diff --git a/config/acme/machines/template.case.run b/config/acme/machines/template.case.run
index ea81a158527..d85c3e15dce 100755
--- a/config/acme/machines/template.case.run
+++ b/config/acme/machines/template.case.run
@@ -55,9 +55,7 @@ formatter_class=argparse.ArgumentDefaultsHelpFormatter
     parser.add_argument("--caseroot",
                         help="Case directory to build")
 
-    args = parser.parse_args()
-
-    CIME.utils.handle_standard_logging_options(args)
+    CIME.utils.parse_args_and.parse_args_and_handle_standard_logging_options(args, parser)
 
     if args.caseroot is not None:
         os.chdir(args.caseroot)
diff --git a/config/acme/machines/template.case.test b/config/acme/machines/template.case.test
index 1c2cf6e49b0..81ccab9cbd1 100755
--- a/config/acme/machines/template.case.test
+++ b/config/acme/machines/template.case.test
@@ -50,9 +50,7 @@ formatter_class=argparse.ArgumentDefaultsHelpFormatter
     parser.add_argument("--caseroot",
                         help="Case directory to build")
 
-    args = parser.parse_args(args[1:])
-
-    CIME.utils.handle_standard_logging_options(args)
+    CIME.utils.parse_args_and_handle_standard_logging_options(args, parser)
 
     if args.caseroot is not None:
         os.chdir(args.caseroot)
diff --git a/config/acme/machines/template.lt_archive b/config/acme/machines/template.lt_archive
index 421cca9325a..0feb5f9d377 100755
--- a/config/acme/machines/template.lt_archive
+++ b/config/acme/machines/template.lt_archive
@@ -49,9 +49,7 @@ formatter_class=argparse.ArgumentDefaultsHelpFormatter
     parser.add_argument("--caseroot", default=os.getcwd(),
                         help="Case directory to build")
 
-    args = parser.parse_args()
-
-    CIME.utils.handle_standard_logging_options(args)
+    CIME.utils.parse_args_and_handle_standard_logging_options(args, parser)
 
     if args.caseroot is not None:
         os.chdir(args.caseroot)
diff --git a/config/acme/machines/template.st_archive b/config/acme/machines/template.st_archive
index 68f008ab3f4..5f830a1e258 100755
--- a/config/acme/machines/template.st_archive
+++ b/config/acme/machines/template.st_archive
@@ -48,9 +48,7 @@ formatter_class=argparse.ArgumentDefaultsHelpFormatter
     parser.add_argument("--caseroot", default=os.getcwd(),
                         help="Case directory to build")
 
-    args = parser.parse_args()
-
-    CIME.utils.handle_standard_logging_options(args)
+    CIME.utils.parse_args_and_handle_standard_logging_options(args, parser)
 
     if args.caseroot is not None:
         os.chdir(args.caseroot)
diff --git a/config/cesm/machines/template.case.run b/config/cesm/machines/template.case.run
index 24162fe4595..7f9d31fc5f5 100755
--- a/config/cesm/machines/template.case.run
+++ b/config/cesm/machines/template.case.run
@@ -52,9 +52,7 @@ formatter_class=argparse.ArgumentDefaultsHelpFormatter
     parser.add_argument("--caseroot",
                         help="Case directory to build")
 
-    args = parser.parse_args()
-
-    CIME.utils.handle_standard_logging_options(args)
+    args = CIME.utils.parse_args_and_handle_standard_logging_options(args, parser)
 
     if args.caseroot is not None:
         os.chdir(args.caseroot)
diff --git a/config/cesm/machines/template.case.test b/config/cesm/machines/template.case.test
index e918de6ec21..13dbb65a4ce 100755
--- a/config/cesm/machines/template.case.test
+++ b/config/cesm/machines/template.case.test
@@ -46,9 +46,7 @@ formatter_class=argparse.ArgumentDefaultsHelpFormatter
     parser.add_argument("--caseroot",
                         help="Case directory to build")
 
-    args = parser.parse_args(args[1:])
-
-    CIME.utils.handle_standard_logging_options(args)
+    args = CIME.utils.parse_args_and_handle_standard_logging_options(args, parser)
 
     if args.caseroot is not None:
         os.chdir(args.caseroot)
diff --git a/config/cesm/machines/template.lt_archive b/config/cesm/machines/template.lt_archive
index 1dd9de1a6bc..9f51cfa886f 100755
--- a/config/cesm/machines/template.lt_archive
+++ b/config/cesm/machines/template.lt_archive
@@ -47,9 +47,7 @@ formatter_class=argparse.ArgumentDefaultsHelpFormatter
     parser.add_argument("--caseroot", default=os.getcwd(),
                         help="Case directory to build")
 
-    args = parser.parse_args()
-
-    CIME.utils.handle_standard_logging_options(args)
+    args = CIME.utils.parse_args_and_handle_standard_logging_options(args, parser)
 
     if args.caseroot is not None:
         os.chdir(args.caseroot)
diff --git a/config/cesm/machines/template.st_archive b/config/cesm/machines/template.st_archive
index 0a1d935d5b0..ec2bc02de34 100755
--- a/config/cesm/machines/template.st_archive
+++ b/config/cesm/machines/template.st_archive
@@ -47,9 +47,7 @@ formatter_class=argparse.ArgumentDefaultsHelpFormatter
     parser.add_argument("--caseroot", default=os.getcwd(),
                         help="Case directory to build")
 
-    args = parser.parse_args()
-
-    CIME.utils.handle_standard_logging_options(args)
+    args = CIME.utils.parse_args_and_handle_standard_logging_options(args, parser)
 
     if args.caseroot is not None:
         os.chdir(args.caseroot)
diff --git a/scripts/Tools/acme_check_env b/scripts/Tools/acme_check_env
index 7abdbcf71fa..e6edf90576c 100755
--- a/scripts/Tools/acme_check_env
+++ b/scripts/Tools/acme_check_env
@@ -30,9 +30,7 @@ formatter_class=argparse.ArgumentDefaultsHelpFormatter
 
