Parallel Computing [alpha]

Barbara Cantalupo

Barbara Canatalupo

Research Engineer
Computer Science Department, University of Turin
Parallel Computing group
Via Pessinetto 12, 10149 Torino – Italy 
E-mail: barbara.cantalupo AT unito.it

Short Bio

Barbara Cantalupo is a Research Engineer at the Computer Science Department of the University of Torino. She received her master’s degree in Computer Science from the University of Pisa (1994), and she has been a researcher in the parallel computing field at University and at the Italian National Research Council (CNR). Afterwards, she has worked for 15 years in several private companies in the area of supercomputing, mobile networks and space, acquiring knowledge on different application fields.

Fields of interest:

  • Workflows, cloud and containers for HPC.

Working on the following European Research project:

Publications

2022

  • I. Colonnelli, B. Casella, G. Mittone, Y. Arfat, B. Cantalupo, R. Esposito, A. R. Martinelli, D. Medić, and M. Aldinucci, “Federated learning meets HPC and cloud,” in Astrophysics and space science proceedings, Catania, Italy, 2022.
    [BibTeX] [Abstract] [Download PDF]

    HPC and AI are fated to meet for several reasons. This article will discuss some of them and argue why this will happen through the set of methods and technologies that underpin cloud computing. As a paradigmatic example, we present a new federated learning system that collaboratively trains a deep learning model in different supercomputing centers. The system is based on the StreamFlow workflow manager designed for hybrid cloud-HPC infrastructures.

    @inproceedings{22:ml4astro,
abstract = {HPC and AI are fated to meet for several reasons. This article will discuss some of them and argue why this will happen through the set of methods and technologies that underpin cloud computing. As a paradigmatic example, we present a new federated learning system that collaboratively trains a deep learning model in different supercomputing centers. The system is based on the StreamFlow workflow manager designed for hybrid cloud-HPC infrastructures.},
address = {Catania, Italy},
author = {Iacopo Colonnelli and Bruno Casella and Gianluca Mittone and Yasir Arfat and Barbara Cantalupo and Roberto Esposito and Alberto Riccardo Martinelli and Doriana Medi\'{c} and Marco Aldinucci},
booktitle = {Astrophysics and Space Science Proceedings},
keywords = {across, eupilot, streamflow},
publisher = {Springer},
title = {Federated Learning meets {HPC} and cloud},
url = {https://iris.unito.it/retrieve/5631da1c-96a0-48c0-a48e-2cdf6b84841d/main.pdf},
year = {2022}
}

  • G. Agosta, M. Aldinucci, C. Alvarez, R. Ammendola, Y. Arfat, O. Beaumont, M. Bernaschi, A. Biagioni, T. Boccali, B. Bramas, C. Brandolese, B. Cantalupo, M. Carrozzo, D. Cattaneo, A. Celestini, M. Celino, I. Colonnelli, P. Cretaro, P. D’Ambra, M. Danelutto, R. Esposito, L. Eyraud-Dubois, A. Filgueras, W. Fornaciari, O. Frezza, A. Galimberti, F. Giacomini, B. Goglin, D. Gregori, A. Guermouche, F. Iannone, M. Kulczewski, F. Lo Cicero, A. Lonardo, A. R. Martinelli, M. Martinelli, X. Martorell, G. Massari, S. Montangero, G. Mittone, R. Namyst, A. Oleksiak, P. Palazzari, P. S. Paolucci, F. Reghenzani, C. Rossi, S. Saponara, F. Simula, F. Terraneo, S. Thibault, M. Torquati, M. Turisini, P. Vicini, M. Vidal, D. Zoni, and G. Zummo, “Towards extreme scale technologies and accelerators for eurohpc hw/sw supercomputing applications for exascale: the textarossa approach,” Microprocessors and microsystems, vol. 95, p. 104679, 2022. doi:10.1016/j.micpro.2022.104679
    [BibTeX] [Abstract]

    In the near future, Exascale systems will need to bridge three technology gaps to achieve high performance while remaining under tight power constraints: energy efficiency and thermal control; extreme computation efficiency via HW acceleration and new arithmetic; methods and tools for seamless integration of reconfigurable accelerators in heterogeneous HPC multi-node platforms. TEXTAROSSA addresses these gaps through a co-design approach to heterogeneous HPC solutions, supported by the integration and extension of HW and SW IPs, programming models, and tools derived from European research.

    @article{textarossa2022micpro:,
abstract = {In the near future, Exascale systems will need to bridge three technology gaps to achieve high performance while remaining under tight power constraints: energy efficiency and thermal control; extreme computation efficiency via HW acceleration and new arithmetic; methods and tools for seamless integration of reconfigurable accelerators in heterogeneous HPC multi-node platforms. TEXTAROSSA addresses these gaps through a co-design approach to heterogeneous HPC solutions, supported by the integration and extension of HW and SW IPs, programming models, and tools derived from European research.},
author = {Giovanni Agosta and Marco Aldinucci and Carlos Alvarez and Roberto Ammendola and Yasir Arfat and Olivier Beaumont and Massimo Bernaschi and Andrea Biagioni and Tommaso Boccali and Berenger Bramas and Carlo Brandolese and Barbara Cantalupo and Mauro Carrozzo and Daniele Cattaneo and Alessandro Celestini and Massimo Celino and Iacopo Colonnelli and Paolo Cretaro and Pasqua D'Ambra and Marco Danelutto and Roberto Esposito and Lionel Eyraud-Dubois and Antonio Filgueras and William Fornaciari and Ottorino Frezza and Andrea Galimberti and Francesco Giacomini and Brice Goglin and Daniele Gregori and Abdou Guermouche and Francesco Iannone and Michal Kulczewski and Francesca {Lo Cicero} and Alessandro Lonardo and Alberto R. Martinelli and Michele Martinelli and Xavier Martorell and Giuseppe Massari and Simone Montangero and Gianluca Mittone and Raymond Namyst and Ariel Oleksiak and Paolo Palazzari and Pier Stanislao Paolucci and Federico Reghenzani and Cristian Rossi and Sergio Saponara and Francesco Simula and Federico Terraneo and Samuel Thibault and Massimo Torquati and Matteo Turisini and Piero Vicini and Miquel Vidal and Davide Zoni and Giuseppe Zummo},
doi = {10.1016/j.micpro.2022.104679},
issn = {0141-9331},
journal = {Microprocessors and Microsystems},
keywords = {textrossa},
pages = {104679},
title = {Towards EXtreme scale technologies and accelerators for euROhpc hw/Sw supercomputing applications for exascale: The TEXTAROSSA approach},
volume = {95},
year = {2022},
bdsk-url-1 = {https://doi.org/10.1016/j.micpro.2022.104679}
}

