5 citations · 9 across the 12 of their papers we have counts for
13 papers
Towards High-Performance and Portable Molecular Docking on CPUs through Vectorization
Gianmarco Accordi, Jens Domke, Theresa Pollinger +2
Recent trends in the HPC field have introduced new CPU architectures with improved vectorization capabilities that require optimization to achieve peak performance and thus pose ch…
Efficient Parameter Tuning for a Structure-Based Virtual Screening HPC Application
Bruno Guindani, Davide Gadioli, Roberto Rocco +2
Virtual screening applications are highly parameterized to optimize the balance between quality and execution performance. While output quality is critical, the entire screening pr…
ZSMILES: an approach for efficient SMILES storage for random access in Virtual Screening
Gianmarco Accordi, Davide Gadioli, Giorgio Seguini +2
Virtual screening is a technique used in drug discovery to select the most promising molecules to test in a lab. To perform virtual screening, we need a large set of molecules as i…
Improving computation efficiency using input and architecture features for a virtual screening application
Gianmarco Accordi, Emanuele Vitali, Davide Gadioli +6
Virtual screening is an early stage of the drug discovery process that selects the most promising candidates. In the urgent computing scenario it is critical to find a solution in…
GPU-optimized Approaches to Molecular Docking-based Virtual Screening in Drug Discovery: A Comparative Analysis
Emanuele Vitali, Federico Ficarelli, Mauro Bisson +4
COVID-19 has shown the importance of having a fast response against pandemics. Finding a novel drug is a very long and complex procedure, and it is possible to accelerate the preli…
A Review on Parallel Virtual Screening Softwares for High Performance Computers
Natarajan Arul Murugan, Artur Podobas, Davide Gadioli +3
Drug discovery is the most expensive, time demanding and challenging project in biopharmaceutical companies which aims at the identification and optimization of lead compounds from…
EXSCALATE: An extreme-scale in-silico virtual screening platform to evaluate 1 trillion compounds in 60 hours on 81 PFLOPS supercomputers
Davide Gadioli, Emanuele Vitali, Federico Ficarelli +7
The social and economic impact of the COVID-19 pandemic demands the reduction of the time required to find a therapeutic cure. In the contest of urgent computing, we re-designed th…
Legio: Fault Resiliency for Embarrassingly Parallel MPI Applications
Roberto Rocco, Davide Gadioli, Gianluca Palermo
Due to the increasing size of HPC machines, the fault presence is becoming an eventuality that applications must face. Natively, MPI provides no support for the execution past the…
Tunable Approximations to Control Time-to-Solution in an HPC Molecular Docking Mini-App
Davide Gadioli, Gianluca Palermo, Stefano Cherubin +7
The drug discovery process involves several tasks to be performed in vivo, in vitro and in silico. Molecular docking is a task typically performed in silico. It aims at finding the…
Exploiting OpenMP & OpenACC to Accelerate a Molecular Docking Mini-App in Heterogeneous HPC Nodes
Emanuele Vitali, Davide Gadioli, Gianluca Palermo +3
In drug discovery, molecular docking is the task in charge of estimating the position of a molecule when interacting with the docking site. This task is usually used to perform scr…
On-line Application Autotuning Exploiting Ensemble Models
Tomas Martinovic, Davide Gadioli, Gianluca Palermo +1
Application autotuning is a promising path investigated in literature to improve computation efficiency. In this context, the end-users define high-level requirements and an autono…
An Efficient Monte Carlo-based Probabilistic Time-Dependent Routing Calculation Targeting a Server-Side Car Navigation System
Emanuele Vitali, Davide Gadioli, Gianluca Palermo +7
Incorporating speed probability distribution to the computation of the route planning in car navigation systems guarantees more accurate and precise responses. In this paper, we pr…
The ANTAREX Domain Specific Language for High Performance Computing
Cristina Silvano, Giovanni Agosta, Andrea Bartolini +19
The ANTAREX project relies on a Domain Specific Language (DSL) based on Aspect Oriented Programming (AOP) concepts to allow applications to enforce extra functional properties such…