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I have large no of variables. Is there any directive to tell compiler not to initiliza vars on startup before disabling watchdog.
It's not just a compiler directive, and of course the tools know nothing about when the watchdog is disabled, but I think you probably want to use UNINIT in the linker scatter file: infocenter.arm.com/.../ka14180.html
Easiest is to find large arrays or structs that can be zero-initialized. Move them to a specific memory region that you specify to be unininialized. Then it's easy to memset() to zero after the watchdog has been kicked.
While you still get the advantage that the startup files can give initial values to the variables you want specific start values for.
Just make sure that you don't on "routine" assign zero to global variables without verifying if the compiler/linker will notice that these assigns can be done by simple zeroing instead of copying explicit values from flash on startup.