  • E. Quiñones, J. Perales, J. Ejarque, A. Badouh, S. Marco, F. Auzanneau, F. Galea, D. González, J. R. Hervás, T. Silva, I. Colonnelli, B. Cantalupo, M. Aldinucci, E. Tartaglione, R. Tornero, J. Flich, J. M. Martinez, D. Rodriguez, I. Catalán, J. Garcia, and C. Hernández, “The DeepHealth HPC infrastructure: leveraging heterogenous HPC and cloud computing infrastructures for IA-based medical solutions,” in HPC, big data, and AI convergence towards exascale: challenge and vision, O. Terzo and J. Martinovič, Eds., Boca Raton, Florida: CRC press, 2022, p. 191–216. doi:10.1201/9781003176664
    [BibTeX] [Abstract] [Download PDF]

    This chapter presents the DeepHealth HPC toolkit for an efficient execution of deep learning (DL) medical application into HPC and cloud-computing infrastructures, featuring many-core, GPU, and FPGA acceleration devices. The toolkit offers to the European Computer Vision Library and the European Distributed Deep Learning Library (EDDL), developed in the DeepHealth project as well, the mechanisms to distribute and parallelize DL operations on HPC and cloud infrastructures in a fully transparent way. The toolkit implements workflow managers used to orchestrate HPC workloads for an efficient parallelization of EDDL training operations on HPC and cloud infrastructures, and includes the parallel programming models for an efficient execution EDDL inference and training operations on many-core, GPUs and FPGAs acceleration devices.

    @incollection{22:deephealth:HPCbook,
abstract = {This chapter presents the DeepHealth HPC toolkit for an efficient execution of deep learning (DL) medical application into HPC and cloud-computing infrastructures, featuring many-core, GPU, and FPGA acceleration devices. The toolkit offers to the European Computer Vision Library and the European Distributed Deep Learning Library (EDDL), developed in the DeepHealth project as well, the mechanisms to distribute and parallelize DL operations on HPC and cloud infrastructures in a fully transparent way. The toolkit implements workflow managers used to orchestrate HPC workloads for an efficient parallelization of EDDL training operations on HPC and cloud infrastructures, and includes the parallel programming models for an efficient execution EDDL inference and training operations on many-core, GPUs and FPGAs acceleration devices.},
address = {Boca Raton, Florida},
author = {Eduardo Qui\~{n}ones and Jesus Perales and Jorge Ejarque and Asaf Badouh and Santiago Marco and Fabrice Auzanneau and Fran\c{c}ois Galea and David Gonz\'{a}lez and Jos\'{e} Ram\'{o}n Herv\'{a}s and Tatiana Silva and Iacopo Colonnelli and Barbara Cantalupo and Marco Aldinucci and Enzo Tartaglione and Rafael Tornero and Jos\'{e} Flich and Jose Maria Martinez and David Rodriguez and Izan Catal\'{a}n and Jorge Garcia and Carles Hern\'{a}ndez},
booktitle = {{HPC}, Big Data, and {AI} Convergence Towards Exascale: Challenge and Vision},
chapter = {10},
doi = {10.1201/9781003176664},
editor = {Olivier Terzo and Jan Martinovi\v{c}},
isbn = {978-1-0320-0984-1},
keywords = {deephealth, streamflow},
pages = {191--216},
publisher = {{CRC} Press},
title = {The {DeepHealth} {HPC} Infrastructure: Leveraging Heterogenous {HPC} and Cloud Computing Infrastructures for {IA}-based Medical Solutions},
url = {https://iris.unito.it/retrieve/handle/2318/1832050/912413/Preprint.pdf},
year = {2022},
bdsk-url-1 = {https://iris.unito.it/retrieve/handle/2318/1832050/912413/Preprint.pdf},
bdsk-url-2 = {https://doi.org/10.1201/9781003176664}
}

  • D. Oniga, B. Cantalupo, E. Tartaglione, D. Perlo, M. Grangetto, M. Aldinucci, F. Bolelli, F. Pollastri, M. Cancilla, L. Canalini, C. Grana, C. M. Alcalde, F. A. Cardillo, and M. Florea, “Applications of AI and HPC in the health domain,” in HPC, big data, and AI convergence towards exascale: challenge and vision, O. Terzo and J. Martinovič, Eds., Boca Raton, Florida: CRC press, 2022, p. 217–239. doi:10.1201/9781003176664
    [BibTeX] [Abstract]

    This chapter presents the applications of artificial intelligence (AI) and high-computing performance (HPC) in the health domain, illustrated by the description of five of the use cases that are developed in the DeepHealth project. In the context of the European Commission supporting the use of AI and HPC in the health sector, DeepHealth Project is helping health experts process large quantities of images, putting at their disposal DeepLearning and computer vision techniques, combined in the DeepHealth toolkit and HPC infrastructures. The DeepHealth toolkit is tested and validated through 15 use cases, each of them representing a biomedical application. The most promising use cases are described in the chapter, which concludes with the value proposition and the benefits that DeepHealth toolkit offers to future end users.

