LIgand Generator and portable drug discovery platform AT Exascale

Resultado final

Final version of D6.2.

Lessons learnt from the LIGATE Project.

Initial Dissemination and Communication Plan

To define the strategy to disseminate and communicate the project results. The activity, led by CHELONIA in tight collaboration with DOMPE, will analyze the strategies and will implement the actions to optimize the dissemination and communication of the project results, beyond the project partners and time-frame.

Validated Platform on Known Dataset

This task is devoted to functionally validate the outcome of the CADD platform enhancement. This task includes the preparation of a dataset composed by known compounds derived from literature and publicly available databases. This dataset will be used as a test-case for the platform for the continuous validation and performance assessment of the platform. The task defines the baseline for the CADD platform validation process and assesses the improvement reached in terms of the selected metrics. A specific action will be carried out to: ● Definition of benchmark datasets for validation of ligand poses and binding affinity calculations; quality control of structures datasets (DOMPE, UNIBAS); ● Evaluation of the baseline of the CADD platform; ● Evaluation and definition of the novel baseline of the intermediate and final tool version (Alpha, Beta, Candidate, Release).

Solution Validation Result

Final validation of the different solution components and of the solution as a whole.

Initial Validation Result

Initial validation of the different solution components and of the solution as a whole

Final runtime and autotuning framework

The final runtime and autotuning report describes the state of the programming model and runtime system after the completion of the autotuning, heterogeneity and energy optimization tasks. It will summarize the framework features, the advancements made in the optimization tasks, and evaluate its performance.

Setup and Maintenance of LIGATE Website & Social Media

Coordination of dissemination (LIGATE webpage, workshops, conferences, articles, and book) and communication (use of social networks such as LinkedIN, Facebook, Twitter and YouTube) activities.

Intermediate runtime and autotuning framework

This intermediate report describes the progress made on runtime system optimization, including autotuning, scheduling and data distribution improvements, as well as energy optimization.

Publicaciones

SYnergy: Fine-grained Energy-Efficient Heterogeneous Computing for Scalable Energy Saving

Autores: Kaijie Fan, Marco D'Antonio, Lorenzo Carpentieri, Biagio Cosenza, Federico Ficarelli, and Daniele Cesarini
Publicado en: Proceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis (SC '23), Edición 69, 2023, Página(s) 1–13
Editor: Association for Computing Machinery
DOI: 10.1145/3581784.3607055

Tunable and Portable Extreme-Scale Drug Discovery Platform at Exascale: the LIGATE Approach

Autores: Gianluca Palermo, Gianmarco Accordi, Davide Gadioli, Emanuele Vitali, Cristina Silvano, Bruno Guindani, Danilo Ardagna, Andrea R. Beccari, Domenico Bonanni, Carmine Talarico, Filippo Lunghini, Jan Martinovic, Paulo Silva, Ada Bohm, Jakub Beranek, Jan Krenek, Branislav Jansik, Luigi Crisci, Biagio, Cosenza, Peter Thoman, Philip Salzmann, Thomas Fahringer, Leila Alexander, Gerardo Tauriello, Torsten
Publicado en: Proceedings of the 20th ACM International Conference on Computing Frontiers (CF '23), 2023, Página(s) 272–278
Editor: Association for Computing Machinery
DOI: 10.1145/3587135.3592172

On the Compilation Performance of Current SYCL Implementations

Autores: Thoman, Peter and Molina Heredia, Facundo and Fahringer, Thomas
Publicado en: IWOCL 22: International Workshop on OpenCL, 2022
Editor: ACM
DOI: 10.1145/3529538.3529548

HEAppE Middleware: From Desktop to HPC

Autores: Jakub Konvička, Václav Svatoň, Jan Křenek
Publicado en: Proceedings of Euro-Par 2023: Parallel Processing Workshops. Lecture Notes in Computer Science, Edición 14352, 2024, Página(s) 252–255, ISBN 978-3-031-48802-3
Editor: Springer
DOI: 10.1007/978-3-031-48803-0_27

