LIgand Generator and portable drug discovery platform AT Exascale

Rezultaty

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.

Publikacje

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

Autorzy: Kaijie Fan, Marco D'Antonio, Lorenzo Carpentieri, Biagio Cosenza, Federico Ficarelli, and Daniele Cesarini
Opublikowane w: Proceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis (SC '23), Numer 69, 2023, Strona(/y) 1–13
Wydawca: Association for Computing Machinery
DOI: 10.1145/3581784.3607055

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

Autorzy: 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
Opublikowane w: Proceedings of the 20th ACM International Conference on Computing Frontiers (CF '23), 2023, Strona(/y) 272–278
Wydawca: Association for Computing Machinery
DOI: 10.1145/3587135.3592172

On the Compilation Performance of Current SYCL Implementations

Autorzy: Thoman, Peter and Molina Heredia, Facundo and Fahringer, Thomas
Opublikowane w: IWOCL 22: International Workshop on OpenCL, 2022
Wydawca: ACM
DOI: 10.1145/3529538.3529548

HEAppE Middleware: From Desktop to HPC

Autorzy: Jakub Konvička, Václav Svatoň, Jan Křenek
Opublikowane w: Proceedings of Euro-Par 2023: Parallel Processing Workshops. Lecture Notes in Computer Science, Numer 14352, 2024, Strona(/y) 252–255, ISBN 978-3-031-48802-3
Wydawca: Springer
DOI: 10.1007/978-3-031-48803-0_27

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

Autorzy: Luigi Crisci, Lorenzo Carpentieri, Peter Thoman, Aksel Alpay, Vincent Heuveline, Biagio Cosenza
Opublikowane w: Proceedings of the 12th International Workshop on OpenCL and SYCL (IWOCL '24), Numer 1, 2024, Strona(/y) 1–12
Wydawca: Association for Computing Machinery
DOI: 10.1145/3648115.3648120

MALIBOO: When Machine Learning meets Bayesian Optimization

Autorzy: Bruno Guindani, Danilo Ardagna, Alessandra Guglielmi
Opublikowane w: Proceedings of IEEE 7th International Conference on Smart Cloud (SmartCloud), 2022, Strona(/y) 1-9, ISBN 978-1-6654-5180-2
Wydawca: IEEE
DOI: 10.1109/smartcloud55982.2022.00008

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

Autorzy: Majid Salimi Beni, Biagio Cosenza
Opublikowane w: Proceedings of Benchmarking, Measuring, and Optimizing: 14th BenchCouncil International Symposium, Bench 2022, 2023, Strona(/y) 123–142
Wydawca: Springer-Verlag
DOI: 10.1007/978-3-031-31180-2_8

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

Autorzy: Kaijie Fan, Biagio Cosenza, Ben H. H. Juurlink
Opublikowane w: ACM International Conference on Computing Frontiers, 2022
Wydawca: ACM
DOI: 10.1145/3528416.3530241

Towards a Portable Drug Discovery Pipeline with SYCL 2020

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

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

Autorzy: Peter Thoman, Fabian Knorr, Luigi Crisci
Opublikowane w: Proceedings of the 12th International Workshop on OpenCL and SYCL (IWOCL '24), Numer 3, 2024, Strona(/y) 1–12
Wydawca: Association for Computing Machinery
DOI: 10.1145/3648115.3648136

Domain-Specific Energy Modeling for Drug Discovery and Magnetohydrodynamics Applications

Autorzy: 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
Opublikowane w: Proceedings of SC-W '23 - International Workshop on the Environmental Sustainability of High-Performance Software, 2023, Strona(/y) 1790–1800
Wydawca: ACM
DOI: 10.1145/3624062.3624261

An Asynchronous Dataflow-Driven Execution Model For Distributed Accelerator Computing

Autorzy: Philip Salzmann, Fabian Knorr, Peter Thoman, Philipp Gschwandtner, Biagio Cosenza, Thomas Fahringer
Opublikowane w: Proceedings of 2023 IEEE/ACM 23rd International Symposium on Cluster, Cloud and Internet Computing (CCGrid), 2023, Strona(/y) 82-93, ISBN 979-8-3503-0120-5
Wydawca: IEEE
DOI: 10.1109/ccgrid57682.2023.00018

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

Autorzy: Fabian Knorr, Peter Thoman, Thomas Fahringer
Opublikowane w: SC '21: Proceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis, 2021
Wydawca: ACM
DOI: 10.1145/3458817.3476224

An extreme-scale virtual screening platform for drug discovery

Autorzy: 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
Opublikowane w: ACM International Conference on Computing Frontiers, 2022
Wydawca: ACM
DOI: 10.1145/3528416.3530872

EMPI: Enhanced Message Passing Interface in Modern C++

Autorzy: Majid Salimi Beni, Luigi Crisci, Biagio Cosenza
Opublikowane w: Proceedings of 2023 IEEE/ACM 23rd International Symposium on Cluster, Cloud and Internet Computing (CCGrid), 2023, Strona(/y) 141-153
Wydawca: IEEE
DOI: 10.1109/ccgrid57682.2023.00023

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

Autorzy: Gianmarco Accordi, Davide Gadioli, Gianluca Palermo, Luigi Crisci, Lorenzo Carpentieri, Biagio Cosenza, Andrea R. Beccari
Opublikowane w: Proceedings of the 12th International Workshop on OpenCL and SYCL (IWOCL '24), Numer 9, 2024, Strona(/y) 1–4
Wydawca: Association for Computing Machinery
DOI: 10.1145/3648115.3648125

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

Autorzy: Stefano Markidis, Davide Gadioli, Emanuele Vitali, Gianluca Palermo
Opublikowane w: 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
Wydawca: IEEE Xplore
DOI: 10.1109/pdsw54622.2021.00007

Command Horizons: Coalescing Data Dependencies while Maintaining Asynchronicity

Autorzy: Peter Thoman, Philipp Salzmann
Opublikowane w: Asynchronous Many-Task Systems and Applications. WAMTA 2023. Lecture Notes in Computer Science, Numer 13861, 2023, Strona(/y) 13–26, ISBN 978-3-031-32315-7
Wydawca: Springer
DOI: 10.1007/978-3-031-32316-4_2

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

Autorzy: Philip Salzmann, Fabian Knorr, Peter Thoman, Biagio Cosenza
Opublikowane w: IWOCL 22: International Workshop on OpenCL, 2022
Wydawca: ACM
DOI: 10.1145/3529538.3530004

Automatic Discovery of Collective Communication Patterns in Parallelized Task Graphs

Autorzy: Fabian Knorr, Philip Salzmann, Peter Thoman, Thomas Fahringer
Opublikowane w: International Journal of Parallel Programming, 2024, ISSN 0885-7458
Wydawca: Kluwer Academic Publishers
DOI: 10.1007/s10766-024-00767-y

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

Autorzy: Knorr Fabian, Thoman Peter, Fahringer Thomas
Opublikowane w: International Journal of Parallel Programming, Numer 51, 2023, Strona(/y) 150–171, ISSN 0885-7458
Wydawca: Kluwer Academic Publishers
DOI: 10.1007/s10766-022-00743-4

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

Autorzy: Peter Thoman, Philip Salzmann
Opublikowane w: SN Computer Science, Numer 5, 2024, Strona(/y) 409, ISSN 2661-8907
Wydawca: Springer Nature
DOI: 10.1007/s42979-024-02749-w

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

Autorzy: Natarajan Arul Murugan, Artur Podobas, Davide Gadioli, Emanuele Vitali, Gianluca Palermo, Stefano Markidis
Opublikowane w: Pharmaceuticals, Numer 15(1):63, 2022, ISSN 1424-8247
Wydawca: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/ph15010063