    @incollection{22:applications:HPCbook,
abstract = {This chapter presents the applications of artificial intelligence (AI) and high-computing performance (HPC) in the health domain, illustrated by the description of five of the use cases that are developed in the DeepHealth project. In the context of the European Commission supporting the use of AI and HPC in the health sector, DeepHealth Project is helping health experts process large quantities of images, putting at their disposal DeepLearning and computer vision techniques, combined in the DeepHealth toolkit and HPC infrastructures. The DeepHealth toolkit is tested and validated through 15 use cases, each of them representing a biomedical application. The most promising use cases are described in the chapter, which concludes with the value proposition and the benefits that DeepHealth toolkit offers to future end users.},
address = {Boca Raton, Florida},
author = {Dana Oniga and Barbara Cantalupo and Enzo Tartaglione and Daniele Perlo and Marco Grangetto and Marco Aldinucci and Federico Bolelli and Federico Pollastri and Michele Cancilla and Laura Canalini and Costantino Grana and Cristina Mu{\~n}oz Alcalde and Franco Alberto Cardillo and Monica Florea},
booktitle = {{HPC}, Big Data, and {AI} Convergence Towards Exascale: Challenge and Vision},
chapter = {11},
doi = {10.1201/9781003176664},
editor = {Olivier Terzo and Jan Martinovi\v{c}},
isbn = {978-1-0320-0984-1},
keywords = {deephealth, streamflow},
pages = {217--239},
publisher = {{CRC} Press},
title = {Applications of {AI} and {HPC} in the Health Domain},
year = {2022},
bdsk-url-1 = {https://doi.org/10.1201/9781003176664}
}

  • I. Colonnelli, M. Aldinucci, B. Cantalupo, L. Padovani, S. Rabellino, C. Spampinato, R. Morelli, R. Di Carlo, N. Magini, and C. Cavazzoni, “Distributed workflows with Jupyter,” Future generation computer systems, vol. 128, pp. 282-298, 2022. doi:10.1016/j.future.2021.10.007
    [BibTeX] [Abstract] [Download PDF]

    The designers of a new coordination interface enacting complex workflows have to tackle a dichotomy: choosing a language-independent or language-dependent approach. Language-independent approaches decouple workflow models from the host code’s business logic and advocate portability. Language-dependent approaches foster flexibility and performance by adopting the same host language for business and coordination code. Jupyter Notebooks, with their capability to describe both imperative and declarative code in a unique format, allow taking the best of the two approaches, maintaining a clear separation between application and coordination layers but still providing a unified interface to both aspects. We advocate the Jupyter Notebooks’ potential to express complex distributed workflows, identifying the general requirements for a Jupyter-based Workflow Management System (WMS) and introducing a proof-of-concept portable implementation working on hybrid Cloud-HPC infrastructures. As a byproduct, we extended the vanilla IPython kernel with workflow-based parallel and distributed execution capabilities. The proposed Jupyter-workflow (Jw) system is evaluated on common scenarios for High Performance Computing (HPC) and Cloud, showing its potential in lowering the barriers between prototypical Notebooks and production-ready implementations.

    @article{21:FGCS:jupyflow,
abstract = {The designers of a new coordination interface enacting complex workflows have to tackle a dichotomy: choosing a language-independent or language-dependent approach. Language-independent approaches decouple workflow models from the host code's business logic and advocate portability. Language-dependent approaches foster flexibility and performance by adopting the same host language for business and coordination code. Jupyter Notebooks, with their capability to describe both imperative and declarative code in a unique format, allow taking the best of the two approaches, maintaining a clear separation between application and coordination layers but still providing a unified interface to both aspects. We advocate the Jupyter Notebooks' potential to express complex distributed workflows, identifying the general requirements for a Jupyter-based Workflow Management System (WMS) and introducing a proof-of-concept portable implementation working on hybrid Cloud-HPC infrastructures. As a byproduct, we extended the vanilla IPython kernel with workflow-based parallel and distributed execution capabilities. The proposed Jupyter-workflow (Jw) system is evaluated on common scenarios for High Performance Computing (HPC) and Cloud, showing its potential in lowering the barriers between prototypical Notebooks and production-ready implementations.},
author = {Iacopo Colonnelli and Marco Aldinucci and Barbara Cantalupo and Luca Padovani and Sergio Rabellino and Concetto Spampinato and Roberto Morelli and Rosario {Di Carlo} and Nicol{\`o} Magini and Carlo Cavazzoni},
doi = {10.1016/j.future.2021.10.007},
issn = {0167-739X},
journal = {Future Generation Computer Systems},
keywords = {streamflow, jupyter-workflow},
pages = {282-298},
title = {Distributed workflows with {Jupyter}},
url = {https://www.sciencedirect.com/science/article/pii/S0167739X21003976},
volume = {128},
year = {2022},
bdsk-url-1 = {https://www.sciencedirect.com/science/article/pii/S0167739X21003976},
bdsk-url-2 = {https://doi.org/10.1016/j.future.2021.10.007}
}

2021

  • G. Agosta, W. Fornaciari, A. Galimberti, G. Massari, F. Reghenzani, F. Terraneo, D. Zoni, C. Brandolese, M. Celino, F. Iannone, P. Palazzari, G. Zummo, M. Bernaschi, P. D’Ambra, S. Saponara, M. Danelutto, M. Torquati, M. Aldinucci, Y. Arfat, B. Cantalupo, I. Colonnelli, R. Esposito, A. R. Martinelli, G. Mittone, O. Beaumont, B. Bramas, L. Eyraud-Dubois, B. Goglin, A. Guermouche, R. Namyst, S. Thibault, A. Filgueras, M. Vidal, C. Alvarez, X. Martorell, A. Oleksiak, M. Kulczewski, A. Lonardo, P. Vicini, F. L. Cicero, F. Simula, A. Biagioni, P. Cretaro, O. Frezza, P. S. Paolucci, M. Turisini, F. Giacomini, T. Boccali, S. Montangero, and R. Ammendola, “TEXTAROSSA: towards extreme scale technologies and accelerators for eurohpc hw/sw supercomputing applications for exascale,” in Proc. of the 24th euromicro conference on digital system design (DSD), Palermo, Italy, 2021. doi:10.1109/DSD53832.2021.00051
    [BibTeX] [Abstract]

    To achieve high performance and high energy effi- ciency on near-future exascale computing systems, three key technology gaps needs to be bridged. These gaps include: en- ergy efficiency and thermal control; extreme computation effi- ciency via HW acceleration and new arithmetics; methods and tools for seamless integration of reconfigurable accelerators in heterogeneous HPC multi-node platforms. TEXTAROSSA aims at tackling this gap through a co-design approach to heterogeneous HPC solutions, supported by the integration and extension of HW and SW IPs, programming models and tools derived from European research.

