From 4ac57eddfa5d18ca3c80c7ffb210bca5fd9918cd Mon Sep 17 00:00:00 2001
From: cookieenick <nikhilr@ucar.edu>
Date: Mon, 24 Mar 2025 22:35:50 -0600
Subject: [PATCH] PFE grouplist + Bug fixes

---
 scripts/makeitso/engage.py                | 11 ++++++-----
 scripts/makeitso/option_descriptions.json |  5 +++++
 scripts/makeitso/template-gtr.pbs         |  7 +++++--
 scripts/makeitso/template.pbs             |  3 +++
 4 files changed, 19 insertions(+), 7 deletions(-)

diff --git a/scripts/makeitso/engage.py b/scripts/makeitso/engage.py
index f3bd1de6..01ed0889 100755
--- a/scripts/makeitso/engage.py
+++ b/scripts/makeitso/engage.py
@@ -469,7 +469,7 @@ def main():
         print(f"options = {options}")
 
     # Save the options dictionary as a JSON file in the current directory.
-    path = f"{engage_options['simulation']['job_name']}-engage.json"
+    path = f"engage_parameters.json"
     if os.path.exists(path):
         if not clobber:
             raise FileExistsError(f"Options file {path} exists!")
@@ -506,6 +506,7 @@ def main():
         makeitso_options["pbs"]["select2"] = str(select2)
         makeitso_options["gamera"]["sim"]["runid"] = engage_options["simulation"]["job_name"]
         makeitso_options["gamera"]["restart"]["resID"] = engage_options["simulation"]["job_name"]
+        path = f"makeitso_parameters.json"
         with open(path, "w", encoding="utf-8") as f:
             json.dump(makeitso_options, f, indent=JSON_INDENT)
         makeitso_args = {'clobber': True, 'debug': False, 'verbose': False, 'options_path': path}
@@ -521,8 +522,8 @@ def main():
  
     with open('makeitso_parameters.json', 'w') as f:
         json.dump(makeitso_options, f, indent=JSON_INDENT)
-        json.dump(makeitso_spinup_pbs_scripts, f, indent=JSON_INDENT)
-        json.dump(makeitso_warmup_pbs_scripts, f, indent=JSON_INDENT)
+        #json.dump(makeitso_spinup_pbs_scripts, f, indent=JSON_INDENT)
+        #json.dump(makeitso_warmup_pbs_scripts, f, indent=JSON_INDENT)
     
 
     # Run the TIEGCMrun
@@ -546,8 +547,8 @@ def main():
     # Save the tiegcm options dictionary as a JSON file in the current directory.
     with open('tiegcmrun_parameters.json', 'w') as f:
         json.dump(tiegcm_options, f, indent=JSON_INDENT)
-        json.dump(tiegcm_pbs_scripts, f, indent=JSON_INDENT)
-        json.dump(tiegcm_inp_scripts, f, indent=JSON_INDENT)
+        #json.dump(tiegcm_pbs_scripts, f, indent=JSON_INDENT)
+        #json.dump(tiegcm_inp_scripts, f, indent=JSON_INDENT)
 
     # Create the PBS job scripts.
     pbs_scripts, submit_all_jobs_script = create_pbs_scripts(engage_options,makeitso_options, makeitso_pbs_scripts, tiegcm_options, tiegcm_inp_scripts, tiegcm_pbs_scripts)
diff --git a/scripts/makeitso/option_descriptions.json b/scripts/makeitso/option_descriptions.json
index 2e61aad8..44f1bb1e 100644
--- a/scripts/makeitso/option_descriptions.json
+++ b/scripts/makeitso/option_descriptions.json
@@ -182,6 +182,11 @@
             }
         },
         "pleiades": {
+            "group_list": {
+                "LEVEL": "BASIC",
+                "prompt": "PBS group list",
+                "default": null
+            },
             "queue": {
                 "LEVEL": "BASIC",
                 "prompt": "PBS queue name",
diff --git a/scripts/makeitso/template-gtr.pbs b/scripts/makeitso/template-gtr.pbs
index 97c3e38f..bff88664 100644
--- a/scripts/makeitso/template-gtr.pbs
+++ b/scripts/makeitso/template-gtr.pbs
@@ -4,6 +4,9 @@
 
 #PBS -N {{ simulation.segment_id }}
 #PBS -A {{ pbs.account_name }}
+{%- if pbs.group_list|default('', true) and pbs.group_list != "None" %}
+#PBS -W group_list={{ pbs.group_list }}
+{%- endif %}
 #PBS -q {{ pbs.queue }}
 #PBS -l walltime={{ pbs.walltime }}
 {%- if pbs.model is defined %}
@@ -62,8 +65,8 @@ echo "The active environment variables are:"
 printenv
 
 # Copy the node file for use by the placer command.
-nodefile=nodefile.$PBS_JOBID
-cp $PBS_NODEFILE $nodefile
+NODEFILE=nodefile.$PBS_JOBID
+cp $PBS_NODEFILE $NODEFILE
 
 {%- if pbs.nodecommand is defined %}
 {{ pbs.nodecommand }}
diff --git a/scripts/makeitso/template.pbs b/scripts/makeitso/template.pbs
index 04780297..a88628d7 100644
--- a/scripts/makeitso/template.pbs
+++ b/scripts/makeitso/template.pbs
@@ -4,6 +4,9 @@
 
 #PBS -N {{ simulation.segment_id }}
 #PBS -A {{ pbs.account_name }}
+{%- if pbs.group_list|default('', true) and pbs.group_list != "None" %}
+#PBS -W group_list={{ pbs.group_list }}
+{%- endif %}
 #PBS -q {{ pbs.queue }}
 #PBS -l walltime={{ pbs.walltime }}
 #PBS -l select={{ pbs.select }}:ncpus={{ pbs.ncpus }}:mpiprocs={{ pbs.mpiprocs }}:ompthreads={{ pbs.ompthreads }}{{ pbs.other }}+{{ pbs.select2 }}:ncpus={{ pbs.ncpus }}:mpiprocs={{ pbs.helper_mpiprocs }}:ompthreads={{ pbs.helper_ompthreads }}{{ pbs.other }}