adaptations in electronic structure calculations in heterogeneous environments
Is Version Of
Modern quantum chemistry deals with electronic structure calculations of
unprecedented complexity and accuracy. They demand full power of
high-performance computing and must be in tune with the given architecture for
superior efficiency. To make such applications resource-aware, it is desirable
to enable their static and dynamic adaptations using some external software
(middleware), which may monitor both system availability and application needs,
rather than mix science with system-related calls inside the application.
The present work investigates scientific application interlinking
with middleware based on the example of the computational chemistry package GAMESS
and middleware NICAN. The existing synchronous model is limited by the possible delays
due to the middleware processing time under the sustainable runtime system conditions.
Proposed asynchronous and hybrid models aim at overcoming this limitation.
When linked with NICAN, the fragment molecular orbital (FMO) method is capable of adapting
statically and dynamically its fragment scheduling policy based on the computing
platform conditions. Significant execution time and throughput gains have been
obtained due to such static adaptations when the compute nodes have very different core counts.
Dynamic adaptations are based on the main memory availability at run time.
NICAN prompts FMO to postpone scheduling certain fragments, if there is not
enough memory for their immediate execution. Hence, FMO may be able to complete
the calculations whereas without such adaptations it aborts.