    @inproceedings{21:DSD:textarossa,
abstract = {To achieve high performance and high energy effi- ciency on near-future exascale computing systems, three key technology gaps needs to be bridged. These gaps include: en- ergy efficiency and thermal control; extreme computation effi- ciency via HW acceleration and new arithmetics; methods and tools for seamless integration of reconfigurable accelerators in heterogeneous HPC multi-node platforms. TEXTAROSSA aims at tackling this gap through a co-design approach to heterogeneous HPC solutions, supported by the integration and extension of HW and SW IPs, programming models and tools derived from European research.},
address = {Palermo, Italy},
author = {Giovanni Agosta and William Fornaciari and Andrea Galimberti and Giuseppe Massari and Federico Reghenzani and Federico Terraneo and Davide Zoni and Carlo Brandolese and Massimo Celino and Francesco Iannone and Paolo Palazzari and Giuseppe Zummo and Massimo Bernaschi and Pasqua D'Ambra and Sergio Saponara and Marco Danelutto and Massimo Torquati and Marco Aldinucci and Yasir Arfat and Barbara Cantalupo and Iacopo Colonnelli and Roberto Esposito and Alberto Riccardo Martinelli and Gianluca Mittone and Olivier Beaumont and Berenger Bramas and Lionel Eyraud-Dubois and Brice Goglin and Abdou Guermouche and Raymond Namyst and Samuel Thibault and Antonio Filgueras and Miquel Vidal and Carlos Alvarez and Xavier Martorell and Ariel Oleksiak and Michal Kulczewski and Alessandro Lonardo and Piero Vicini and Francesco Lo Cicero and Francesco Simula and Andrea Biagioni and Paolo Cretaro and Ottorino Frezza and Pier Stanislao Paolucci and Matteo Turisini and Francesco Giacomini and Tommaso Boccali and Simone Montangero and Roberto Ammendola},
booktitle = {Proc. of the 24th Euromicro Conference on Digital System Design ({DSD})},
date-added = {2021-09-04 12:07:42 +0200},
date-modified = {2021-09-04 12:23:41 +0200},
doi = {10.1109/DSD53832.2021.00051},
keywords = {textarossa, streamflow},
month = aug,
publisher = {IEEE},
title = {{TEXTAROSSA}: Towards EXtreme scale Technologies and Accelerators for euROhpc hw/Sw Supercomputing Applications for exascale},
year = {2021},
bdsk-url-1 = {https://doi.org/10.1109/DSD53832.2021.00051}
}

  • M. Aldinucci, V. Cesare, I. Colonnelli, A. R. Martinelli, G. Mittone, and B. Cantalupo, “Practical parallelizazion of a Laplace solver with MPI,” in Enea cresco in the fight against covid-19, 2021, p. 21–24.
    [BibTeX] [Abstract]

    This work exposes a practical methodology for the semi-automatic parallelization of existing code. We show how a scientific sequential code can be parallelized through our approach. The obtained parallel code is only slightly different from the starting sequential one, providing an example of how little re-designing our methodology involves. The performance of the parallelized code, executed on the CRESCO6 cluster, is then exposed and discussed. We also believe in the educational value of this approach and suggest its use as a teaching device for students.

    @inproceedings{21:laplace:enea,
abstract = {This work exposes a practical methodology for the semi-automatic parallelization of existing code. We show how a scientific sequential code can be parallelized through our approach. The obtained parallel code is only slightly different from the starting sequential one, providing an example of how little re-designing our methodology involves. The performance of the parallelized code, executed on the CRESCO6 cluster, is then exposed and discussed. We also believe in the educational value of this approach and suggest its use as a teaching device for students.},
author = {Aldinucci, Marco and Cesare, Valentina and Colonnelli, Iacopo and Martinelli, Alberto Riccardo and Mittone, Gianluca and Cantalupo, Barbara},
booktitle = {ENEA CRESCO in the fight against COVID-19},
editor = {Francesco Iannone},
keywords = {hpc4ai},
pages = {21--24},
publisher = {ENEA},
title = {Practical Parallelizazion of a {Laplace} Solver with {MPI}},
year = {2021}
}

  • I. Colonnelli, B. Cantalupo, C. Spampinato, M. Pennisi, and M. Aldinucci, “Bringing ai pipelines onto cloud-hpc: setting a baseline for accuracy of covid-19 diagnosis,” in Enea cresco in the fight against covid-19, 2021. doi:10.5281/zenodo.5151511
    [BibTeX] [Abstract] [Download PDF]

    HPC is an enabling platform for AI. The introduction of AI workloads in the HPC applications basket has non-trivial consequences both on the way of designing AI applications and on the way of providing HPC computing. This is the leitmotif of the convergence between HPC and AI. The formalized definition of AI pipelines is one of the milestones of HPC-AI convergence. If well conducted, it allows, on the one hand, to obtain portable and scalable applications. On the other hand, it is crucial for the reproducibility of scientific pipelines. In this work, we advocate the StreamFlow Workflow Management System as a crucial ingredient to define a parametric pipeline, called “CLAIRE COVID-19 Universal Pipeline”, which is able to explore the optimization space of methods to classify COVID-19 lung lesions from CT scans, compare them for accuracy, and therefore set a performance baseline. The universal pipeline automatizes the training of many different Deep Neural Networks (DNNs) and many different hyperparameters. It, therefore, requires a massive computing power, which is found in traditional HPC infrastructure thanks to the portability-by-design of pipelines designed with StreamFlow. Using the universal pipeline, we identified a DNN reaching over 90\% accuracy in detecting COVID-19 lesions in CT scans.

