From 847bcfa89c4fab074f23e3c27c5a7c80b8865d7d Mon Sep 17 00:00:00 2001
From: Dana Singh <115384427+singhd789@users.noreply.github.com>
Date: Tue, 22 Oct 2024 10:36:05 -0400
Subject: [PATCH 1/2] Fix LD_LIBRARY_PATH env. var. name

---
 fre/make/gfdlfremake/buildDocker.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/fre/make/gfdlfremake/buildDocker.py b/fre/make/gfdlfremake/buildDocker.py
index 15b77476..6d33d0d2 100644
--- a/fre/make/gfdlfremake/buildDocker.py
+++ b/fre/make/gfdlfremake/buildDocker.py
@@ -154,7 +154,7 @@ def writeRunscript(self,RUNenv,containerRun,runOnDisk):
         """
         #create runscript in tmp - create spack environment, install necessary packages,
         self.createscript = ["#!/bin/bash \n",
-                             "export BACKUP_LD_LIBRARY_PATH=$LD_LIBRARY\n",
+                             "export BACKUP_LD_LIBRARY_PATH=$LD_LIBRARY_PATH\n",
                              "# Set up spack loads\n",
                              RUNenv[0]+"\n"]
         with open(runOnDisk,"w") as f:

From be0192248f33afaf501a2b11980314d8fec1e058 Mon Sep 17 00:00:00 2001
From: Dana Singh <Dana.Singh@noaa.gov>
Date: Fri, 25 Oct 2024 15:41:19 -0400
Subject: [PATCH 2/2]  #212 Make compile and checkout scripts executable

- make scripts executable after creating
- moved `chmod` lines earlier in scripts
---
 fre/make/gfdlfremake/buildBaremetal.py | 4 +++-
 fre/make/gfdlfremake/checkout.py       | 4 +++-
 2 files changed, 6 insertions(+), 2 deletions(-)

diff --git a/fre/make/gfdlfremake/buildBaremetal.py b/fre/make/gfdlfremake/buildBaremetal.py
index f0279a11..fdb4e2d8 100644
--- a/fre/make/gfdlfremake/buildBaremetal.py
+++ b/fre/make/gfdlfremake/buildBaremetal.py
@@ -110,6 +110,9 @@ def writeScript(self):
         self.f.write(self.make+"\n")
         self.f.close()
 
+        # Make compile script executable
+        os.chmod(self.bld+"/compile.sh", 0o744)
+
 ## TODO run as a batch job on the login cluster
     def run(self):
         """
@@ -118,7 +121,6 @@ def run(self):
             - self : The dockerfile object
         """
 ###### TODO make the Makefile
-        os.chmod(self.bld+"/compile.sh", 0o744)
         command = [self.bld+"/compile.sh","|","tee",self.bld+"/log.compile"]
         try:
             subprocess.run(args=command, check=True)
diff --git a/fre/make/gfdlfremake/checkout.py b/fre/make/gfdlfremake/checkout.py
index 3a1ffa9b..4e4c905c 100644
--- a/fre/make/gfdlfremake/checkout.py
+++ b/fre/make/gfdlfremake/checkout.py
@@ -108,6 +108,9 @@ def finish (self,pc):
         else:
             self.checkoutScript.close()
 
+        # Make checkout script executable
+        os.chmod(self.src+"/"+self.fname, 0o744)
+
 ## TODO: batch script building
     def run (self):
         """
@@ -115,7 +118,6 @@ def run (self):
         Param:
             - self The checkout script object
         """
-        os.chmod(self.src+"/"+self.fname, 0o744)
         try:
             subprocess.run(args=[self.src+"/"+self.fname], check=True)
         except: