Performance models for message passing architectures

1993 ◽  
Vol 140 (1) ◽  
pp. 19
Author(s):  
S. Gudvangen ◽  
A.G.J. Holt
2011 ◽  
pp. 1116-1116
Author(s):  
David Padua ◽  
Amol Ghoting ◽  
John A. Gunnels ◽  
Mark S. Squillante ◽  
José Meseguer ◽  
...  

2014 ◽  
Vol 22 (2) ◽  
pp. 75-91 ◽  
Author(s):  
Robert Gerstenberger ◽  
Maciej Besta ◽  
Torsten Hoefler

Modern interconnects offer remote direct memory access (RDMA) features. Yet, most applications rely on explicit message passing for communications albeit their unwanted overheads. The MPI-3.0 standard defines a programming interface for exploiting RDMA networks directly, however, it's scalability and practicability has to be demonstrated in practice. In this work, we develop scalable bufferless protocols that implement the MPI-3.0 specification. Our protocols support scaling to millions of cores with negligible memory consumption while providing highest performance and minimal overheads. To arm programmers, we provide a spectrum of performance models for all critical functions and demonstrate the usability of our library and models with several application studies with up to half a million processes. We show that our design is comparable to, or better than UPC and Fortran Coarrays in terms of latency, bandwidth and message rate. We also demonstrate application performance improvements with comparable programming complexity.


2000 ◽  
Vol 147 (3) ◽  
pp. 61 ◽  
Author(s):  
V. Cortellessa ◽  
G. Iazeolla ◽  
R. Mirandola

2020 ◽  
Author(s):  
Ali Raza ◽  
Arni Sturluson ◽  
Cory Simon ◽  
Xiaoli Fern

Virtual screenings can accelerate and reduce the cost of discovering metal-organic frameworks (MOFs) for their applications in gas storage, separation, and sensing. In molecular simulations of gas adsorption/diffusion in MOFs, the adsorbate-MOF electrostatic interaction is typically modeled by placing partial point charges on the atoms of the MOF. For the virtual screening of large libraries of MOFs, it is critical to develop computationally inexpensive methods to assign atomic partial charges to MOFs that accurately reproduce the electrostatic potential in their pores. Herein, we design and train a message passing neural network (MPNN) to predict the atomic partial charges on MOFs under a charge neutral constraint. A set of ca. 2,250 MOFs labeled with high-fidelity partial charges, derived from periodic electronic structure calculations, serves as training examples. In an end-to-end manner, from charge-labeled crystal graphs representing MOFs, our MPNN machine-learns features of the local bonding environments of the atoms and learns to predict partial atomic charges from these features. Our trained MPNN assigns high-fidelity partial point charges to MOFs with orders of magnitude lower computational cost than electronic structure calculations. To enhance the accuracy of virtual screenings of large libraries of MOFs for their adsorption-based applications, we make our trained MPNN model and MPNN-charge-assigned computation-ready, experimental MOF structures publicly available.<br>


Author(s):  
Michael Withnall ◽  
Edvard Lindelöf ◽  
Ola Engkvist ◽  
Hongming Chen

We introduce Attention and Edge Memory schemes to the existing Message Passing Neural Network framework for graph convolution, and benchmark our approaches against eight different physical-chemical and bioactivity datasets from the literature. We remove the need to introduce <i>a priori</i> knowledge of the task and chemical descriptor calculation by using only fundamental graph-derived properties. Our results consistently perform on-par with other state-of-the-art machine learning approaches, and set a new standard on sparse multi-task virtual screening targets. We also investigate model performance as a function of dataset preprocessing, and make some suggestions regarding hyperparameter selection.


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