     CIME.utils.setup_standard_logging_options(parser)
 
-    args = parser.parse_args(args[1:])
-
-    CIME.utils.handle_standard_logging_options(args)
+    args = CIME.utils.parse_args_and_handle_standard_logging_options(args, parser)
 
 ###############################################################################
 def check_sh():
diff --git a/scripts/Tools/bless_test_results b/scripts/Tools/bless_test_results
index 4b01e4768f8..ceca60cf51f 100755
--- a/scripts/Tools/bless_test_results
+++ b/scripts/Tools/bless_test_results
@@ -89,9 +89,7 @@ formatter_class=argparse.ArgumentDefaultsHelpFormatter
     parser.add_argument("bless_tests", nargs="*",
                         help="When blessing, limit the bless to tests matching these regex")
 
-    args = parser.parse_args(args[1:])
-
-    CIME.utils.handle_standard_logging_options(args)
+    args = CIME.utils.parse_args_and_handle_standard_logging_options(args, parser)
 
     expect(not (args.report_only and args.force),
            "Makes no sense to use -r and -f simultaneously")
diff --git a/scripts/Tools/case.build b/scripts/Tools/case.build
index 7fba3c18d61..8caee2ee579 100755
--- a/scripts/Tools/case.build
+++ b/scripts/Tools/case.build
@@ -56,9 +56,7 @@ OR
     parser.add_argument("--clean-all", action="store_true",
                         help="clean all objects including sharedlibobjects that may be used by other builds")
 
-    args = parser.parse_args(args[1:])
-
-    CIME.utils.handle_standard_logging_options(args)
+    args = CIME.utils.parse_args_and_handle_standard_logging_options(args, parser)
 
     cleanlist = args.clean if args.clean is None or len(args.clean) else comps
 
diff --git a/scripts/Tools/case.cmpgen_namelists b/scripts/Tools/case.cmpgen_namelists
index e874121a205..999ba075a45 100755
--- a/scripts/Tools/case.cmpgen_namelists
+++ b/scripts/Tools/case.cmpgen_namelists
@@ -49,9 +49,7 @@ OR
                         help="Force generation to use baselines with this name. "
                         "Default will be to follow the case specification")
 
-    args = parser.parse_args(args[1:])
-
-    CIME.utils.handle_standard_logging_options(args)
+    args = CIME.utils.parse_args_and_handle_standard_logging_options(args, parser)
 
     return args.caseroot, args.compare, args.generate, args.compare_name, args.generate_name
 
diff --git a/scripts/Tools/case.setup b/scripts/Tools/case.setup
index 3aca10bb130..7fb4eaae6da 100755
--- a/scripts/Tools/case.setup
+++ b/scripts/Tools/case.setup
@@ -45,9 +45,7 @@ OR
     parser.add_argument("-r", "--reset", action="store_true",
                         help="Does a clean followed by setup")
 
-    args = parser.parse_args(args[1:])
-
-    CIME.utils.handle_standard_logging_options(args)
+    args = CIME.utils.parse_args_and_handle_standard_logging_options(args, parser)
 
     return args.caseroot, args.clean, args.test_mode, args.reset
 
diff --git a/scripts/Tools/case.submit b/scripts/Tools/case.submit
index c307035dc43..3ea9d21b287 100755
--- a/scripts/Tools/case.submit
+++ b/scripts/Tools/case.submit
@@ -48,12 +48,10 @@ OR
     parser.add_argument("-a", "--batch-args",
                         help="Used to pass additional arguments to batch system. ")
 
-    args = parser.parse_args(args[1:])
+    args = CIME.utils.parse_args_and_handle_standard_logging_options(args, parser)
 
     CIME.utils.expect(args.prereq is None, "--prereq not currently supported")
 
-    CIME.utils.handle_standard_logging_options(args)
-
     return args.caseroot, args.job, args.no_batch, args.resubmit, args.batch_args
 
 ###############################################################################
diff --git a/scripts/Tools/case_diff b/scripts/Tools/case_diff
index 6cd5db1b706..4ad7da8da80 100755
--- a/scripts/Tools/case_diff
+++ b/scripts/Tools/case_diff
@@ -42,9 +42,7 @@ formatter_class=argparse.ArgumentDefaultsHelpFormatter
     parser.add_argument("-b", "--show-binary", action="store_true",
                         help="Show binary diffs")
 
-    args = parser.parse_args(args[1:])
-
-    CIME.utils.handle_standard_logging_options(args)
+    args = CIME.utils.parse_args_and_handle_standard_logging_options(args, parser)
 
     return args.case1, args.case2, args.show_binary, args.skip_list
 
diff --git a/scripts/Tools/check_case b/scripts/Tools/check_case
index 2553e1a197f..0c360e41e87 100755
--- a/scripts/Tools/check_case
+++ b/scripts/Tools/check_case
@@ -38,9 +38,7 @@ formatter_class=argparse.ArgumentDefaultsHelpFormatter
 
     CIME.utils.setup_standard_logging_options(parser)
 
-    args = parser.parse_args(args[1:])
-
-    CIME.utils.handle_standard_logging_options(args)
+    args = CIME.utils.parse_args_and_handle_standard_logging_options(args, parser)
 
