Deliverables
Final version of D6.2.
Lessons Learnt from the LIGATE ProjectLessons learnt from the LIGATE Project.
Initial Dissemination and Communication PlanTo 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 DatasetThis 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 ResultFinal validation of the different solution components and of the solution as a whole.
Initial Validation ResultInitial validation of the different solution components and of the solution as a whole
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 MediaCoordination 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 frameworkThis intermediate report describes the progress made on runtime system optimization, including autotuning, scheduling and data distribution improvements, as well as energy optimization.
Publications
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
Author(s):
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
Published in:
Computational and Structural Biotechnology Journal, Issue 23, 2024, Page(s) 2141-2151, ISSN 2001-0370
Publisher:
Elsevier
DOI:
10.1016/j.csbj.2024.05.024
Author(s):
Jakub Beránek, Ada Böhm, Gianluca Palermo, Jan Martinovič, Branislav Jansík
Published in:
SoftwareX, Issue 27, 2024, Page(s) 101814, ISSN 2352-7110
Publisher:
Elsevier BV
DOI:
10.1016/j.softx.2024.101814
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
Author(s):
Davide Gadioli, Gianmarco Accordi, Jan Krenek, Martin Golasowski, Ladislav Foltyn, Jan Martinovic, Andrea R. Beccari, Gianluca Palermo
Published in:
Procedia Computer Science, Issue 240, 2024, Page(s) 42-51, ISSN 1877-0509
Publisher:
Elsevier
DOI:
10.1016/j.procs.2024.07.007
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
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
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
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
DOI:
10.5281/zenodo.7298549
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