The Modular Supercomputing Architecture (MSA) is a blueprint for heterogeneous HPC systems supporting the highest efficiency and scalability. The MSA developed throughout the DEEP projects integrates different compute modules with specific performance characteristics for different workloads. To cope with the high computing and memory heterogeneity of modern HPC architectures and the MSA in particular, an adapted and optimised software stack is required: The modular approach provides substantial benefits to heterogeneous applications and workflows. Each part of a code can be executed on the most suitable platform, improving both time to solution and energy efficiency. Extracting the maximum performance from the diverse pool of compute resources requires the applications to be adapted. The innovative DEEP-SEA SW stack enables applications to effectively harness modularity. It supports memory hierarchies and a wide range of accelerators. DEEP-SEA builds on the results of the DEEP project series and is linked to the partner project RED-SEA to cover HPC interconnect topics, and also to IO-SEA to address system-level I/O and storage management.