 ###############################################################################
 def _main_func(description):
@@ -68,4 +66,3 @@ def _main_func(description):
 
 if __name__ == "__main__":
     _main_func(__doc__)
-
diff --git a/scripts/Tools/check_input_data b/scripts/Tools/check_input_data
index 7795c063cac..dc127720490 100755
--- a/scripts/Tools/check_input_data
+++ b/scripts/Tools/check_input_data
@@ -52,9 +52,7 @@ formatter_class=argparse.ArgumentDefaultsHelpFormatter
     parser.add_argument("--download", action="store_true",
                         help="Attempt to download missing input files")
 
-    args = parser.parse_args(args[1:])
-
-    CIME.utils.handle_standard_logging_options(args)
+    args = CIME.utils.parse_args_and_handle_standard_logging_options(args, parser)
 
     return args.svn_loc, args.input_data_root, args.data_list_dir, args.download
 
@@ -78,4 +76,3 @@ def _main_func(description):
 
 if (__name__ == "__main__"):
     _main_func(__doc__)
-
diff --git a/scripts/Tools/check_lockedfiles b/scripts/Tools/check_lockedfiles
index 39b68a1bd90..46f509e4721 100755
--- a/scripts/Tools/check_lockedfiles
+++ b/scripts/Tools/check_lockedfiles
@@ -29,9 +29,7 @@ OR
     parser.add_argument("--caseroot", default=os.getcwd(),
                         help="Case directory to build")
 
-    args = parser.parse_args(args[1:])
-
-    CIME.utils.handle_standard_logging_options(args)
+    args = CIME.utils.parse_args_and_handle_standard_logging_options(args, parser)
 
     return args.caseroot
 
diff --git a/scripts/Tools/cime_bisect b/scripts/Tools/cime_bisect
index 6e2b37e93bd..53d1d830412 100755
--- a/scripts/Tools/cime_bisect
+++ b/scripts/Tools/cime_bisect
@@ -74,9 +74,7 @@ formatter_class=argparse.ArgumentDefaultsHelpFormatter
     parser.add_argument("-a", "--all-commits", action="store_true",
                         help="Test all commits, not just merges")
 
-    args = parser.parse_args(args[1:])
-
-    CIME.utils.handle_standard_logging_options(args)
+    args = CIME.utils.parse_args_and_handle_standard_logging_options(args, parser)
 
     if (args.test_root is None):
         args.test_root = os.path.join(_MACHINE.get_value("CIME_OUTPUT_ROOT"), "cime_bisect")
diff --git a/scripts/Tools/code_checker b/scripts/Tools/code_checker
index a81908a9951..79191d2d2bf 100755
--- a/scripts/Tools/code_checker
+++ b/scripts/Tools/code_checker
@@ -46,9 +46,7 @@ formatter_class=argparse.ArgumentDefaultsHelpFormatter
     parser.add_argument("files", nargs="*",
                         help="Restrict checking to specific files. Relative name is fine.")
 
-    args = parser.parse_args(args[1:])
-
-    CIME.utils.handle_standard_logging_options(args)
+    args = CIME.utils.parse_args_and_handle_standard_logging_options(args, parser)
 
     return args.num_procs, args.files
 
diff --git a/scripts/Tools/compare_namelists b/scripts/Tools/compare_namelists
index 69f86659afc..fcfbc481a2c 100755
--- a/scripts/Tools/compare_namelists
+++ b/scripts/Tools/compare_namelists
@@ -40,9 +40,7 @@ formatter_class=argparse.ArgumentDefaultsHelpFormatter
     parser.add_argument("-c", "--case", action="store", dest="case", default=None,
                         help="The case base id (<TESTCASE>.<GRID>.<COMPSET>). Helps us normalize data.")
 
-    args = parser.parse_args(args[1:])
-
-    CIME.utils.handle_standard_logging_options(args)
+    args = CIME.utils.parse_args_and_handle_standard_logging_options(args, parser)
 
     # Normalize case
     if (args.case is not None):
diff --git a/scripts/Tools/compare_test_results b/scripts/Tools/compare_test_results
index ae3ac037b14..7307c74e0c8 100755
--- a/scripts/Tools/compare_test_results
+++ b/scripts/Tools/compare_test_results
@@ -90,9 +90,7 @@ formatter_class=argparse.ArgumentDefaultsHelpFormatter
     parser.add_argument("compare_tests", nargs="*",
                         help="When comparing, limit the comparison to tests matching these regex")
 
-    args = parser.parse_args(args[1:])
-
-    CIME.utils.handle_standard_logging_options(args)
+    args = CIME.utils.parse_args_and_handle_standard_logging_options(args, parser)
 
     return args.baseline_name, args.baseline_root, args.test_root, args.compiler, args.test_id, args.compare_tests, args.namelists_only, args.hist_only
 
diff --git a/scripts/Tools/component_compare_baseline b/scripts/Tools/component_compare_baseline
index ea8e43343a7..a809e12acfe 100755
--- a/scripts/Tools/component_compare_baseline
+++ b/scripts/Tools/component_compare_baseline
@@ -35,9 +35,7 @@ OR
     parser.add_argument("-b", "--baseline-dir",
                         help="Use custom baseline dir")
 
-    args = parser.parse_args(args[1:])
-
-    CIME.utils.handle_standard_logging_options(args)
+    args = CIME.utils.parse_args_and_handle_standard_logging_options(args, parser)
 
     return args.caseroot, args.baseline_dir
 
diff --git a/scripts/Tools/component_compare_copy b/scripts/Tools/component_compare_copy
index 209358ff604..db3574cad57 100755
--- a/scripts/Tools/component_compare_copy
+++ b/scripts/Tools/component_compare_copy
@@ -36,9 +36,7 @@ OR
     parser.add_argument("caseroot", nargs="?", default=os.getcwd(),
                         help="Case directory")
 
