From da0f257deb8bc73f52241c3a6b8cb03c15c57f73 Mon Sep 17 00:00:00 2001
From: Lee de Mora <ledm@pml.ac.uk>
Date: Fri, 24 Nov 2023 14:13:11 +0000
Subject: [PATCH] testing sbatch

---
 bgcval2/parrellel_timeseries.py | 13 +++++++++---
 lotus_timeseries.sh             | 35 +++++++++++----------------------
 2 files changed, 22 insertions(+), 26 deletions(-)

diff --git a/bgcval2/parrellel_timeseries.py b/bgcval2/parrellel_timeseries.py
index fc98c324..e914eb84 100644
--- a/bgcval2/parrellel_timeseries.py
+++ b/bgcval2/parrellel_timeseries.py
@@ -31,6 +31,7 @@
 """
 import argparse
 import subprocess
+from getpass import getuser
 
 from bgcval2.analysis_compare import load_comparison_yml
 
@@ -75,17 +76,23 @@ def submits_lotus(compare_yml, config_user, dry_run=False):
     details = load_comparison_yml(compare_yml)
     jobs = details['jobs']
 
-    user='ldemora'
+    user = getuser()
     out = str(subprocess.check_output(["squeue", "--user="+user]))
 
     for job in jobs:
         suites = details['suites'][job]
+
         if out.find(job) > -1:
             print("That job exists already: skipping", job)
+
+        command_txt = ['sbatch', '-J', job, 'lotus_timeseries.sh', job]
+        for suite in suites:
+            command_txt.append(suite)
         if dry_run:
-            print(' '.join(['sbatch', 'lotus_timeseries.sh', job, suites]) )
+            print(' '.join(command_txt))
         else:
-            command1 = subprocess.Popen(['sbatch', 'lotus_timeseries.sh', job, suites])
+            # Submit job:
+            command1 = subprocess.Popen(command_txt)
 
 
 def main():
diff --git a/lotus_timeseries.sh b/lotus_timeseries.sh
index c2e21e32..92488145 100644
--- a/lotus_timeseries.sh
+++ b/lotus_timeseries.sh
@@ -7,25 +7,10 @@
 
 
 ######################
-# First make a copy of this file:
-# rysnc -av lotus_bgcval2.sh lotus_bgcval2_$USER.sh
-#
-# Then edit your new copy (lotus_bgcval2_$USER.sh):
-#
-#  1. Check the name of your conda environment: CONDA_ENV
-#     "bgcval2" is the default, but may have a different one.
-#
-#  2. Check the path to your bgcval2 directory: BGCVAL2_PATH
-#
-#  3. Change the analyses to run: BGCVAL2_SUITE
-#     You can add several suites here if needed.
-#
-#  4. Submit this script with with:
-#     sbatch lotus_bgcval2_$USER.sh
-#
-#  5. Monitor progress with:
-#     squeue | grep $USER
+# This script runs a single time series job.
 #
+# Runs:
+#    lotus_timeseries.sh jobID suite1 suite2 etc...
 #########################
 
 
@@ -61,11 +46,15 @@ conda activate ${CONDA_ENV}
 #cd $BGCVAL2_PATH
 #pwd
 
-jobID=$1
-keys=$2
-
-echo "analysis timeseries -j $jobID -k $2"
-#analysis_timeseries -j $jobID -k $2
+##########################
+# Load command line arguments:
+args=$@
+jobID="${a%% *}"
+suites="${@:2}"
+echo $suites
+
+echo "analysis timeseries -j $jobID -k $suites"
+#analysis_timeseries -j $jobID -k $suites
 #########################
 # Add one or more input_yml files here
 #cho analysis_timeseries -y $BGCVAL2_SUITE