diff --git a/tools/configure b/tools/configure
index ae60efc625f..97d7e6adcb8 100755
--- a/tools/configure
+++ b/tools/configure
@@ -108,6 +108,19 @@ def parse_command_line(args):
            % compiler)
     opts['compiler'] = compiler
     opts['os'] = machobj.get_value('OS')
+
+    if args.clean:
+        files = ["Macros.make", "Macros.cmake", "env_mach_specific.xml", ".env_mach_specific.sh",
+                 ".env_mach_specific.csh", "Depends.%s"%compiler, "Depends.%s"%args.machine,
+                  "Depends.%s.%s"%(args.machine,compiler)]
+        for file_ in files:
+            if os.path.isfile(file_):
+                logger.warn("Removing file %s"%file_)
+                os.remove(file_)
+        if argcnt == 2:
+            opts['clean_only'] = True
+            return opts
+
     # Set MPI library.
     if args.mpilib is not None:
         mpilib = args.mpilib
@@ -134,17 +147,6 @@ def parse_command_line(args):
     opts['debug'] = debug
 
 
-    if args.clean:
-        files = ["Macros.make", "Macros.cmake", "env_mach_specific.xml", ".env_mach_specific.sh",
-                 ".env_mach_specific.csh", "Depends.%s"%compiler, "Depends.%s"%args.machine,
-                  "Depends.%s.%s"%(args.machine,compiler)]
-        for file_ in files:
-            if os.path.isfile(file_):
-                logger.warn("Removing file %s"%file_)
-                os.remove(file_)
-        if argcnt == 2:
-            opts['clean_only'] = True
-
     return opts
 
 def _main():