-    args = parser.parse_args(args[1:])
-
-    CIME.utils.handle_standard_logging_options(args)
+    args = CIME.utils.parse_args_and_handle_standard_logging_options(args, parser)
 
     return args.suffix, args.caseroot
 
diff --git a/scripts/Tools/component_compare_test b/scripts/Tools/component_compare_test
index aae11911e49..07e6c17b199 100755
--- a/scripts/Tools/component_compare_test
+++ b/scripts/Tools/component_compare_test
@@ -38,9 +38,7 @@ OR
     parser.add_argument("caseroot", nargs="?", default=os.getcwd(),
                         help="Case directory")
 
-    args = parser.parse_args(args[1:])
-
-    CIME.utils.handle_standard_logging_options(args)
+    args = CIME.utils.parse_args_and_handle_standard_logging_options(args, parser)
 
     return args.suffix1, args.suffix2, args.caseroot
 
diff --git a/scripts/Tools/component_generate_baseline b/scripts/Tools/component_generate_baseline
index 0dcca7681c8..311537438df 100755
--- a/scripts/Tools/component_generate_baseline
+++ b/scripts/Tools/component_generate_baseline
@@ -40,9 +40,7 @@ OR
                         "will raise an error. Specifying this option allows "
                         "existing baseline directories to be silently overwritten.")
 
-    args = parser.parse_args(args[1:])
-
-    CIME.utils.handle_standard_logging_options(args)
+    args = CIME.utils.parse_args_and_handle_standard_logging_options(args, parser)
 
     return args.caseroot, args.baseline_dir, args.allow_baseline_overwrite
 
diff --git a/scripts/Tools/getTiming b/scripts/Tools/getTiming
index a2ba123ec3b..22878582ee5 100755
--- a/scripts/Tools/getTiming
+++ b/scripts/Tools/getTiming
@@ -21,8 +21,8 @@ def parse_command_line(args, description):
                         default="999999-999999")
     parser.add_argument("--caseroot", default=os.getcwd(),
                         help="Case directory to get timing for")
-    args = parser.parse_args(args[1:])
-    CIME.utils.handle_standard_logging_options(args)
+
+    args = CIME.utils.parse_args_and_handle_standard_logging_options(args, parser)
     return args.caseroot, args.lid
 
 def __main_func(description):
diff --git a/scripts/Tools/jenkins_generic_job b/scripts/Tools/jenkins_generic_job
index 5e4ae54369d..a31ff82fb8e 100755
--- a/scripts/Tools/jenkins_generic_job
+++ b/scripts/Tools/jenkins_generic_job
@@ -84,9 +84,7 @@ formatter_class=argparse.ArgumentDefaultsHelpFormatter
                         help="Number of tasks create_test should perform simultaneously. Default "
                         "will be min(num_cores, num_tests).")
 
-    args = parser.parse_args(args[1:])
-
-    CIME.utils.handle_standard_logging_options(args)
+    args = CIME.utils.parse_args_and_handle_standard_logging_options(args, parser)
 
     expect(not (args.submit_to_cdash and args.generate_baselines),
            "Does not make sense to use --generate-baselines and --submit-to-cdash together")
diff --git a/scripts/Tools/list_acme_tests b/scripts/Tools/list_acme_tests
index 915f0a380e1..c7f2cefba51 100755
--- a/scripts/Tools/list_acme_tests
+++ b/scripts/Tools/list_acme_tests
@@ -43,9 +43,7 @@ formatter_class=argparse.ArgumentDefaultsHelpFormatter
     parser.add_argument("categories", nargs="*",
                         help="The test categories to list. Default will list all. Test categories: %s" % (", ".join(update_acme_tests.get_test_suites())))
 
-    args = parser.parse_args(args[1:])
-
-    CIME.utils.handle_standard_logging_options(args)
+    args = CIME.utils.parse_args_and_handle_standard_logging_options(args, parser)
 
     if (not args.categories):
         args.categories = update_acme_tests.get_test_suites()
diff --git a/scripts/Tools/normalize_cases b/scripts/Tools/normalize_cases
index 1eca9367d5d..693c4861e67 100755
--- a/scripts/Tools/normalize_cases
+++ b/scripts/Tools/normalize_cases
@@ -38,9 +38,7 @@ formatter_class=argparse.ArgumentDefaultsHelpFormatter
 
     parser.add_argument("case2", help="Second case. This one will not be changed")
 
-    args = parser.parse_args(args[1:])
-
-    CIME.utils.handle_standard_logging_options(args)
+    args = CIME.utils.parse_args_and_handle_standard_logging_options(args, parser)
 
     return args.case1, args.case2
 
diff --git a/scripts/Tools/pelayout b/scripts/Tools/pelayout
index 64848d3a64e..50736a52832 100755
--- a/scripts/Tools/pelayout
+++ b/scripts/Tools/pelayout
@@ -68,9 +68,7 @@ def parse_command_line(args):
     parser.add_argument("-caseroot" , "--caseroot", default=os.getcwd(),
                         help="Case directory to reference")
 
-    args = parser.parse_args(args[1:])
-
-    CIME.utils.handle_standard_logging_options(args)
+    args = CIME.utils.parse_args_and_handle_standard_logging_options(args, parser)
 
     if (args.no_header):
         args.header = None
diff --git a/scripts/Tools/preview_namelists b/scripts/Tools/preview_namelists
index 2d3f8efcbf0..4bece0ee573 100755
--- a/scripts/Tools/preview_namelists
+++ b/scripts/Tools/preview_namelists
@@ -27,9 +27,7 @@ def parse_command_line(args, description):
     parser.add_argument('--test', action='store_true',
                         help="Run preview_namelist in test mode.")
 