SYCL-Bench 2020: Benchmarking SYCL 2020 on AMD, Intel, and NVIDIA GPUs

Autores: Luigi Crisci, Lorenzo Carpentieri, Peter Thoman, Aksel Alpay, Vincent Heuveline, Biagio Cosenza
Publicado en: Proceedings of the 12th International Workshop on OpenCL and SYCL (IWOCL '24), Edición 1, 2024, Página(s) 1–12
Editor: Association for Computing Machinery
DOI: 10.1145/3648115.3648120

MALIBOO: When Machine Learning meets Bayesian Optimization

Autores: Bruno Guindani, Danilo Ardagna, Alessandra Guglielmi
Publicado en: Proceedings of IEEE 7th International Conference on Smart Cloud (SmartCloud), 2022, Página(s) 1-9, ISBN 978-1-6654-5180-2
Editor: IEEE
DOI: 10.1109/smartcloud55982.2022.00008

An Analysis of Long-Tailed Network Latency Distribution and Background Traffic on Dragonfly+

Autores: Majid Salimi Beni, Biagio Cosenza
Publicado en: Proceedings of Benchmarking, Measuring, and Optimizing: 14th BenchCouncil International Symposium, Bench 2022, 2023, Página(s) 123–142
Editor: Springer-Verlag
DOI: 10.1007/978-3-031-31180-2_8

FLEXDP: flexible frequency scaling for energy-delay product optimization of GPU applications

Autores: Kaijie Fan, Biagio Cosenza, Ben H. H. Juurlink
Publicado en: ACM International Conference on Computing Frontiers, 2022
Editor: ACM
DOI: 10.1145/3528416.3530241

Towards a Portable Drug Discovery Pipeline with SYCL 2020

Autores: Luigi Crisci, Majid Salimi Beni, Biagio Cosenza, Nicolò Scipione, Davide Gadioli, Emanuele Vitali,Gianluca Palermo, Andrea Rosario Beccari
Publicado en: IWOCL 22: International Workshop on OpenCL, 2021
Editor: ACM
DOI: 10.1145/3529538.3529688

SimSYCL: A SYCL Implementation Targeting Development, Debugging, Simulation and Conformance

Autores: Peter Thoman, Fabian Knorr, Luigi Crisci
Publicado en: Proceedings of the 12th International Workshop on OpenCL and SYCL (IWOCL '24), Edición 3, 2024, Página(s) 1–12
Editor: Association for Computing Machinery
DOI: 10.1145/3648115.3648136

Domain-Specific Energy Modeling for Drug Discovery and Magnetohydrodynamics Applications

Autores: Lorenzo Carpentieri, Marco D'Antonio, Kaijie Fan, Luigi Crisci, Biagio Cosenza, Federico Ficarelli, Daniele Cesarini, Gianmarco Accordi, Davide Gadioli, Gianluca Palermo, Peter Thoman, Philip Salzmann, Philipp Gschwandtner, Markus Wippler, Filippo Marchetti, Daniele Gregori, Andrea Rosario Beccari
Publicado en: Proceedings of SC-W '23 - International Workshop on the Environmental Sustainability of High-Performance Software, 2023, Página(s) 1790–1800
Editor: ACM
DOI: 10.1145/3624062.3624261

An Asynchronous Dataflow-Driven Execution Model For Distributed Accelerator Computing

Autores: Philip Salzmann, Fabian Knorr, Peter Thoman, Philipp Gschwandtner, Biagio Cosenza, Thomas Fahringer
Publicado en: Proceedings of 2023 IEEE/ACM 23rd International Symposium on Cluster, Cloud and Internet Computing (CCGrid), 2023, Página(s) 82-93, ISBN 979-8-3503-0120-5
Editor: IEEE
DOI: 10.1109/ccgrid57682.2023.00018

ndzip-gpu: efficient lossless compression of scientific floating-point data on GPUs

Autores: Fabian Knorr, Peter Thoman, Thomas Fahringer
Publicado en: SC '21: Proceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis, 2021
Editor: ACM
DOI: 10.1145/3458817.3476224

An extreme-scale virtual screening platform for drug discovery

Autores: Gadioli, Davide and Vitali, Emanuele and Ficarelli, Federico and Latini, Chiara and Manelfi, Candida and Talarico, Carmine and Silvano, Cristina and Beccari, Andrea. R. and Palermo, Gianluca
Publicado en: ACM International Conference on Computing Frontiers, 2022
Editor: ACM
DOI: 10.1145/3528416.3530872