    @inproceedings{21:covi:enea,
abstract = {HPC is an enabling platform for AI. The introduction of AI workloads in the HPC applications basket has non-trivial consequences both on the way of designing AI applications and on the way of providing HPC computing. This is the leitmotif of the convergence between HPC and AI. The formalized definition of AI pipelines is one of the milestones of HPC-AI convergence. If well conducted, it allows, on the one hand, to obtain portable and scalable applications. On the other hand, it is crucial for the reproducibility of scientific pipelines. In this work, we advocate the StreamFlow Workflow Management System as a crucial ingredient to define a parametric pipeline, called ``CLAIRE COVID-19 Universal Pipeline'', which is able to explore the optimization space of methods to classify COVID-19 lung lesions from CT scans, compare them for accuracy, and therefore set a performance baseline. The universal pipeline automatizes the training of many different Deep Neural Networks (DNNs) and many different hyperparameters. It, therefore, requires a massive computing power, which is found in traditional HPC infrastructure thanks to the portability-by-design of pipelines designed with StreamFlow. Using the universal pipeline, we identified a DNN reaching over 90\% accuracy in detecting COVID-19 lesions in CT scans.},
author = {Colonnelli, Iacopo and Cantalupo, Barbara and Spampinato, Concetto and Pennisi, Matteo and Aldinucci, Marco},
booktitle = {ENEA CRESCO in the fight against COVID-19},
doi = {10.5281/zenodo.5151511},
editor = {Francesco Iannone},
keywords = {streamflow},
publisher = {ENEA},
title = {Bringing AI pipelines onto cloud-HPC: setting a baseline for accuracy of COVID-19 diagnosis},
url = {https://iris.unito.it/retrieve/handle/2318/1796029/779853/21_AI-pipelines_ENEA-COVID19.pdf},
year = {2021},
bdsk-url-1 = {https://iris.unito.it/retrieve/handle/2318/1796029/779853/21_AI-pipelines_ENEA-COVID19.pdf},
bdsk-url-2 = {https://doi.org/10.5281/zenodo.5151511}
}

  • Y. Arfat, G. Mittone, R. Esposito, B. Cantalupo, G. M. De Ferrari, and M. Aldinucci, “A review of machine learning for cardiology,” Minerva cardiology and angiology, 2021. doi:10.23736/s2724-5683.21.05709-4
    [BibTeX] [Abstract] [Download PDF]

    This paper reviews recent cardiology literature and reports how Artificial Intelligence Tools (specifically, Machine Learning techniques) are being used by physicians in the field. Each technique is introduced with enough details to allow the understanding of how it works and its intent, but without delving into details that do not add immediate benefits and require expertise in the field. We specifically focus on the principal Machine Learning based risk scores used in cardiovascular research. After introducing them and summarizing their assumptions and biases, we discuss their merits and shortcomings. We report on how frequently they are adopted in the field and suggest why this is the case based on our expertise in Machine Learning. We complete the analysis by reviewing how corresponding statistical approaches compare with them. Finally, we discuss the main open issues in applying Machine Learning tools to cardiology tasks, also drafting possible future directions. Despite the growing interest in these tools, we argue that there are many still underutilized techniques: while Neural Networks are slowly being incorporated in cardiovascular research, other important techniques such as Semi-Supervised Learning and Federated Learning are still underutilized. The former would allow practitioners to harness the information contained in large datasets that are only partially labeled, while the latter would foster collaboration between institutions allowing building larger and better models.

    @article{21:ai4numbers:minerva,
abstract = {This paper reviews recent cardiology literature and reports how Artificial Intelligence Tools (specifically, Machine Learning techniques) are being used by physicians in the field. Each technique is introduced with enough details to allow the understanding of how it works and its intent, but without delving into details that do not add immediate benefits and require expertise in the field. We specifically focus on the principal Machine Learning based risk scores used in cardiovascular research. After introducing them and summarizing their assumptions and biases, we discuss their merits and shortcomings. We report on how frequently they are adopted in the field and suggest why this is the case based on our expertise in Machine Learning. We complete the analysis by reviewing how corresponding statistical approaches compare with them. Finally, we discuss the main open issues in applying Machine Learning tools to cardiology tasks, also drafting possible future directions. Despite the growing interest in these tools, we argue that there are many still underutilized techniques: while Neural Networks are slowly being incorporated in cardiovascular research, other important techniques such as Semi-Supervised Learning and Federated Learning are still underutilized. The former would allow practitioners to harness the information contained in large datasets that are only partially labeled, while the latter would foster collaboration between institutions allowing building larger and better models.},
author = {Yasir Arfat and Gianluca Mittone and Roberto Esposito and Barbara Cantalupo and Gaetano Maria {De Ferrari} and Marco Aldinucci},
date-added = {2021-08-09 23:00:12 +0200},
date-modified = {2021-08-09 23:05:36 +0200},
doi = {10.23736/s2724-5683.21.05709-4},
journal = {Minerva cardiology and angiology},
keywords = {deephealth, hpc4ai},
title = {A Review of Machine Learning for Cardiology},
url = {https://iris.unito.it/retrieve/handle/2318/1796298/780512/21_AI4numbers-preprint.pdf},
year = {2021},
bdsk-url-1 = {https://iris.unito.it/retrieve/handle/2318/1796298/780512/21_AI4numbers-preprint.pdf},
bdsk-url-2 = {https://doi.org/10.23736/s2724-5683.21.05709-4}
}

  • M. Aldinucci, V. Cesare, I. Colonnelli, A. R. Martinelli, G. Mittone, B. Cantalupo, C. Cavazzoni, and M. Drocco, “Practical parallelization of scientific applications with OpenMP, OpenACC and MPI,” Journal of parallel and distributed computing, vol. 157, pp. 13-29, 2021. doi:10.1016/j.jpdc.2021.05.017
    [BibTeX] [Abstract] [Download PDF]

    This work aims at distilling a systematic methodology to modernize existing sequential scientific codes with a little re-designing effort, turning an old codebase into \emph{modern} code, i.e., parallel and robust code. We propose a semi-automatic methodology to parallelize scientific applications designed with a purely sequential programming mindset, possibly using global variables, aliasing, random number generators, and stateful functions. We demonstrate that the same methodology works for the parallelization in the shared memory model (via OpenMP), message passing model (via MPI), and General Purpose Computing on GPU model (via OpenACC). The method is demonstrated parallelizing four real-world sequential codes in the domain of physics and material science. The methodology itself has been distilled in collaboration with MSc students of the Parallel Computing course at the University of Torino, that applied it for the first time to the project works that they presented for the final exam of the course. Every year the course hosts some special lectures from industry representatives, who present how they use parallel computing and offer codes to be parallelized.

