Intra annual Variability of the Arabian Sea high salinity water mass in the South Eastern Arabian Sea during 2016 17

Intra-annual variability of the Arabian Sea high salinity water mass (ASHSW) in the South Eastern Arabian Sea (SEAS) and Gulf of Mannar (GoM) are addressed in this paper by utilisng the monthly missions carried out onboard INS Sagardhwani during 2016-17. Our observations revealed that the ASHSW was evident along the SEAS irrespective of seasons, whereas in the GoM the presence of ASHSW was observed during winter. The processes such as downwelling/up-welling, coastal currents, intrusion of low saline waters, stratification are clearly affects the spreading of the ASHSW. The characteristics such as core salinity value, depth and thickness of ASHSW exhibited remarkable spatio-temporal variability. Lateral mixing with the low saline waters in the region during winter reduces its core salinity. The intrusion of low saline waters was clearly seen upto 15 ON but the intrusion of low saline waters is not flowing through the GoM. The interface between the ASHSW and the prevailing low saline waters showed strong horizontal gradients of salinity. The presence of the ASHSW makes difference in the SLD and the below layer gradient which is sufficient to complicate or influence sound transmission. The spatio temporal variability of the ASHSW and its acoustic relevance are documented in this paper

MINIO : an I/O benchmark for investigating high level parallel libraries

Input/output (I/O) operations are one of the biggest challenges facing scientific computing as it transitions to exascale. The traditional software stack – com- prising of parallel file systems, middlewares and high level libraries – has evolved to enable applications to better cope with the demands of enormous datasets. This software stack makes high performance parallel I/O easily accessible to application engineers, however it is important to ensure best performance is not compromised through attempts to enrich these libraries. We present MINIO, a benchmark for the investigation of I/O behaviour focusing on understanding overheads and inefficiencies in high level library usage. MINIO uses HDF5 and TyphonIO to explore I/O at scale using different application behavioural pat- terns. A case study is performed using MINIO to identify performance limiting characteristics present in the TyphonIO library as an example of performance discrepancies in the I/O stack

Enabling portable I/O analysis of commercially sensitive HPC applications through workload replication

Benchmarking and analyzing I/O performance across high performance computing (HPC) platforms is necessary to identify performance bottlenecks and guide effective use of new and existing storage systems. Doing this with large production applications, which can often be commercially sensitive and lack portability, is not a straightforward task and the availability of a representative proxy for I/O workloads can help to provide a solution. We use Darshan I/O characterization and the MACSio proxy application to replicate five production workloads, showing how these can be used effectively to investigate I/O performance when migrating between HPC systems ranging from small local clusters to leadership scale machines. Preliminary results indicate that it is possible to generate datasets that match the target application with a good degree of accuracy. This enables a predictive performance analysis study of a representative workload to be conducted on five different systems. The results of this analysis are used to identify how workloads exhibit different I/O footprints on a file system and what effect file system configuration can have on performance

Replicating HPC I/O workloads with proxy applications

Large scale simulation performance is dependent on a number of components, however the task of investigation and optimization has long favored computational and communication elements above I/O. Manually extracting the pattern of I/O behavior from a parent application is a useful way of working to address performance issues on a per-application basis, but developing workflows with some degree of automation and flexibility provides a more powerful approach to tackling current and future I/O challenges. In this paper we describe a workload replication workflow that extracts the I/O pattern of an application and recreates its behavior with a flexible proxy application. We demonstrate how simple lightweight characterization can be translated to provide an effective representation of a physics application, and show how a proxy replication can be used as a tool for investigating I/O library paradigms

BookLeaf: An Unstructured Hydrodynamics Mini-application

With the age of Exascale computing causing a diversification away from traditional CPU-based homogeneous clusters, it is becoming increasingly difficult to ensure that computationally complex codes are able to run on these emerging architectures. This is especially important for large physics simulations that are themselves becoming increasingly complex and computationally expensive. One proposed solution to the problem of ensuring these applications can run on the desired architectures is to develop representative mini-applications that are simpler and so can be ported to new frameworks more easily, but which are also representative of the algorithmic and performance characteristics of the original applications. In this paper we present BookLeaf, an unstructured Arbitrary Lagrangian-Eulerian mini-application to add to the suite of representative applications developed and maintained by the UK Mini-App Consortium (UK-MAC). First, we outline the reference implementation of our application in Fortran. We then discuss a number of alternative implementations using a variety of parallel programming models and discuss the issues that arise when porting such an application to new architectures. To demonstrate our implementation, we present a study of the performance of BookLeaf on number of platforms using alternative designs, and we document a scaling study showing the behaviour of the application at scale

Higher-order particle representation for particle-in-cell simulations

In this paper we present an alternative approach to the representation of simulation particles for unstructured electrostatic and electromagnetic PIC simulations. In our modified PIC algorithm we represent particles as having a smooth shape function limited by some specified finite radius, . A unique feature of our approach is the representation of this shape by surrounding simulation particles with a set of virtual particles with delta shape, with fixed offsets and weights derived from Gaussian quadrature rules and the value of . As the virtual particles are purely computational, they provide the additional benefit of increasing the arithmetic intensity of traditionally memory bound particle kernels. The modified algorithm is implemented within Sandia National Laboratories' unstructured EMPIRE-PIC code, for electrostatic and electromagnetic simulations, using periodic boundary conditions. We show results for a representative set of benchmark problems, including electron orbit, a transverse electromagnetic wave propagating through a plasma, numerical heating, and a plasma slab expansion. Good error reduction across all of the chosen problems is achieved as the particles are made progressively smoother, with the optimal particle radius appearing to be problem-dependent

Full-System Modeling and Simulation: Contributions Towards Coupling Contention and I/O

Production machine performance has large variability. On the UK National Supercomputing Service, the time a job takes to complete can vary by as much as 53%. Load imbalance and shared resource contention are largely responsible, but we find that previous efforts to model application/architecture performance do not typically take these into account. In this research we model and simulate network contention, which allows us to explore the impact of multiple interacting jobs and approaches to alleviate these effects, including network re-design and communication-staging within applications. We show the utility of this work on a variety of systems and interacting applications

Warwick Data Store : a data structure abstraction library

With the increasing complexity of memory architectures and scientific applications, developing data structures that are performant, portable, scalable, and support developer productivity, is a challenging task. In this paper, we present Warwick Data Store (WDS), a lightweight and extensible C++ template library designed to manage these complexities and allow rapid prototyping. WDS is designed to abstract details of the underlying data structures away from the user, thus easing application development and optimisation. We show that using WDS does not significantly impact achieved performance across a variety of different scientific benchmarks and proxy-applications, compilers, and different architectures. The overheads are largely below 30% for smaller problems, with the overhead deceasing to below 10% when using larger problems. This shows that the library does not significantly impact the performance, while providing additional functionality to data structures, and the ability to optimise data structures without changing the application code

Computational modelling of epithelial cell interactions

EThOS - Electronic Theses Online ServiceGBUnited Kingdo