-    args = parser.parse_args()
-
-    CIME.utils.handle_standard_logging_options(args)
+    args = CIME.utils.parse_args_and_handle_standard_logging_options(args, parser)
 
     return args
 
diff --git a/scripts/Tools/save_provenance b/scripts/Tools/save_provenance
index 885c55a4eb6..fa3ae37b869 100755
--- a/scripts/Tools/save_provenance
+++ b/scripts/Tools/save_provenance
@@ -42,9 +42,7 @@ OR
     parser.add_argument("-l", "--lid",
                         help="Force system to save provenance with this LID")
 
-    args = parser.parse_args(args[1:])
-
-    CIME.utils.handle_standard_logging_options(args)
+    args = CIME.utils.parse_args_and_handle_standard_logging_options(args, parser)
 
     return args.mode, args.caseroot, args.lid
 
diff --git a/scripts/Tools/simple_compare b/scripts/Tools/simple_compare
index 47b465c14fa..a72ebe398bc 100755
--- a/scripts/Tools/simple_compare
+++ b/scripts/Tools/simple_compare
@@ -40,9 +40,7 @@ formatter_class=argparse.ArgumentDefaultsHelpFormatter
     parser.add_argument("-c", "--case", action="store", dest="case", default=None,
                         help="The case base id (<TESTCASE>.<GRID>.<COMPSET>). Helps us normalize data.")
 
-    args = parser.parse_args(args[1:])
-
-    CIME.utils.handle_standard_logging_options(args)
+    args = CIME.utils.parse_args_and_handle_standard_logging_options(args, parser)
 
     # Normalize case
     if (args.case is not None):
diff --git a/scripts/Tools/testreporter.py b/scripts/Tools/testreporter.py
index 4ea6666dc24..bc5188ab41c 100755
--- a/scripts/Tools/testreporter.py
+++ b/scripts/Tools/testreporter.py
@@ -43,7 +43,7 @@ def parse_command_line(args):
     parser.add_argument("--dumpxml",action="store_true", 
                         help="Dump XML test results to sceen.")
     args = parser.parse_args()
-    CIME.utils.handle_standard_logging_options(args)
+    CIME.utils.parse_args_and_handle_standard_logging_options(args)
 
 
     return args.testroot, args.testid, args.tagname, args.testtype, args.dryrun, args.dumpxml
diff --git a/scripts/Tools/update_acme_tests b/scripts/Tools/update_acme_tests
index f5aeb4a0207..588c5132160 100755
--- a/scripts/Tools/update_acme_tests
+++ b/scripts/Tools/update_acme_tests
@@ -48,9 +48,7 @@ formatter_class=argparse.ArgumentDefaultsHelpFormatter
     parser.add_argument("-p", "--platform",
                         help="Only add tests for a specific platform, format=machine,compiler. Useful for adding new platforms.")
 
-    args = parser.parse_args(args[1:])
-
-    CIME.utils.handle_standard_logging_options(args)
+    args = CIME.utils.parse_args_and_handle_standard_logging_options(args, parser)
 
     expect(os.path.isfile(args.test_list_path),
            "'%s' is not a valid file" % args.test_list_path)
diff --git a/scripts/Tools/wait_for_tests b/scripts/Tools/wait_for_tests
index 3e1b88d343f..7b4e698f3fa 100755
--- a/scripts/Tools/wait_for_tests
+++ b/scripts/Tools/wait_for_tests
@@ -66,9 +66,7 @@ formatter_class=argparse.ArgumentDefaultsHelpFormatter
     parser.add_argument("-g", "--cdash-build-group", default=CIME.wait_for_tests.CDASH_DEFAULT_BUILD_GROUP,
                         help="The build group to be used to display results on the CDash dashboard.")
 
-    args = parser.parse_args(args[1:])
-
-    CIME.utils.handle_standard_logging_options(args)
+    args = CIME.utils.parse_args_and_handle_standard_logging_options(args, parser)
 
     return args.paths, args.no_wait, args.check_throughput, args.check_memory, args.ignore_namelist_diffs, args.ignore_memleak, args.cdash_build_name, args.cdash_project, args.cdash_build_group
 
diff --git a/scripts/Tools/xmlchange b/scripts/Tools/xmlchange
index a8686fac4a0..f32bf556c0d 100755
--- a/scripts/Tools/xmlchange
+++ b/scripts/Tools/xmlchange
@@ -78,9 +78,7 @@ formatter_class=argparse.ArgumentDefaultsHelpFormatter
     parser.add_argument("-f","--force", action="store_true",
                         help="ignore typing checks and store value")
 
-    args = parser.parse_args(args[1:])
-
-    CIME.utils.handle_standard_logging_options(args)
+    args = CIME.utils.parse_args_and_handle_standard_logging_options(args, parser)
 
     listofsettings = []
     if( len(args.listofsettings )):
diff --git a/scripts/Tools/xmlconvertors/config_pes_converter.py b/scripts/Tools/xmlconvertors/config_pes_converter.py
index a0d0746c227..c453ee4c31b 100755
--- a/scripts/Tools/xmlconvertors/config_pes_converter.py
+++ b/scripts/Tools/xmlconvertors/config_pes_converter.py
@@ -28,9 +28,7 @@ def parse_command_line(args):
     parser.add_argument("-cime2file", "--cime2file", help="location of config_grid.xml file in CIME2 repository")
     parser.add_argument("-cime5file", "--cime5file", help="location of config_grids.xml file in CIME5 repository")
 