    @article{21:jpdc:loop,
abstract = {This work aims at distilling a systematic methodology to modernize existing sequential scientific codes with a little re-designing effort, turning an old codebase into \emph{modern} code, i.e., parallel and robust code. We propose a semi-automatic methodology to parallelize scientific applications designed with a purely sequential programming mindset, possibly using global variables, aliasing, random number generators, and stateful functions. We demonstrate that the same methodology works for the parallelization in the shared memory model (via OpenMP), message passing model (via MPI), and General Purpose Computing on GPU model (via OpenACC). The method is demonstrated parallelizing four real-world sequential codes in the domain of physics and material science. The methodology itself has been distilled in collaboration with MSc students of the Parallel Computing course at the University of Torino, that applied it for the first time to the project works that they presented for the final exam of the course. Every year the course hosts some special lectures from industry representatives, who present how they use parallel computing and offer codes to be parallelized. },
author = {Aldinucci, Marco and Cesare, Valentina and Colonnelli, Iacopo and Martinelli, Alberto Riccardo and Mittone, Gianluca and Cantalupo, Barbara and Cavazzoni, Carlo and Drocco, Maurizio},
date-added = {2021-06-10 22:05:54 +0200},
date-modified = {2021-06-10 22:30:05 +0200},
doi = {10.1016/j.jpdc.2021.05.017},
journal = {Journal of Parallel and Distributed Computing},
keywords = {saperi},
pages = {13-29},
title = {Practical Parallelization of Scientific Applications with {OpenMP, OpenACC and MPI}},
url = {https://iris.unito.it/retrieve/handle/2318/1792557/770851/Practical_Parallelization_JPDC_preprint.pdf},
volume = {157},
year = {2021},
bdsk-url-1 = {https://iris.unito.it/retrieve/handle/2318/1792557/770851/Practical_Parallelization_JPDC_preprint.pdf},
bdsk-url-2 = {https://doi.org/10.1016/j.jpdc.2021.05.017}
}

  • I. Colonnelli, B. Cantalupo, R. Esposito, M. Pennisi, C. Spampinato, and M. Aldinucci, “HPC Application Cloudification: The StreamFlow Toolkit,” in 12th workshop on parallel programming and run-time management techniques for many-core architectures and 10th workshop on design tools and architectures for multicore embedded computing platforms (parma-ditam 2021), Dagstuhl, Germany, 2021, p. 5:1–5:13. doi:10.4230/OASIcs.PARMA-DITAM.2021.5
    [BibTeX] [Abstract] [Download PDF]

    Finding an effective way to improve accessibility to High-Performance Computing facilities, still anchored to SSH-based remote shells and queue-based job submission mechanisms, is an open problem in computer science. This work advocates a cloudification of HPC applications through a cluster-as-accelerator pattern, where computationally demanding portions of the main execution flow hosted on a Cloud Finding an effective way to improve accessibility to High-Performance Computing facilities, still anchored to SSH-based remote shells and queue-based job submission mechanisms, is an open problem in computer science. This work advocates a cloudification of HPC applications through a cluster-as-accelerator pattern, where computationally demanding portions of the main execution flow hosted on a Cloud infrastructure can be offloaded to HPC environments to speed them up. We introduce StreamFlow, a novel Workflow Management System that supports such a design pattern and makes it possible to run the steps of a standard workflow model on independent processing elements with no shared storage. We validated the proposed approach’s effectiveness on the CLAIRE COVID-19 universal pipeline, i.e. a reproducible workflow capable of automating the comparison of (possibly all) state-of-the-art pipelines for the diagnosis of COVID-19 interstitial pneumonia from CT scans images based on Deep Neural Networks (DNNs).

    @inproceedings{colonnelli_et_al:OASIcs.PARMA-DITAM.2021.5,
abstract = {Finding an effective way to improve accessibility to High-Performance Computing facilities, still anchored to SSH-based remote shells and queue-based job submission mechanisms, is an open problem in computer science. This work advocates a cloudification of HPC applications through a cluster-as-accelerator pattern, where computationally demanding portions of the main execution flow hosted on a Cloud Finding an effective way to improve accessibility to High-Performance Computing facilities, still anchored to SSH-based remote shells and queue-based job submission mechanisms, is an open problem in computer science. This work advocates a cloudification of HPC applications through a cluster-as-accelerator pattern, where computationally demanding portions of the main execution flow hosted on a Cloud infrastructure can be offloaded to HPC environments to speed them up. We introduce StreamFlow, a novel Workflow Management System that supports such a design pattern and makes it possible to run the steps of a standard workflow model on independent processing elements with no shared storage. We validated the proposed approach's effectiveness on the CLAIRE COVID-19 universal pipeline, i.e. a reproducible workflow capable of automating the comparison of (possibly all) state-of-the-art pipelines for the diagnosis of COVID-19 interstitial pneumonia from CT scans images based on Deep Neural Networks (DNNs).},
address = {Dagstuhl, Germany},
annote = {Keywords: cloud computing, distributed computing, high-performance computing, streamflow, workflow management systems},
author = {Colonnelli, Iacopo and Cantalupo, Barbara and Esposito, Roberto and Pennisi, Matteo and Spampinato, Concetto and Aldinucci, Marco},
booktitle = {12th Workshop on Parallel Programming and Run-Time Management Techniques for Many-core Architectures and 10th Workshop on Design Tools and Architectures for Multicore Embedded Computing Platforms (PARMA-DITAM 2021)},
doi = {10.4230/OASIcs.PARMA-DITAM.2021.5},
editor = {Bispo, Jo\~{a}o and Cherubin, Stefano and Flich, Jos\'{e}},
isbn = {978-3-95977-181-8},
issn = {2190-6807},
keywords = {deephealth, hpc4ai, streamflow},
pages = {5:1--5:13},
publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
series = {Open Access Series in Informatics (OASIcs)},
title = {{HPC Application Cloudification: The StreamFlow Toolkit}},
url = {https://drops.dagstuhl.de/opus/volltexte/2021/13641/pdf/OASIcs-PARMA-DITAM-2021-5.pdf},
urn = {urn:nbn:de:0030-drops-136419},
volume = {88},
year = {2021},
bdsk-url-1 = {https://drops.dagstuhl.de/opus/volltexte/2021/13641/pdf/OASIcs-PARMA-DITAM-2021-5.pdf},
bdsk-url-2 = {https://doi.org/10.4230/OASIcs.PARMA-DITAM.2021.5}
}