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

Autorzy: Bruno Guindani, Danilo Ardagna, Alessandra Guglielmi, Roberto Rocco, Gianluca Palermo
Opublikowane w: IEEE Transactions on Cloud Computing, Numer 12(1), 2024, Strona(/y) 277-294, ISSN 2168-7161
Wydawca: 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

Autorzy: 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
Opublikowane w: Computational and Structural Biotechnology Journal, Numer 23, 2024, Strona(/y) 2141-2151, ISSN 2001-0370
Wydawca: Elsevier
DOI: 10.1016/j.csbj.2024.05.024

HyperQueue: Efficient and ergonomic task graphs on HPC clusters

Autorzy: Jakub Beránek, Ada Böhm, Gianluca Palermo, Jan Martinovič, Branislav Jansík
Opublikowane w: SoftwareX, Numer 27, 2024, Strona(/y) 101814, ISSN 2352-7110
Wydawca: Elsevier BV
DOI: 10.1016/j.softx.2024.101814

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

Autorzy: Gianmarco Accordi, Davide Gadioli, Emanele Vitali, Luigi Crisci, Biagio Cosenza, Andrea Beccari, Gianluca Palermo
Opublikowane w: Journal of Supercomputing, Numer 80, 2024, Strona(/y) 11798–11815, ISSN 0920-8542
Wydawca: Kluwer Academic Publishers
DOI: 10.1007/s11227-023-05884-y

A Portable Drug Discovery Platform for Urgent Computing

Autorzy: Davide Gadioli, Gianmarco Accordi, Jan Krenek, Martin Golasowski, Ladislav Foltyn, Jan Martinovic, Andrea R. Beccari, Gianluca Palermo
Opublikowane w: Procedia Computer Science, Numer 240, 2024, Strona(/y) 42-51, ISSN 1877-0509
Wydawca: Elsevier
DOI: 10.1016/j.procs.2024.07.007

Automated benchmarking of combined protein structure and ligand conformation prediction

Autorzy: Michèle Leemann, Ander Sagasta, Jerome Eberhardt, Torsten Schwede, Xavier Robin, Janani Durairaj
Opublikowane w: Proteins, Numer 91(12), 2023, Strona(/y) 1912-1924, ISSN 0887-3585
Wydawca: Wiley-Liss Inc
DOI: 10.1002/prot.26605

Enabling performance portability on the LiGen drug discovery pipeline

Autorzy: Luigi Crisci, Lorenzo Carpentieri, Biagio Cosenza, Gianmarco Accordi, Davide Gadioli, Emanuele Vitali, Gianluca Palermo, Andrea Rosario Beccari
Opublikowane w: Future Generation Computer Systems, Numer 158, 2024, Strona(/y) 44-59, ISSN 0167-739X
Wydawca: 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

Autorzy: Emanuele Vitali, Federico Ficarelli, Mauro Bisson, Davide Gadioli, Massimiliano Fatica, Andrea R. Beccari, Gianluca Palermo
Opublikowane w: Journal of Parallel and Distributed Computing, Numer 186, 2024, ISSN 0743-7315
Wydawca: Academic Press
DOI: 10.1016/j.jpdc.2023.104819

Poster: HyperQueue: Overcoming Limitations of HPC Job Managers

Autorzy: Stanislav Böhm, Jakub Beránek, Vojtěch Cima, Roman Macháček, Vyomkesh Jha, Alfréd Kočí, Branislav Jansík, Jan Martinovič
Opublikowane w: SC 21, The International Conference for High Performance Computing, Networking, Storage, and Analysis, 2021
Wydawca: 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

Autorzy: Jakub Konvička, Václav Svatoň, Jan Křenek
Opublikowane w: Euro-Par 2023: Parallel Processing Workshops, 2024
Wydawca: Springer
DOI: 10.5281/zenodo.11080405

Rezultaty

Publikacje

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