-    args = parser.parse_args(args[1:])
-
-    CIME.utils.handle_standard_logging_options(args)
+    CIME.utils.parse_args_and_handle_standard_logging_options(args, parser)
 
     if args.cime2file is None or args.cime5file is None:
         parser.print_help()
@@ -187,8 +185,8 @@ def __init__(self, xmlfilename):
             tempxml = StringIO.StringIO(t3)
             super(PesTree, self).__init__(tempxml)
             tempxml.close()
-        
-        
+
+
     def populate(self):
         xmlnodes = self.root.findall('grid')
         nodeclass = Cime5PesNode
diff --git a/scripts/Tools/xmlconvertors/grid_xml_converter.py b/scripts/Tools/xmlconvertors/grid_xml_converter.py
index 28fb95f49b5..988727a3edc 100755
--- a/scripts/Tools/xmlconvertors/grid_xml_converter.py
+++ b/scripts/Tools/xmlconvertors/grid_xml_converter.py
@@ -33,9 +33,7 @@ def parse_command_line(args):
     parser.add_argument("-cime2file", "--cime2file", help="location of config_grid.xml file in CIME2 repository")
     parser.add_argument("-cime5file", "--cime5file", help="location of config_grids.xml file in CIME5 repository")
 
-    args = parser.parse_args(args[1:])
-
-    CIME.utils.handle_standard_logging_options(args)
+    CIME.utils.parse_args_and_handle_standard_logging_options(args, parser)
 
     if args.cime2file is None or args.cime5file is None:
         parser.print_help()
diff --git a/scripts/Tools/xmlquery b/scripts/Tools/xmlquery
index 95bb0996fc7..26b6b23d788 100755
--- a/scripts/Tools/xmlquery
+++ b/scripts/Tools/xmlquery
@@ -105,9 +105,7 @@ epilog=textwrap.dedent(__doc__))
     group.add_argument("--valid-values", default=False, action="store_true",
                         help="Print the valid values associated with this variable if defined")
 
-    args = parser.parse_args(args[1:])
-
-    CIME.utils.handle_standard_logging_options(args)
+    args = CIME.utils.parse_args_and_handle_standard_logging_options(args, parser)
 
     if (len(sys.argv) == 1) :
         parser.print_help()
diff --git a/scripts/create_clone b/scripts/create_clone
index 968848a7a42..74c7bedfee5 100755
--- a/scripts/create_clone
+++ b/scripts/create_clone
@@ -40,9 +40,7 @@ def parse_command_line(args):
                         help="Specify the root output directory"
 			"default: setting in case, create_clone will fail if this directory is not writable")
 
-    args = parser.parse_args()
-
-    CIME.utils.handle_standard_logging_options(args)
+    args = CIME.utils.parse_args_and_handle_standard_logging_options(args, parser)
 
     if args.case is None:
         expect(False,
diff --git a/scripts/create_newcase b/scripts/create_newcase
index 1524e76d958..6d0f79cfcac 100755
--- a/scripts/create_newcase
+++ b/scripts/create_newcase
@@ -121,9 +121,7 @@ OR
     parser.add_argument("-i", "--input-dir",
                         help="Use a non-default location for input files")
 
-    args = parser.parse_args()
-
-    CIME.utils.handle_standard_logging_options(args)
+    args = CIME.utils.parse_args_and_handle_standard_logging_options(args, parser)
 
     if args.srcroot is not None:
         expect(os.path.isdir(args.srcroot),
diff --git a/scripts/create_test b/scripts/create_test
index 3ed88253cce..fb8ce394b44 100755
--- a/scripts/create_test
+++ b/scripts/create_test
@@ -226,9 +226,7 @@ OR
     parser.add_argument("-i", "--input-dir",
                         help="Use a non-default location for input files")
 
-    args = parser.parse_args(args[1:])
-
-    CIME.utils.handle_standard_logging_options(args)
+    args = CIME.utils.parse_args_and_handle_standard_logging_options(args, parser)
 
     # generate and compare flags may not point to the same directory
     if model == "cesm":
diff --git a/scripts/fortran_unit_testing/run_tests.py b/scripts/fortran_unit_testing/run_tests.py
index 715a98f7fde..9ce19b2d453 100755
--- a/scripts/fortran_unit_testing/run_tests.py
+++ b/scripts/fortran_unit_testing/run_tests.py
@@ -127,8 +127,8 @@ def parse_command_line(args):
         "--xml-test-list",
         help="""Path to an XML file listing directories to run tests from."""
         )
-    args = parser.parse_args()
-    CIME.utils.handle_standard_logging_options(args)
+
+    args = CIME.utils.parse_args_and_handle_standard_logging_options(args, parser)
     output = Printer(color=args.color)
 
     if args.xml_test_list is None and args.test_spec_dir is None:
diff --git a/scripts/lib/CIME/XML/env_mach_specific.py b/scripts/lib/CIME/XML/env_mach_specific.py
index 8e3ef188c71..e5d80ee4bdb 100644
--- a/scripts/lib/CIME/XML/env_mach_specific.py
+++ b/scripts/lib/CIME/XML/env_mach_specific.py
@@ -336,7 +336,7 @@ def get_mpirun(self, case, attribs, check_members=None, job="case.run", exe_only
         best_num_matched = -1
         default_match = None
         best_num_matched_default = -1
-        args = {}
+        args = []
         for mpirun_node in mpirun_nodes:
             xml_attribs = mpirun_node.attrib
             all_match = True
@@ -388,7 +388,7 @@ def get_mpirun(self, case, attribs, check_members=None, job="case.run", exe_only
                                                subgroup=job,
                                                check_members=check_members,
                                                default=arg_node.get("default"))
-                    args[arg_node.get("name")] = arg_value
+                    args.append(arg_value)
 
         exec_node = self.get_node("executable", root=the_match)
         expect(exec_node is not None,"No executable found")
diff --git a/scripts/lib/CIME/buildlib.py b/scripts/lib/CIME/buildlib.py
index 33b4ffce959..cc775e7bbbf 100644
--- a/scripts/lib/CIME/buildlib.py
+++ b/scripts/lib/CIME/buildlib.py
@@ -3,7 +3,7 @@
 """
 
 from CIME.XML.standard_module_setup import *
-from CIME.utils import handle_standard_logging_options, setup_standard_logging_options
+from CIME.utils import parse_args_and_handle_standard_logging_options, setup_standard_logging_options
 from CIME.case  import Case
 import sys, os, argparse, doctest
 
@@ -30,9 +30,7 @@ def parse_input(argv):
     parser.add_argument("bldroot",
                         help="root for building library")
 
-    args = parser.parse_args()
-
-    handle_standard_logging_options(args)
+    args = parse_args_and_handle_standard_logging_options(argv, parser)
 
     return args.caseroot, args.libroot, args.bldroot
 
diff --git a/scripts/lib/CIME/buildnml.py b/scripts/lib/CIME/buildnml.py
index 34f863155b6..0fa84fa578e 100644
--- a/scripts/lib/CIME/buildnml.py
+++ b/scripts/lib/CIME/buildnml.py
@@ -5,7 +5,7 @@
 """
 
 from CIME.XML.standard_module_setup import *
-from CIME.utils import expect, handle_standard_logging_options, setup_standard_logging_options
+from CIME.utils import expect, parse_args_and_handle_standard_logging_options, setup_standard_logging_options
 import sys, os, argparse, doctest
 
 logger = logging.getLogger(__name__)
@@ -25,9 +25,7 @@ def parse_input(argv):
     parser.add_argument("caseroot", default=os.getcwd(),
                         help="Case directory")
 
-    args = parser.parse_args()
-
-    handle_standard_logging_options(args)
+    args = parse_args_and_handle_standard_logging_options(argv, parser)
 
     return args.caseroot
 
diff --git a/scripts/lib/CIME/case.py b/scripts/lib/CIME/case.py
index 9e143418fd5..8fc3d2b26a6 100644
--- a/scripts/lib/CIME/case.py
+++ b/scripts/lib/CIME/case.py
@@ -1129,21 +1129,21 @@ def get_mpirun_cmd(self, job="case.run"):
             "unit_testing" : False
             }
 
-        executable, args = env_mach_specific.get_mpirun(self, mpi_attribs, job=job)
+        executable, mpi_arg_list = env_mach_specific.get_mpirun(self, mpi_attribs, job=job)
 
         # special case for aprun
-        if  executable is not None and "aprun" in executable:
+        if executable is not None and "aprun" in executable:
             aprun_args, num_nodes = get_aprun_cmd_for_case(self, run_exe)
             expect(num_nodes == self.num_nodes, "Not using optimized num nodes")
             return executable + aprun_args + " " + run_misc_suffix
 
         else:
-            mpi_arg_string = " ".join(args.values())
+            mpi_arg_string = " ".join(mpi_arg_list)
 
-            if self.get_value("BATCH_SYSTEM") == "cobalt":
-                mpi_arg_string += " : "
+        if self.get_value("BATCH_SYSTEM") == "cobalt":
+            mpi_arg_string += " : "
 
-            return "%s %s %s" % (executable if executable is not None else "", mpi_arg_string, run_suffix)
+        return "%s %s %s" % (executable if executable is not None else "", mpi_arg_string, run_suffix)
 
     def set_model_version(self, model):
         version = "unknown"
diff --git a/scripts/lib/CIME/case_setup.py b/scripts/lib/CIME/case_setup.py
index f17ef584e07..dd815e39dce 100644
--- a/scripts/lib/CIME/case_setup.py
+++ b/scripts/lib/CIME/case_setup.py
@@ -155,7 +155,6 @@ def _case_setup_impl(case, caseroot, clean=False, test_mode=False, reset=False):
             logger.debug("at update TOTALPES = %s"%pestot)
             case.set_value("TOTALPES", pestot)
             thread_count = env_mach_pes.get_max_thread_count(models)
-            build_threaded = case.get_build_threaded()
             cost_pes = env_mach_pes.get_cost_pes(pestot, thread_count, machine=case.get_value("MACH"))
             case.set_value("COST_PES", cost_pes)
 
diff --git a/scripts/lib/CIME/utils.py b/scripts/lib/CIME/utils.py
index 247b04c6f61..6d79bce0543 100644
--- a/scripts/lib/CIME/utils.py
+++ b/scripts/lib/CIME/utils.py
@@ -637,7 +637,7 @@ def filter(self, record):
         #non-zero return means we log this message
         return 1 if record.levelno < self.max_level else 0
 
-def handle_standard_logging_options(args):
+def parse_args_and_handle_standard_logging_options(args, parser=None):
     """
     Guide to logging in CIME.
 
@@ -660,6 +660,11 @@ def handle_standard_logging_options(args):
     stderr_stream_handler = logging.StreamHandler(stream=sys.stderr)
     stderr_stream_handler.setLevel(logging.WARNING)
 
+    # scripts_regression_tests is the only thing that should pass a None argument in parser
+    if parser is not None:
+        _check_for_invalid_args(args[1:])
+        args = parser.parse_args(args[1:])
+
     # --verbose adds to the message format but does not impact the log level
     if args.verbose:
         stdout_stream_handler.setFormatter(verbose_formatter)
@@ -682,6 +687,8 @@ def handle_standard_logging_options(args):
         root_logger.setLevel(logging.WARN)
     else:
         root_logger.setLevel(logging.INFO)
+    return args
+
 
 def get_logging_options():
     """
@@ -1229,6 +1236,16 @@ def run_and_log_case_status(func, phase, caseroot='.'):
 
     return rv
 
+def _check_for_invalid_args(args):
+    for arg in args:
+        if arg.startswith("--"):
+            continue
+        if arg.startswith("-") and len(arg) > 2:
+            if arg == "-value" or arg == "-noecho":
+                logger.warn("This argument is depricated, please use -%s"%arg)
+            else:
+                expect(False, "Invalid argument %s\n  Multi-character arguments should begin with \"--\" and single character with \"-\"\n  Use --help for a complete list of available options"%arg)
+
 class SharedArea(object):
     """
     Enable 0002 umask within this manager
diff --git a/scripts/manage_case b/scripts/manage_case
index c561d6cede4..40f6a8fc280 100755
--- a/scripts/manage_case
+++ b/scripts/manage_case
@@ -140,9 +140,7 @@ def parse_command_line(args):
     parser.add_argument("--long", action="store_true",
                         help="Provide long output for queries")
 