  • F. D’Ascenzo, O. De Filippo, G. Gallone, G. Mittone, M. A. Deriu, M. Iannaccone, A. Ariza-Solé, C. Liebetrau, S. Manzano-Fernández, G. Quadri, T. Kinnaird, G. Campo, J. P. Simao Henriques, J. M. Hughes, A. Dominguez-Rodriguez, M. Aldinucci, U. Morbiducci, G. Patti, S. Raposeiras-Roubin, E. Abu-Assi, G. M. De Ferrari, F. Piroli, A. Saglietto, F. Conrotto, P. Omedé, A. Montefusco, M. Pennone, F. Bruno, P. P. Bocchino, G. Boccuzzi, E. Cerrato, F. Varbella, M. Sperti, S. B. Wilton, L. Velicki, I. Xanthopoulou, A. Cequier, A. Iniguez-Romo, I. Munoz Pousa, M. Cespon Fernandez, B. Caneiro Queija, R. Cobas-Paz, A. Lopez-Cuenca, A. Garay, P. F. Blanco, A. Rognoni, G. Biondi Zoccai, S. Biscaglia, I. Nunez-Gil, T. Fujii, A. Durante, X. Song, T. Kawaji, D. Alexopoulos, Z. Huczek, J. R. Gonzalez Juanatey, S. Nie, M. Kawashiri, I. Colonnelli, B. Cantalupo, R. Esposito, S. Leonardi, W. Grosso Marra, A. Chieffo, U. Michelucci, D. Piga, M. Malavolta, S. Gili, M. Mennuni, C. Montalto, L. Oltrona Visconti, and Y. Arfat, “Machine learning-based prediction of adverse events following an acute coronary syndrome (PRAISE): a modelling study of pooled datasets,” The lancet, vol. 397, iss. 10270, pp. 199-207, 2021. doi:10.1016/S0140-6736(20)32519-8
    [BibTeX] [Abstract] [Download PDF]

    Background The accuracy of current prediction tools for ischaemic and bleeding events after an acute coronary syndrome (ACS) remains insufficient for individualised patient management strategies. We developed a machine learning-based risk stratification model to predict all-cause death, recurrent acute myocardial infarction, and major bleeding after ACS. Methods Different machine learning models for the prediction of 1-year post-discharge all-cause death, myocardial infarction, and major bleeding (defined as Bleeding Academic Research Consortium type 3 or 5) were trained on a cohort of 19826 adult patients with ACS (split into a training cohort [80%] and internal validation cohort [20%]) from the BleeMACS and RENAMI registries, which included patients across several continents. 25 clinical features routinely assessed at discharge were used to inform the models. The best-performing model for each study outcome (the PRAISE score) was tested in an external validation cohort of 3444 patients with ACS pooled from a randomised controlled trial and three prospective registries. Model performance was assessed according to a range of learning metrics including area under the receiver operating characteristic curve (AUC). Findings The PRAISE score showed an AUC of 0.82 (95% CI 0.78-0.85) in the internal validation cohort and 0.92 (0.90-0.93) in the external validation cohort for 1-year all-cause death; an AUC of 0.74 (0.70-0.78) in the internal validation cohort and 0.81 (0.76-0.85) in the external validation cohort for 1-year myocardial infarction; and an AUC of 0.70 (0.66-0.75) in the internal validation cohort and 0.86 (0.82-0.89) in the external validation cohort for 1-year major bleeding. Interpretation A machine learning-based approach for the identification of predictors of events after an ACS is feasible and effective. The PRAISE score showed accurate discriminative capabilities for the prediction of all-cause death, myocardial infarction, and major bleeding, and might be useful to guide clinical decision making.

