Merge branch 'main' into 204-improve-fre-cmor-run-functionality

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)

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:

fre/make/gfdlfremake/checkout.py

@@ -108,14 +108,16 @@ 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):
         """
         Brief: Changes the permission on the checkout script and runs it
         Param:
             - self The checkout script object
         """
-        os.chmod(self.src+"/"+self.fname, 0o744)
         try:
             subprocess.run(args=[self.src+"/"+self.fname], check=True)
         except: