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Software-controlled caches, often called scratch-pad memories (SPM), are being increasingly used due to their efficiency. And to exploit all the advantages of SPMs an efficient allocation must be done in software. In this work we propose a runtime operating system management approach for SPMs that do not require compiler support, application profiling or hardware support. The OS will use annotations, inserted into the code by the programmer, as hints to choose the most appropriate level in the memory hierarchy to allocate the data. The results showed that we were able to implement a run-time SPM allocation technique without adding any significant overhead to the system when compared with manual allocation.