Energy consumption of parallel algorithms for solving linear systems on HPC architecture

Modern High-Performance Computing HPC systems are gradually increasing in size and complexity due to the correspondent demand of larger simulations requiring more complicated tasks and higher accuracy. However, as side effects of the Dennard’s scaling approaching its ultimate power limit, the efficiency of software plays also an important role in increasing the overall performance of a computation. Tools to measure application performance in these increasingly complex environments provide insights into the intricate ways in which software and hardware interact. The monitoring of the power consumption in order to save energy is possible through processors interfaces like Intel Running Average Power Limit RAPL. Given the low level of these interfaces, they are often paired with an application-level tool like Performance Application Programming Interface PAPI. Since several problems in many heterogeneous fields can be represented as a complex linear system, an optimized and scalable linear system solver algorithm can decrease significantly the time spent to compute its resolution. One of the most widely used algorithms deployed for the resolution of large simulation is the Gaussian Elimination, which has its most popular implementation for HPC systems in the Scalable Linear Algebra PACKage ScaLAPACK library. However, another relevant algorithm, which is increasing in popularity in the academic field, is the Inhibition Method. This thesis compares the energy consumption of the Inhibition Method and Gaussian Elimination from ScaLAPACK to profile their execution during the resolution of linear systems above the HPC architecture offered by CINECA. Moreover, it also collates the energy and power values for different ranks, nodes, and sockets configurations. The monitoring tools employed to track the energy consumption of these algorithms are PAPI and RAPL, that will be integrated with the parallel execution of the algorithms managed with the Message Passing Interface MPI.

Antibody-Antigen Interface Characterization with Contextualized Pre-trained Embeddings

Artificial Intelligence (AI) has substantially influenced numerous disciplines in recent years. Biology, chemistry, and bioinformatics are among them, with significant advances in protein structure prediction, paratope prediction, protein-protein interactions (PPIs), and antibody-antigen interactions. Understanding PPIs is critical since they are responsible for practically everything living and have several uses in vaccines, cancer, immunology, and inflammatory illnesses. Machine Learning (ML) offers enormous potential for effectively simulating antibody-antigen interactions and improving in-silico optimization of therapeutic antibodies for desired features, including binding activity, stability, and low immunogenicity. This research looks at the use of AI algorithms to better understand antibody-antigen interactions, and it further expands and explains several difficulties encountered in the field. Furthermore, we contribute by presenting a method that outperforms existing state-of-the-art strategies in paratope prediction from sequence data.