Related papers: A Communication Avoiding and Reducing Algorithm fo…
The use of hybrid scheme combining the message passing programming models for inter-node parallelism and the shared memory programming models for node-level parallelism is widely spread. Existing extensive practices on hybrid Message…
Mass spectrometry (MS) based omics data analysis require significant time and resources. To date, few parallel algorithms have been proposed for deducing peptides from mass spectrometry-based data. However, these parallel algorithms were…
Modern compute nodes in high-performance computing provide a tremendous level of parallelism and processing power. However, as arithmetic performance has been observed to increase at a faster rate relative to memory and network bandwidths,…
Supercomputers getting ever larger and energy-efficient is at odds with the reliability of the used hardware. Thus, the time intervals between component failures are decreasing. Contrarily, the latencies for individual operations of…
We present and evaluate the ExaNeSt Prototype, a liquid-cooled rack prototype consisting of 256 Xilinx ZU9EG MPSoCs, 4 TBytes of DRAM, 16 TBytes of SSD, and configurable interconnection 10-Gbps hardware. We developed this testbed in…
We present scalable parallel algorithms with sublinear per-processor communication volume and low latency for several fundamental problems related to finding the most relevant elements in a set, for various notions of relevance: We begin…
With the ever-increasing computing power of supercomputers and the growing scale of scientific applications, the efficiency of MPI collective communications turns out to be a critical bottleneck in large-scale distributed and parallel…
We present our recent code modernizations of the of the ab initio molecular dynamics program CPMD (www.cpmd.org) with a special focus on the ultra-soft pseudopotential (USPP) code path. Following the internal instrumentation of CPMD, all…
Analytic, first-principles performance modeling of distributed-memory parallel codes is notoriously imprecise. Even for applications with extremely regular and homogeneous compute-communicate phases, simply adding communication time to…
The Simplex tableau has been broadly used and investigated in the industry and academia. With the advent of the big data era, ever larger problems are posed to be solved in ever larger machines whose architecture type did not exist in the…
In this paper, we address the problem of designing a distributed application meant to run both classical and asynchronous iterations. MPI libraries are very popular and widely used in the scientific community, however asynchronous iterative…
Parallel implementations of linear iterative solvers generally alternate between phases of data exchange and phases of local computation. Increasingly large problem sizes on more heterogeneous systems make load balancing and network layout…
In this work, we consider the integration of MPI one-sided communication and non-blocking I/O in HPC-centric MapReduce frameworks. Using a decoupled strategy, we aim to overlap the Map and Reduce phases of the algorithm by allowing…
We explore an approach due to Nievergelt of decomposing a time-evolution equation along the time dimension and solving it in parallel with as little communication as possible between the processors. This method computes a map from initial…
Communication and topology aware process mapping is a powerful approach to reduce communication time in parallel applications with known communication patterns on large, distributed memory systems. We address the problem as a quadratic…
Exact diagonalization is a well-established method for simulating small quantum systems. Its applicability is limited by the exponential growth of the so-called Hamiltonian matrix that needs to be diagonalized. Physical symmetries are…
On many parallel machines, the time LQCD applications spent in communication is a significant contribution to the total wall-clock time, especially in the strong-scaling limit. We present a novel high-performance communication library that…
Matrix factorizations are among the most important building blocks of scientific computing. State-of-the-art libraries, however, are not communication-optimal, underutilizing current parallel architectures. We present novel algorithms for…
In this work we present a robust interface coupling algorithm called Compact Interface quasi-Newton (CIQN). It is designed for computationally intensive applications using an MPI multi-code partitioned scheme. The algorithm allows to reuse…
Recent increased interest in Cloud computing emphasizes the need to find an adequate solution to the load-balancing problem in parallel computing -- efficiently running several jobs concurrently on a cluster of shared computers (nodes). One…