LIgand Generator and portable drug discovery platform AT Exascale

Project Information

LIGATE

Grant agreement ID: 956137

DOI 10.3030/956137

Project closed

EC signature date 16 December 2020

Start date 1 January 2021

End date 30 April 2024

Funded under

• INDUSTRIAL LEADERSHIP - Leadership in enabling and industrial technologies - Information and Communication Technologies (ICT)

Total cost € 5 938 656,25

EU contribution € 2 612 060,85

Coordinated by

DOMPE FARMACEUTICI SPA
Italy

Deliverables

Other (1)

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.

Documents, reports (1)

Initial Validation Result

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

Publications

Conference proceedings (16)

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

Author(s): Kaijie Fan, Marco D'Antonio, Lorenzo Carpentieri, Biagio Cosenza, Federico Ficarelli, and Daniele Cesarini
Published in: Proceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis (SC '23), Issue 69, 2023, Page(s) 1–13
Publisher: Association for Computing Machinery
DOI: 10.1145/3581784.3607055

On the Compilation Performance of Current SYCL Implementations

Author(s): Thoman, Peter and Molina Heredia, Facundo and Fahringer, Thomas
Published in: IWOCL 22: International Workshop on OpenCL, 2022
Publisher: ACM
DOI: 10.1145/3529538.3529548

HEAppE Middleware: From Desktop to HPC

Author(s): Jakub Konvička, Václav Svatoň, Jan Křenek
Published in: Proceedings of Euro-Par 2023: Parallel Processing Workshops. Lecture Notes in Computer Science, Issue 14352, 2024, Page(s) 252–255, ISBN 978-3-031-48802-3
Publisher: Springer
DOI: 10.1007/978-3-031-48803-0_27

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

Author(s): Luigi Crisci, Lorenzo Carpentieri, Peter Thoman, Aksel Alpay, Vincent Heuveline, Biagio Cosenza
Published in: Proceedings of the 12th International Workshop on OpenCL and SYCL (IWOCL '24), Issue 1, 2024, Page(s) 1–12
Publisher: Association for Computing Machinery
DOI: 10.1145/3648115.3648120

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

Author(s): Kaijie Fan, Biagio Cosenza, Ben H. H. Juurlink
Published in: ACM International Conference on Computing Frontiers, 2022
Publisher: ACM
DOI: 10.1145/3528416.3530241

Towards a Portable Drug Discovery Pipeline with SYCL 2020

Author(s): Luigi Crisci, Majid Salimi Beni, Biagio Cosenza, Nicolò Scipione, Davide Gadioli, Emanuele Vitali,Gianluca Palermo, Andrea Rosario Beccari
Published in: IWOCL 22: International Workshop on OpenCL, 2021
Publisher: ACM
DOI: 10.1145/3529538.3529688

HyperQueue: Overcoming Limitations of HPC Job Managers

Author(s): Stanislav Böhm, Jakub Beránek, Vojtěch Cima, Roman Macháček, Vyomkesh Jha, Alfréd Kočí, Branislav Jansík, Jan Martinovič
Published in: SC 21, The International Conference for High Performance Computing, Networking, Storage, and Analysis, 2021
Publisher: SC 21, The International Conference for High Performance Computing, Networking, Storage, and Analysis

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

Author(s): Peter Thoman, Fabian Knorr, Luigi Crisci
Published in: Proceedings of the 12th International Workshop on OpenCL and SYCL (IWOCL '24), Issue 3, 2024, Page(s) 1–12
Publisher: Association for Computing Machinery
DOI: 10.1145/3648115.3648136

Command Horizons: Coalescing Data Dependencies while Maintaining Asynchronicity

Author(s): Thoman, Peter; Salzmann, Philipp
Published in: Asynchronous Many-Task Systems and Applications. WAMTA 2023. Lecture Notes in Computer Science, Issue 13861, 2023, Page(s) 13–26, ISBN 978-3-031-32315-7
Publisher: Springer
DOI: 10.1007/978-3-031-32316-4_2

HEAppE Middleware: From Desktop to HPC

Author(s): Konvička, Jakub; Svatoň, Václav; Krenek, Jan
Published in: Euro-Par 2023: Parallel Processing Workshops. Euro-Par 2023. Lecture Notes in Computer Science, Issue 14352, 2024, Page(s) 252–255, ISBN 978-3-031-48802-3
Publisher: Springer
DOI: 10.1007/978-3-031-48803-0_27

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

Author(s): Fabian Knorr, Peter Thoman, Thomas Fahringer
Published in: SC '21: Proceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis, 2021
Publisher: ACM
DOI: 10.1145/3458817.3476224

An extreme-scale virtual screening platform for drug discovery

Author(s): 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
Published in: ACM International Conference on Computing Frontiers, 2022
Publisher: ACM
DOI: 10.1145/3528416.3530872

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

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

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

Author(s): Stefano Markidis, Davide Gadioli, Emanuele Vitali, Gianluca Palermo
Published in: 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
Publisher: IEEE Xplore
DOI: 10.1109/pdsw54622.2021.00007

Command Horizons: Coalescing Data Dependencies while Maintaining Asynchronicity

Author(s): Peter Thoman, Philipp Salzmann
Published in: Asynchronous Many-Task Systems and Applications. WAMTA 2023. Lecture Notes in Computer Science, Issue 13861, 2023, Page(s) 13–26, ISBN 978-3-031-32315-7
Publisher: Springer
DOI: 10.1007/978-3-031-32316-4_2

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

Author(s): Philip Salzmann, Fabian Knorr, Peter Thoman, Biagio Cosenza
Published in: IWOCL 22: International Workshop on OpenCL, 2022
Publisher: ACM
DOI: 10.1145/3529538.3530004

Peer reviewed articles (10)

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

Author(s): Knorr Fabian, Thoman Peter, Fahringer Thomas
Published in: International Journal of Parallel Programming, Issue 51, 2023, Page(s) 150–171, ISSN 0885-7458
Publisher: Kluwer Academic Publishers
DOI: 10.1007/s10766-022-00743-4

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

Author(s): Peter Thoman, Philip Salzmann
Published in: SN Computer Science, Issue 5, 2024, Page(s) 409, ISSN 2661-8907
Publisher: Springer Nature
DOI: 10.1007/s42979-024-02749-w

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

Author(s): Knorr, Fabian; Thoman, Peter; Fahringer, Thomas
Published in: International Journal of Parallel Programming, Issue 51, 2023, Page(s) 150–171, ISSN 0885-7458
Publisher: Kluwer Academic Publishers
DOI: 10.1007/s10766-022-00743-4

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

Author(s): Natarajan Arul Murugan, Artur Podobas, Davide Gadioli, Emanuele Vitali, Gianluca Palermo, Stefano Markidis
Published in: Pharmaceuticals, Issue 15(1):63, 2022, ISSN 1424-8247
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/ph15010063

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

Author(s): Bruno Guindani, Danilo Ardagna, Alessandra Guglielmi, Roberto Rocco, Gianluca Palermo
Published in: IEEE Transactions on Cloud Computing, Issue 12(1), 2024, Page(s) 277-294, ISSN 2168-7161
Publisher: Institute of Electrical and Electronics Engineers Inc.
DOI: 10.1109/tcc.2024.3361070

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

Author(s): Bruno Guindani; Danilo Ardagna; Alessandra Guglielmi; Roberto Rocco; Gianluca Palermo
Published in: IEEE Transactions on Cloud Computing, Issue 12(1), 2024, Page(s) 277 - 294, ISSN 2168-7161
Publisher: Institute of Electrical and Electronics Engineers Inc.
DOI: 10.1109/tcc.2024.3361070

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

Author(s): Gianmarco Accordi, Davide Gadioli, Emanele Vitali, Luigi Crisci, Biagio Cosenza, Andrea Beccari, Gianluca Palermo
Published in: Journal of Supercomputing, Issue 80, 2024, Page(s) 11798–11815, ISSN 0920-8542
Publisher: Kluwer Academic Publishers
DOI: 10.1007/s11227-023-05884-y

Automated benchmarking of combined protein structure and ligand conformation prediction

Author(s): Michèle Leemann, Ander Sagasta, Jerome Eberhardt, Torsten Schwede, Xavier Robin, Janani Durairaj
Published in: Proteins, Issue 91(12), 2023, Page(s) 1912-1924, ISSN 0887-3585
Publisher: Wiley-Liss Inc
DOI: 10.1002/prot.26605

Enabling performance portability on the LiGen drug discovery pipeline

Author(s): Luigi Crisci, Lorenzo Carpentieri, Biagio Cosenza, Gianmarco Accordi, Davide Gadioli, Emanuele Vitali, Gianluca Palermo, Andrea Rosario Beccari
Published in: Future Generation Computer Systems, Issue 158, 2024, Page(s) 44-59, ISSN 0167-739X
Publisher: 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

Author(s): Emanuele Vitali, Federico Ficarelli, Mauro Bisson, Davide Gadioli, Massimiliano Fatica, Andrea R. Beccari, Gianluca Palermo
Published in: Journal of Parallel and Distributed Computing, Issue 186, 2024, ISSN 0743-7315
Publisher: Academic Press
DOI: 10.1016/j.jpdc.2023.104819