EMPI: Enhanced Message Passing Interface in Modern C++

Autores: Majid Salimi Beni, Luigi Crisci, Biagio Cosenza
Publicado en: Proceedings of 2023 IEEE/ACM 23rd International Symposium on Cluster, Cloud and Internet Computing (CCGrid), 2023, Página(s) 141-153
Editor: IEEE
DOI: 10.1109/ccgrid57682.2023.00023

Unlocking performance portability on LUMI-G supercomputer: A virtual screening case study

Autores: Gianmarco Accordi, Davide Gadioli, Gianluca Palermo, Luigi Crisci, Lorenzo Carpentieri, Biagio Cosenza, Andrea R. Beccari
Publicado en: Proceedings of the 12th International Workshop on OpenCL and SYCL (IWOCL '24), Edición 9, 2024, Página(s) 1–4
Editor: Association for Computing Machinery
DOI: 10.1145/3648115.3648125

Understanding the I/O Impact on the Performance of High-Throughput Molecular Docking

Autores: Stefano Markidis, Davide Gadioli, Emanuele Vitali, Gianluca Palermo
Publicado en: PDSW 2021 (SC21 Workshop) 6TH INTERNATIONAL PARALLEL DATA SYSTEMS WORKSHOP (HELD IN CONJUNCTION WITH SC21: THE INTERNATIONAL CONFERENCE FOR HIGH PERFORMANCE COMPUTING, NETWORKING, STORAGE AND ANALYSIS), 2021
Editor: IEEE Xplore
DOI: 10.1109/pdsw54622.2021.00007

Command Horizons: Coalescing Data Dependencies while Maintaining Asynchronicity

Autores: Peter Thoman, Philipp Salzmann
Publicado en: Asynchronous Many-Task Systems and Applications. WAMTA 2023. Lecture Notes in Computer Science, Edición 13861, 2023, Página(s) 13–26, ISBN 978-3-031-32315-7
Editor: Springer
DOI: 10.1007/978-3-031-32316-4_2

Celerity: How (Well) Does the SYCL API Translate to Distributed Clusters?

Autores: Philip Salzmann, Fabian Knorr, Peter Thoman, Biagio Cosenza
Publicado en: IWOCL 22: International Workshop on OpenCL, 2022
Editor: ACM
DOI: 10.1145/3529538.3530004

Automatic Discovery of Collective Communication Patterns in Parallelized Task Graphs

Autores: Fabian Knorr, Philip Salzmann, Peter Thoman, Thomas Fahringer
Publicado en: International Journal of Parallel Programming, 2024, ISSN 0885-7458
Editor: Kluwer Academic Publishers
DOI: 10.1007/s10766-024-00767-y

Declarative Data Flow in a Graph-Based Distributed Memory Runtime System

Autores: Knorr Fabian, Thoman Peter, Fahringer Thomas
Publicado en: International Journal of Parallel Programming, Edición 51, 2023, Página(s) 150–171, ISSN 0885-7458
Editor: Kluwer Academic Publishers
DOI: 10.1007/s10766-022-00743-4

Balancing Tracking Granularity and Parallelism in Many-Task Systems: The Horizons Approach

Autores: Peter Thoman, Philip Salzmann
Publicado en: SN Computer Science, Edición 5, 2024, Página(s) 409, ISSN 2661-8907
Editor: Springer Nature
DOI: 10.1007/s42979-024-02749-w

A Review on Parallel Virtual Screening Softwares for High-Performance Computers

Autores: Natarajan Arul Murugan, Artur Podobas, Davide Gadioli, Emanuele Vitali, Gianluca Palermo, Stefano Markidis
Publicado en: Pharmaceuticals, Edición 15(1):63, 2022, ISSN 1424-8247
Editor: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/ph15010063

Integrating Bayesian Optimization and Machine Learning for the Optimal Configuration of Cloud Systems

Autores: Bruno Guindani, Danilo Ardagna, Alessandra Guglielmi, Roberto Rocco, Gianluca Palermo
Publicado en: IEEE Transactions on Cloud Computing, Edición 12(1), 2024, Página(s) 277-294, ISSN 2168-7161
Editor: Institute of Electrical and Electronics Engineers Inc.
DOI: 10.1109/tcc.2024.3361070