-    args = parser.parse_args()
-
-    CIME.utils.handle_standard_logging_options(args)
+    args = CIME.utils.parse_args_and_handle_standard_logging_options(args, parser)
 
     return args
 
diff --git a/scripts/manage_pes b/scripts/manage_pes
index 6258b76e6d6..9f0f86e52cf 100755
--- a/scripts/manage_pes
+++ b/scripts/manage_pes
@@ -98,8 +98,8 @@ def parse_command_line(args, description):
                         help=queryhelp)
     parser.add_argument("-machine", "--machine", default=None,
                         help="can be a supported machine name")
-    args = parser.parse_args(args[1:])
-    CIME.utils.handle_standard_logging_options(args)
+
+    args = CIME.utils.parse_args_and_handle_standard_logging_options(args, parser)
     CIME.utils.expect(args.add or args.query,
                       "Either --query or --add must be on command line")
 
diff --git a/scripts/query_testlists b/scripts/query_testlists
index 12d3fc0c3eb..d9c5f3a31d3 100755
--- a/scripts/query_testlists
+++ b/scripts/query_testlists
@@ -11,7 +11,7 @@ from CIME.utils import expect
 logger = logging.getLogger(__name__)
 
 ###############################################################################
-def parse_command_line(description):
+def parse_command_line(args, description):
 ###############################################################################
     parser = argparse.ArgumentParser(
         description=description)
@@ -45,9 +45,7 @@ def parse_command_line(description):
     parser.add_argument("--xml-testlist",
                         help="Use this testlist to lookup tests, default specified in config_files.xml")
 
-    args = parser.parse_args()
-
-    CIME.utils.handle_standard_logging_options(args)
+    args = CIME.utils.parse_args_and_handle_standard_logging_options(args, parser)
 
     expect(not(args.count and args.list_type),
            "Cannot specify both --count and --list arguments.")
@@ -149,7 +147,7 @@ def list_test_data(test_data, list_type):
 ###############################################################################
 def _main_func(description):
 ###############################################################################
-    args = parse_command_line(description)
+    args = parse_command_line(sys.argv, description)
 
     test_data = get_tests_from_xml(
         xml_machine = args.xml_machine,
diff --git a/scripts/tests/scripts_regression_tests.py b/scripts/tests/scripts_regression_tests.py
index 7dac780e46d..380b0f19fdf 100755
--- a/scripts/tests/scripts_regression_tests.py
+++ b/scripts/tests/scripts_regression_tests.py
@@ -2217,7 +2217,7 @@ def _main_func():
         else:
             setattr(args, log_param, False)
 
-    CIME.utils.handle_standard_logging_options(args)
+    args = CIME.utils.parse_args_and_handle_standard_logging_options(args, None)
 
     write_provenance_info()
 
diff --git a/src/build_scripts/buildlib.gptl b/src/build_scripts/buildlib.gptl
index 2a5fea6f852..b92c788d396 100755
--- a/src/build_scripts/buildlib.gptl
+++ b/src/build_scripts/buildlib.gptl
@@ -6,8 +6,8 @@
 
 cd $CASEROOT # CASEROOT is always assumed to be an environment variable
 
-set CIMEROOT	= `./xmlquery  CIMEROOT	-value `
-set GMAKE	= `./xmlquery  GMAKE	-value `
+set CIMEROOT	= `./xmlquery  CIMEROOT -value `
+set GMAKE	= `./xmlquery  GMAKE	--value `
 
 # NOTE- (mv, 2015-01-02) SHAREDPATH is an environment variable set in
 # the $CASE.build script
diff --git a/src/build_scripts/buildlib.pio b/src/build_scripts/buildlib.pio
index cb4d29e40bf..5b6909b0ddf 100755
--- a/src/build_scripts/buildlib.pio
+++ b/src/build_scripts/buildlib.pio
@@ -38,9 +38,7 @@ formatter_class=argparse.ArgumentDefaultsHelpFormatter
     parser.add_argument("caseroot", nargs="?", default=os.getcwd(),
                         help="Case directory to build")
 
-    args = parser.parse_args(args[1:])
-
-    CIME.utils.handle_standard_logging_options(args)
+    args = CIME.utils.parse_args_and_handle_standard_logging_options(args, parser)
 
     return args.buildroot, args.installpath, args.caseroot
 
@@ -144,7 +142,7 @@ def _main_func(description):
         case.set_valid_values("PIO_TYPENAME",valid_values)
         # nothing means use the general default
         valid_values += ",nothing"
-        
+
         for comp in case.get_values("COMP_CLASSES"):
             comp_pio_typename = "%s_PIO_TYPENAME"%comp
             case.set_valid_values(comp_pio_typename,valid_values)
diff --git a/tools/configure b/tools/configure
index bba14b82d70..997b1d3e524 100755
--- a/tools/configure
+++ b/tools/configure
@@ -69,7 +69,7 @@ def parse_command_line(args):
 
     argcnt = len(args)
     args = parser.parse_args()
-    CIME.utils.handle_standard_logging_options(args)
+    CIME.utils.parse_args_and_handle_standard_logging_options(args)
 
     opts = {}
     if args.machines_dir is not None: