Rapid technological advancements in sequencing technologies allow producing cost effective and high volume sequencing data. Processing this data for real-time clinical diagnosis is potentially time-consuming if done on a single computing node. This work presents a complete variant calling workflow, implemented using the Message Passing Interface (MPI) to leverage the benefits of high bandwidth interconnects. This solution (GenMPI) is portable and flexible, meaning it can be deployed to any private or public cluster/cloud infrastructure. Any alignment or variant calling application can be used with minimal adaptation. To achieve high performance, compressed input data can be streamed in parallel to alignment applications while uncompressed data can use internal file seek functionality to eliminate the bottleneck of streaming input data from a single node. Alignment output can be directly stored in multiple chromosome-specific SAM files or a single SAM file. After alignment, a distributed queue using MPI RMA (Remote Memory Access) atomic operations is created for sorting, indexing, marking of duplicates (if necessary) and variant calling applications. We ensure the accuracy of variants as compared to the original single node methods. We also show that for 300x coverage data, alignment scales almost linearly up to 64 nodes (8192 CPU cores). Overall, this work outperforms existing Big Data based workflows by a factor of two and is almost 20% faster than other MPI-based implementations for alignment without any extra memory overheads. Sorting, indexing, duplicate removal and variant calling is also scalable up to 8 nodes cluster. For pair-end short-reads (Illumina) data, we integrated the BWA-MEM aligner and three variant callers (GATK HaplotypeCaller, DeepVariant and Octopus), while for long-reads data, we integrated the Minimap2 aligner and three different variant callers (DeepVariant, DeepVariant with WhatsHap for phasing (PacBio) and Clair3 (ONT)).

Abstract Since the C++ bindings were deleted in 2008, the Message Passing Interface (MPI) community has recently revived efforts in building high-level modern C++ interfaces. Such interfaces are either built to serve specific scientific application needs (with limited coverage to the underlying MPI functionality), or as an exercise in general-purpose programming model building, with the hope that bespoke interfaces can be broadly adopted to construct a variety of distributed-memory scientific applications. However, with the advent of modern C++-based heterogeneous programming models, GPUs and widespread Machine Learning (ML) usage in contemporary scientific computing, the role of prospective community-standardized high-level C++ interfaces to MPI is evolving. The success of such an interface clearly will depend on providing robust abstractions and features adhering to the generic programming principles that underpin the C++ programming language, without compromising on either performance or portability, the core principles upon which MPI was founded. However, there is a tension between idiomatic C++ handling of types and lifetimes and MPI’s loose interpretation of object lifetimes/ownership and insistence on maintaining global states. Instead of proposing “yet another” high-level C++ interface to MPI, overlooking or providing partial solutions to work around the key issues concerning the dissonance between MPI semantics and idiomatic C++, this paper focuses on the three fundamental aspects of a high-level interface: type system, object lifetimes, and communication buffers, while also identifying inconsistencies in the MPI specification. Presumptive solutions can be unrefined, and we hope the broader MPI and C++ communities will engage with us in productive exchange of ideas and concerns.

This reproducibility report provides details about the artifact evaluation done with regards to the Artifact Description and Evaluation appendix of SC25 paper “X-MoE: Enabling Scalable Training for Emerging Mixture-of-Experts Architectures on HPC Platforms” by Sajal Dash, Minjia Zhang, Feiyi Wang, Jianping Li, Yueming Yuan, and Ahan Gupta. The work was done as part of the Reproducibility Initiative of SC25. The author is a member of the SC25 Reproducibilty Committee.

MPI is the most widely used interface for high-performance computing (HPC) workloads. Its success lies in its embrace of libraries and ability to evolve while maintaining backward compatibility for older codes, enabling them to run on new architectures for many years. In this paper, we propose a new level of MPI compatibility: a standard Application Binary Interface (ABI). We review the history of MPI implementation ABIs, identify the constraints from the MPI standard and ISO C, and summarize recent efforts to develop a standard ABI for MPI. We provide the current proposal from the MPI Forum’s ABI working group, which has been prototyped both within MPICH and as an independent abstraction layer called Mukautuva. We also list several use cases that would benefit from the definition of an ABI while outlining the remaining constraints.

Performance benchmarks are an integral part of the development and evaluation of parallel algorithms, both in distributed applications as well as MPI implementations themselves. The initial step of the benchmark process is to obtain a common timestamp to mark the start of an operation across all involved processes, and the state-of-the-art in many applications and widely used MPI benchmark suites is the use of MPI barriers. In this paper, we show that the synchronization in space provided by an MPI_Barrier is insufficient for proper benchmark results of parallel distributed algorithms, using MPI collective operations as examples. The resulting lack of a global start timestamp for an operation leads to skewed results, with a significant impact of the used barrier algorithm. In order to mitigate these issues, we propose and discuss the implementation of MPIX_Harmonize, which extends the synchronization in space provided by MPI_Barrier with a time synchronization to guarantee a common starting timestamp across all involved processes. By replacing the use of MPI_Barrier with MPIX_Harmonize, benchmark implementors can eliminate skews resulting from barrier algorithms and achieve stable performance benchmark results. We will show that the proper time synchronization can have significant impact on the benchmark results for various implementations of MPI_Allreduce, MPI_Reduce, and MPI_Bcast.