Addressing docking pose selection with structure-based deep learning: Recent advances, challenges and opportunities

Autores: Serena Vittorio, Filippo Lunghini, Pietro Morerio, Davide Gadioli, Sergio Orlandini, Paulo Silva, null Jan Martinovic, Alessandro Pedretti, Domenico Bonanni, Alessio Del Bue, Gianluca Palermo, Giulio Vistoli, Andrea R. Beccari
Publicado en: Computational and Structural Biotechnology Journal, Edición 23, 2024, Página(s) 2141-2151, ISSN 2001-0370
Editor: Elsevier
DOI: 10.1016/j.csbj.2024.05.024

HyperQueue: Efficient and ergonomic task graphs on HPC clusters

Autores: Jakub Beránek, Ada Böhm, Gianluca Palermo, Jan Martinovič, Branislav Jansík
Publicado en: SoftwareX, Edición 27, 2024, Página(s) 101814, ISSN 2352-7110
Editor: Elsevier BV
DOI: 10.1016/j.softx.2024.101814

Out of kernel tuning and optimizations for portable large-scale docking experiments on GPUs

Autores: Gianmarco Accordi, Davide Gadioli, Emanele Vitali, Luigi Crisci, Biagio Cosenza, Andrea Beccari, Gianluca Palermo
Publicado en: Journal of Supercomputing, Edición 80, 2024, Página(s) 11798–11815, ISSN 0920-8542
Editor: Kluwer Academic Publishers
DOI: 10.1007/s11227-023-05884-y

A Portable Drug Discovery Platform for Urgent Computing

Autores: Davide Gadioli, Gianmarco Accordi, Jan Krenek, Martin Golasowski, Ladislav Foltyn, Jan Martinovic, Andrea R. Beccari, Gianluca Palermo
Publicado en: Procedia Computer Science, Edición 240, 2024, Página(s) 42-51, ISSN 1877-0509
Editor: Elsevier
DOI: 10.1016/j.procs.2024.07.007

Automated benchmarking of combined protein structure and ligand conformation prediction

Autores: Michèle Leemann, Ander Sagasta, Jerome Eberhardt, Torsten Schwede, Xavier Robin, Janani Durairaj
Publicado en: Proteins, Edición 91(12), 2023, Página(s) 1912-1924, ISSN 0887-3585
Editor: Wiley-Liss Inc
DOI: 10.1002/prot.26605

Enabling performance portability on the LiGen drug discovery pipeline

Autores: Luigi Crisci, Lorenzo Carpentieri, Biagio Cosenza, Gianmarco Accordi, Davide Gadioli, Emanuele Vitali, Gianluca Palermo, Andrea Rosario Beccari
Publicado en: Future Generation Computer Systems, Edición 158, 2024, Página(s) 44-59, ISSN 0167-739X
Editor: Elsevier BV
DOI: 10.1016/j.future.2024.03.045

GPU-optimized Approaches to Molecular Docking-based Virtual Screening in Drug Discovery: A Comparative Analysis

Autores: Emanuele Vitali, Federico Ficarelli, Mauro Bisson, Davide Gadioli, Massimiliano Fatica, Andrea R. Beccari, Gianluca Palermo
Publicado en: Journal of Parallel and Distributed Computing, Edición 186, 2024, ISSN 0743-7315
Editor: Academic Press
DOI: 10.1016/j.jpdc.2023.104819

Poster: HyperQueue: Overcoming Limitations of HPC Job Managers

Autores: Stanislav Böhm, Jakub Beránek, Vojtěch Cima, Roman Macháček, Vyomkesh Jha, Alfréd Kočí, Branislav Jansík, Jan Martinovič
Publicado en: SC 21, The International Conference for High Performance Computing, Networking, Storage, and Analysis, 2021
Editor: SC 21, The International Conference for High Performance Computing, Networking, Storage, and Analysis
DOI: 10.5281/zenodo.7298549

Poster: HEAppE Middleware: From Desktop to HPC

Autores: Jakub Konvička, Václav Svatoň, Jan Křenek
Publicado en: Euro-Par 2023: Parallel Processing Workshops, 2024
Editor: Springer
DOI: 10.5281/zenodo.11080405

Resultado final

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