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Challenges at Petascale for Pseudo-Spectral Methods on Spheres (A Last Hurrah?)

Conclusions: a) Proper software abstractions should enable rapid-exploration of platform-specific optimizations/ tradeoffs. b) Pseudo-spectra! methods are marginally viable for at least some classes of petascaie problems. i.e., GPU based machine with good bisection would be best. c) Scalability at exascale is possible, but the necessary resolution will make algorithm prohibitively expensive. Efficient implementations of realistic global transposes are mtricate and tedious in MPI. PS at petascaie requires exploration of a variety of strategies for spreading local and remote communic3tions. PGAS allows far simpler implementation and thus rapid exploration of variants.

Clune, Thomas↗

Testing Scientific Software: Challenges and Remedies

Over the past two decades, the emergence of highly effective software testing frameworks has greatly simplified the development and use of unit tests and has led to new software development paradigms such as test driven development (TDD). However, scientific computing introduces a number of unique testing challenges, including numerical algorithms, distributed parallelism, and exascale environments. This presentation will begin with a brief introduction to unit testing, testing frameworks, and some simple examples using pFUnit, a unit testing framework for Fortran + MPI. I will then take a closer look at several of the obstacles one faces when testing technical software and suggest methodologies that can mitigate these difficulties.

Clune, Tom↗

Testing Fortran Software with pFunit

Over the past two decades, the emergence of highly effective software testing frameworks has greatly simplified the development and use of unit tests and has led to new software development paradigms such as test driven development (TDD). However, technical computing introduces a number of unique testing challenges, including distributed parallelism and numerical accuracy. This webinar will begin with a basic introduction to the use of pFUnit (parallel Fortran Unit testing framework) to develop tests for Message Passing Interface (MPI) plus Fortran (MPI+Fortran) software and then present some of the new capabilities in the latest release. We will also discuss some specialized methodologies for testing numerical algorithms and speculate about future framework capabilities that may improve our ability to test at exascale.

Clune, Tom↗

Methodology and Application of HPC I/O Characterization with MPIProf and IOT

Combining the strengths of MPIProf and IOT, an efficient and systematic method is devised for I/O characterization at the per-job, per-rank, per-file and per-call levels of HPC programs running on the NASA Advanced Supercomputing Center. This method is applied to answer four I/O questions in this paper. A total of 13 MPI programs and 15 cases, ranging from 24 to 5968 ranks, are analyzed to establish the I/O landscape from answers to the four questions. Four of the 13 programs use MPI I/O and the behavior of their collective writes depends on the specific implementation of the MPI library used. The SGI MPT library, the prevailing MPI library for our systems, was found to gather small writes from a large number of ranks to perform larger writes by a small subset of collective buffering ranks. The number of collective buffering ranks invoked by MPT depends on the Lustre stripe count and the number of nodes used for the run. A demonstration of varying the stripe count to achieve double-digit speedup of one program's I/O was presented. Another program, which concurrently opens private files by all ranks and could potentially create a heavy load on the Lustre servers, was identified. The ability to systematically characterize I/O for a large number of programs running on a supercomputer, seek I/O optimization opportunity and identify programs that could cause a high load and instability on the filesystems is important for pursuing exascale in a real production environment.

Characterization↗

GEOS Atmospheric Model: Challenges at Exascale

The Goddard Earth Observing System (GEOS) model at NASA's Global Modeling and Assimilation Office (GMAO) is used to simulate the multi-scale variability of the Earth's weather and climate, and is used primarily to assimilate conventional and satellite-based observations for weather forecasting and reanalysis. In addition, assimilations coupled to an ocean model are used for longer-term forecasting (e.g., El Nino) on seasonal to interannual times-scales. The GMAO's research activities, including system development, focus on numerous time and space scales, as detailed on the GMAO website, where they are tabbed under five major themes: Weather Analysis and Prediction; Seasonal-Decadal Analysis and Prediction; Reanalysis; Global Mesoscale Modeling, and Observing System Science. A brief description of the GEOS systems can also be found at the GMAO website. GEOS executes as a collection of earth system components connected through the Earth System Modeling Framework (ESMF). The ESMF layer is supplemented with the MAPL (Modeling, Analysis, and Prediction Layer) software toolkit developed at the GMAO, which facilitates the organization of the computational components into a hierarchical architecture. GEOS systems run in parallel using a horizontal decomposition of the Earth's sphere into processing elements (PEs). Communication between PEs is primarily through a message passing framework, using the message passing interface (MPI), and through explicit use of node-level shared memory access via the SHMEM (Symmetric Hierarchical Memory access) protocol. Production GEOS weather prediction systems currently run at 12.5-kilometer horizontal resolution with 72 vertical levels decomposed into PEs associated with 5,400 MPI processes. Research GEOS systems run at resolutions as fine as 1.5 kilometers globally using as many as 30,000 MPI processes. Looking forward, these systems can be expected to see a 2 times increase in horizontal resolution every two to three years, as well as less frequent increases in vertical resolution. Coupling these resolution changes with increases in complexity, the computational demands on the GEOS production and research systems should easily increase 100-fold over the next five years. Currently, our 12.5 kilometer weather prediction system narrowly meets the time-to-solution demands of a near-real-time production system. Work is now in progress to take advantage of a hybrid MPI-OpenMP parallelism strategy, in an attempt to achieve a modest two-fold speed-up to accommodate an immediate demand due to increased scientific complexity and an increase in vertical resolution. Pursuing demands that require a 10- to 100-fold increases or more, however, would require a detailed exploration of the computational profile of GEOS, as well as targeted solutions using more advanced high-performance computing technologies. Increased computing demands of 100-fold will be required within five years based on anticipated changes in the GEOS production systems, increases of 1000-fold can be anticipated over the next ten years.

ESMF↗