    @article{21:lancet,
abstract = {Background The accuracy of current prediction tools for ischaemic and bleeding events after an acute coronary syndrome (ACS) remains insufficient for individualised patient management strategies. We developed a machine learning-based risk stratification model to predict all-cause death, recurrent acute myocardial infarction, and major bleeding after ACS.
Methods Different machine learning models for the prediction of 1-year post-discharge all-cause death, myocardial infarction, and major bleeding (defined as Bleeding Academic Research Consortium type 3 or 5) were trained on a cohort of 19826 adult patients with ACS (split into a training cohort [80%] and internal validation cohort [20%]) from the BleeMACS and RENAMI registries, which included patients across several continents. 25 clinical features routinely assessed at discharge were used to inform the models. The best-performing model for each study outcome (the PRAISE score) was tested in an external validation cohort of 3444 patients with ACS pooled from a randomised controlled trial and three prospective registries. Model performance was assessed according to a range of learning metrics including area under the receiver operating characteristic curve (AUC).
Findings The PRAISE score showed an AUC of 0.82 (95% CI 0.78-0.85) in the internal validation cohort and 0.92 (0.90-0.93) in the external validation cohort for 1-year all-cause death; an AUC of 0.74 (0.70-0.78) in the internal validation cohort and 0.81 (0.76-0.85) in the external validation cohort for 1-year myocardial infarction; and an AUC of 0.70 (0.66-0.75) in the internal validation cohort and 0.86 (0.82-0.89) in the external validation cohort for 1-year major bleeding.
Interpretation A machine learning-based approach for the identification of predictors of events after an ACS is feasible and effective. The PRAISE score showed accurate discriminative capabilities for the prediction of all-cause death, myocardial infarction, and major bleeding, and might be useful to guide clinical decision making.},
author = {Fabrizio D'Ascenzo and Ovidio {De Filippo} and Guglielmo Gallone and Gianluca Mittone and Marco Agostino Deriu and Mario Iannaccone and Albert Ariza-Sol\'e and Christoph Liebetrau and Sergio Manzano-Fern\'andez and Giorgio Quadri and Tim Kinnaird and Gianluca Campo and Jose Paulo {Simao Henriques} and James M Hughes and Alberto Dominguez-Rodriguez and Marco Aldinucci and Umberto Morbiducci and Giuseppe Patti and Sergio Raposeiras-Roubin and Emad Abu-Assi and Gaetano Maria {De Ferrari} and Francesco Piroli and Andrea Saglietto and Federico Conrotto and Pierluigi Omed\'e and Antonio Montefusco and Mauro Pennone and Francesco Bruno and Pier Paolo Bocchino and Giacomo Boccuzzi and Enrico Cerrato and Ferdinando Varbella and Michela Sperti and Stephen B. Wilton and Lazar Velicki and Ioanna Xanthopoulou and Angel Cequier and Andres Iniguez-Romo and Isabel {Munoz Pousa} and Maria {Cespon Fernandez} and Berenice {Caneiro Queija} and Rafael Cobas-Paz and Angel Lopez-Cuenca and Alberto Garay and Pedro Flores Blanco and Andrea Rognoni and Giuseppe {Biondi Zoccai} and Simone Biscaglia and Ivan Nunez-Gil and Toshiharu Fujii and Alessandro Durante and Xiantao Song and Tetsuma Kawaji and Dimitrios Alexopoulos and Zenon Huczek and Jose Ramon {Gonzalez Juanatey} and Shao-Ping Nie and Masa-aki Kawashiri and Iacopo Colonnelli and Barbara Cantalupo and Roberto Esposito and Sergio Leonardi and Walter {Grosso Marra} and Alaide Chieffo and Umberto Michelucci and Dario Piga and Marta Malavolta and Sebastiano Gili and Marco Mennuni and Claudio Montalto and Luigi {Oltrona Visconti} and Yasir Arfat},
date-modified = {2021-03-26 23:53:19 +0100},
doi = {10.1016/S0140-6736(20)32519-8},
issn = {0140-6736},
journal = {The Lancet},
keywords = {deephealth, hpc4ai},
number = {10270},
pages = {199-207},
title = {Machine learning-based prediction of adverse events following an acute coronary syndrome {(PRAISE)}: a modelling study of pooled datasets},
url = {https://www.researchgate.net/profile/James_Hughes3/publication/348501148_Machine_learning-based_prediction_of_adverse_events_following_an_acute_coronary_syndrome_PRAISE_a_modelling_study_of_pooled_datasets/links/6002a81ba6fdccdcb858b6c2/Machine-learning-based-prediction-of-adverse-events-following-an-acute-coronary-syndrome-PRAISE-a-modelling-study-of-pooled-datasets.pdf},
volume = {397},
year = {2021},
bdsk-url-1 = {https://www.researchgate.net/profile/James_Hughes3/publication/348501148_Machine_learning-based_prediction_of_adverse_events_following_an_acute_coronary_syndrome_PRAISE_a_modelling_study_of_pooled_datasets/links/6002a81ba6fdccdcb858b6c2/Machine-learning-based-prediction-of-adverse-events-following-an-acute-coronary-syndrome-PRAISE-a-modelling-study-of-pooled-datasets.pdf},
bdsk-url-2 = {https://doi.org/10.1016/S0140-6736(20)32519-8}
}

  • I. Colonnelli, B. Cantalupo, I. Merelli, and M. Aldinucci, “StreamFlow: cross-breeding cloud with HPC,” IEEE Transactions on Emerging Topics in Computing, vol. 9, iss. 4, p. 1723–1737, 2021. doi:10.1109/TETC.2020.3019202
    [BibTeX] [Abstract] [Download PDF]

    Workflows are among the most commonly used tools in a variety of execution environments. Many of them target a specific environment; few of them make it possible to execute an entire workflow in different environments, e.g. Kubernetes and batch clusters. We present a novel approach to workflow execution, called StreamFlow, that complements the workflow graph with the declarative description of potentially complex execution environments, and that makes it possible the execution onto multiple sites not sharing a common data space. StreamFlow is then exemplified on a novel bioinformatics pipeline for single cell transcriptomic data analysis workflow.

    @article{20Lstreamflow:tetc,
abstract = {Workflows are among the most commonly used tools in a variety of execution environments. Many of them target a specific environment; few of them make it possible to execute an entire workflow in different environments, e.g. Kubernetes and batch clusters. We present a novel approach to workflow execution, called StreamFlow, that complements the workflow graph with the declarative description of potentially complex execution environments, and that makes it possible the execution onto multiple sites not sharing a common data space. StreamFlow is then exemplified on a novel bioinformatics pipeline for single cell transcriptomic data analysis workflow.},
author = {Iacopo Colonnelli and Barbara Cantalupo and Ivan Merelli and Marco Aldinucci},
date-added = {2020-08-27 09:29:49 +0200},
date-modified = {2020-08-27 09:36:33 +0200},
doi = {10.1109/TETC.2020.3019202},
journal = {{IEEE} {T}ransactions on {E}merging {T}opics in {C}omputing},
keywords = {deephealth, hpc4ai, streamflow},
number = {4},
pages = {1723--1737},
title = {{StreamFlow}: cross-breeding cloud with {HPC}},
url = {https://arxiv.org/pdf/2002.01558},
volume = {9},
year = {2021},
bdsk-url-1 = {https://arxiv.org/pdf/2002.01558},
bdsk-url-2 = {https://doi.org/10.1109/TETC.2020.3019202}
}