The EU Center of Excellence for Exascale in Solid Earth (ChEESE) develops exascale transition capabilities in the domain of Solid Earth, an area of geophysics rich in computational challenges embracing different approaches to exascale (capability, capacity, and urgent computing). The first implementation phase of the project (ChEESE-1P; 2018–2022) addressed scientific and technical computational challenges in seismology, tsunami science, volcanology, and magnetohydrodynamics, in order to understand the phenomena, anticipate the impact of natural disasters, and contribute to risk management. The project initiated the optimisation of 10 community flagship codes for the upcoming exascale systems and implemented 12 Pilot Demonstrators that combine the flagship codes with dedicated workflows in order to address the underlying capability and capacity computational challenges. Pilot Demonstrators reaching more mature Technology Readiness Levels (TRLs) were further enabled in operational service environments on critical aspects of geohazards such as long-term and short-term probabilistic hazard assessment, urgent computing, and early warning and probabilistic forecasting. Partnership and service co-design with members of the project Industry and User Board (IUB) leveraged the uptake of results across multiple research institutions, academia, industry, and public governance bodies (e.g. civil protection agencies). This article summarises the implementation strategy and the results from ChEESE-1P, outlining also the underpinning concepts and the roadmap for the on-going second project implementation phase (ChEESE-2P; 2023–2026).

Shared memory parallel programming models strive to provide low-overhead execution environments. Task-based programming models, in particular, are well-suited to cope with the ubiquitous multi- and many-core systems since they allow applications to express all available concurrency to a scheduler, which is tasked with exploiting the available hardware resources. It is general consensus that atomic operations should be preferred over locks and mutexes to avoid inter-thread serialization and the resulting loss in efficiency. However, even atomic operations may serialize threads if not used judiciously. In this work, we will discuss several optimizations applied to TTG and the underlying PaRSEC runtime system aiming at removing contentious atomic operations to reduce the overhead of task management to a few hundred clock cycles. The result is an optimized data-flow programming system that seamlessly scales from a single node to distributed execution and which is able to compete with OpenMP in shared memory.

We present and evaluate TTG, a novel programming model and its C++ implementation that by marrying the ideas of control and data flowgraph programming supports compact specification and efficient distributed execution of dynamic and irregular applications. Programming interfaces that support task-based execution often only support shared memory parallel environments; a few support distributed memory environments, either by discovering the entire DAG of tasks on all processes, or by introducing explicit communications. The first approach limits scalability, while the second increases the complexity of programming. We demonstrate how TTG can address these issues without sacrificing scalability or programmability by providing higher-level abstractions than conventionally provided by task-centric programming systems, without impeding the ability of these runtimes to manage task creation and execution as well as data and resource management efficiently. TTG supports distributed memory execution over 2 different task runtimes, PaRSEC and MADNESS. Performance of four paradigmatic applications (in graph analytics, dense and block-sparse linear algebra, and numerical integrodifferential calculus) with various degrees of irregularity implemented in TTG is illustrated on large distributed-memory platforms and compared to the state-of-the-art implementations.

Asynchronous programming models (APM) are gaining more and more traction, allowing applications to expose the available concurrency to a runtime system tasked with coordinating the execution. While MPI has long provided support for multi-threaded communication and non-blocking operations, it falls short of adequately supporting APMs as correctly and efficiently handling MPI communication in different models is still a challenge. Meanwhile, new low-level implementations of light-weight, cooperatively scheduled execution contexts (fibers, aka user-level threads (ULT)) are meant to serve as a basis for higher-level APMs and their integration in MPI implementations has been proposed as a replacement for traditional POSIX thread support to alleviate these challenges.

In both the embedded systems and High Performance Computing domains, energy-efficiency has become one of the main design criteria. Efficiently utilizing the resources provided in computing systems ranging from embedded systems to current petascale and future Exascale HPC systems will be a challenging task. Suboptimal designs can potentially cause large amounts of underutilized resources and wasted energy. In both domains, a promising potential for improving efficiency of scalable applications stems from the significant degree of dynamic behaviour, e.g., runtime alternation in application resource requirements and workloads. Manually detecting and leveraging this dynamism to improve performance and energy-efficiency is a tedious task that is commonly neglected by developers. However, using an automatic optimization approach, application dynamism can be analysed at design time and used to optimize system configurations at runtime. The European Union Horizon 2020 READEX (Runtime Exploitation of Application Dynamism for Energy-efficient eX-ascale computing) project will develop a tools-aided auto-tuning methodology inspired by the system scenario methodology used in embedded systems. Dynamic behaviour of HPC applications will be exploited to achieve improved energy-efficiency and performance. Driven by a consortium of European experts from academia, HPC resource providers, and industry, the READEX project aims at developing the first of its kind generic framework to split design time and runtime automatic tuning while targeting heterogeneous system at the Exascale level. This paper describes plans for the project as well as early results achieved during its first year. Furthermore, it is shown how project results will be brought back into the embedded systems domain.

We present a particle-in-cell simulation of the relativistic Kelvin-Helmholtz Instability (KHI) that for the first time delivers angularly resolved radiation spectra of the particle dynamics during the formation of the KHI. This enables studying the formation of the KHI with unprecedented spatial, angular and spectral resolution. Our results are of great importance for understanding astrophysical jet formation and comparable plasma phenomena by relating the particle motion observed in the KHI to its radiation signature.

Event tracing is an important tool for understanding the performance of parallel applications. As concurrency increases in leadership-class computing systems, the quantity of performance log data can overload the parallel file system, perturbing the application being observed. In this work we present a solution for event tracing at leadership scales. We enhance the I/O forwarding system software to aggregate and reorganize log data prior to writing to the storage system, significantly reducing the burden on the underlying file system for this type of traffic. Furthermore, we augment the I/O forwarding system with a write buffering capability to limit the impact of artificial perturbations from log data accesses on traced applications. To validate the approach, we modify the Vampir tracing toolset to take advantage of this new capability and show that the approach increases the maximum traced application size by a factor of 5x to more than 200,000 processes.