diff -r f5b374b08180 src/sys/objects/options.c
--- a/src/sys/objects/options.c	Mon Jul 23 12:27:02 2012 -0500
+++ b/src/sys/objects/options.c	Tue Jul 24 08:35:27 2012 -0500
@@ -646,13 +646,6 @@ PetscErrorCode  PetscOptionsInsert(int *
     }
   }
 
-#if defined(PETSC_HAVE_YAML)
-  char yaml_file[PETSC_MAX_PATH_LEN];
-  PetscBool yaml_flg = PETSC_FALSE;
-  ierr = PetscOptionsGetString(PETSC_NULL,"-options_file_yaml",yaml_file,PETSC_MAX_PATH_LEN,&yaml_flg);CHKERRQ(ierr);
-  if (yaml_flg) ierr = PetscOptionsInsertFile_YAML(PETSC_COMM_WORLD,yaml_file,PETSC_TRUE);CHKERRQ(ierr);
-#endif
-
   /* insert command line options again because they take precedence over arguments in petscrc/environment */
   if (argc && args && *argc) {ierr = PetscOptionsInsertArgs_Private(*argc,*args);CHKERRQ(ierr);}
 
diff -r f5b374b08180 src/sys/objects/pinit.c
--- a/src/sys/objects/pinit.c	Mon Jul 23 12:27:02 2012 -0500
+++ b/src/sys/objects/pinit.c	Tue Jul 24 08:35:27 2012 -0500
@@ -830,6 +830,14 @@ PetscErrorCode  PetscInitialize(int *arg
   ierr = PetscThreadCommInitializePackage(PETSC_NULL);CHKERRQ(ierr);
 #endif
 
+#if defined(PETSC_HAVE_YAML)
+  char yaml_file[PETSC_MAX_PATH_LEN];
+  PetscBool yaml_flg = PETSC_FALSE;
+  ierr = PetscOptionsGetString(PETSC_NULL,"-options_file_yaml",yaml_file,PETSC_MAX_PATH_LEN,&yaml_flg);CHKERRQ(ierr);
+  if (yaml_flg) ierr = PetscOptionsInsertFile_YAML(PETSC_COMM_WORLD,yaml_file,PETSC_TRUE);CHKERRQ(ierr);
+#endif
+
+
   /*
       Once we are completedly initialized then we can set this variables
   */