job_id = cfg.submit(job, script)
 
-                # Logging
-                job_end_time = datetime.now()
-                job_duration = job_end_time - job_launch_time
-                cfg.log_job_status(job, 'FINISH', job_end_time, job_duration)
-                # This needs to be done by the job
-                #shutil.copy(logfile, logfile_finish)
-
         # wait for previous chunk to be done
         cfg.wait_for_previous()
         # cycle
@@ -496,8 +487,7 @@ def main():
         )
 
         if cfg.logging:
-            launch_time = datetime.now()
-            cfg.log_job_status('chain', 'START', launch_time)
+            launch_time = cfg.init_time_logging('chain')
 
         # Check for restart compatibility and spinup
         if 'restart' in cfg.workflow['features']:
@@ -516,9 +506,8 @@ def main():
             run_chunk(cfg=cfg, force=args.force, resume=args.resume)
 
     if cfg.logging:
-        end_time = datetime.now()
-        duration = end_time - launch_time
-        cfg.log_job_status('chain', 'FINISH', end_time, duration)
+        cfg.finish_time_logging('chain', launch_time)
+
     print('>>> Finished the processing chain successfully <<<')