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Book ; Online: Fault-Aware Non-Collective Communication Creation and Reparation in MPI

Rocco, Roberto / Palermo, Gianluca

2022

Abstract: The increasing size of HPC architectures makes the faults' presence a more and more frequent eventuality. This issue becomes especially relevant since MPI, the de-facto standard for inter-process communication, lacks proper fault management ... ...

Abstract	The increasing size of HPC architectures makes the faults' presence a more and more frequent eventuality. This issue becomes especially relevant since MPI, the de-facto standard for inter-process communication, lacks proper fault management functionalities. Past efforts produced extensions to the MPI standard that enabled fault management, including ULFM. While providing powerful tools to handle faults, it still faces limitations like the collectiveness of the repair procedure. With this paper, we overcome those limitations and achieve fault-aware non-collective communicator creation and reparation. We integrate our solution into an existing fault resiliency framework and measure the overhead introduced in the application code. The experimental campaign shows that our solution is scalable and introduces a limited overhead, and the non-collective reparation is a viable opportunity for ULFM-based applications.
Keywords	Computer Science - Distributed ; Parallel ; and Cluster Computing
Subject code	005
Publishing date	2022-09-05
Publishing country	us
Document type	Book ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Book ; Online: Fault Awareness in the MPI 4.0 Session Model

Rocco, Roberto / Palermo, Gianluca / Gregori, Daniele

2023

Abstract: The latest version of MPI introduces new functionalities like the Session model, but it still lacks fault management mechanisms. Past efforts produced tools and MPI standard extensions to manage fault presence, including ULFM. These measures are ... ...

Abstract	The latest version of MPI introduces new functionalities like the Session model, but it still lacks fault management mechanisms. Past efforts produced tools and MPI standard extensions to manage fault presence, including ULFM. These measures are effective against faults but do not fully support the new additions to the standard. In this paper, we combine the fault management possibilities of ULFM with the new Session model functionality introduced in version 4.0 of the standard. We focus on the communicator creation procedure, highlighting criticalities and proposing a method to circumvent them. The experimental campaign shows that the proposed solution does not significantly affect applications' execution time and scalability while better managing the insurgence of faults.
Keywords	Computer Science - Distributed ; Parallel ; and Cluster Computing
Publishing date	2023-03-06
Publishing country	us
Document type	Book ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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

Murugan, Natarajan Arul / Podobas, Artur / Gadioli, Davide / Vitali, Emanuele / Palermo, Gianluca / Markidis, Stefano

Pharmaceuticals (Basel, Switzerland)

2022 Volume 15, Issue 1

Abstract: Drug discovery is the most expensive, time-demanding, and challenging project in biopharmaceutical companies which aims at the identification and optimization of lead compounds from large-sized chemical libraries. The lead compounds should have high- ... ...

Abstract	Drug discovery is the most expensive, time-demanding, and challenging project in biopharmaceutical companies which aims at the identification and optimization of lead compounds from large-sized chemical libraries. The lead compounds should have high-affinity binding and specificity for a target associated with a disease, and, in addition, they should have favorable pharmacodynamic and pharmacokinetic properties (grouped as ADMET properties). Overall, drug discovery is a multivariable optimization and can be carried out in supercomputers using a reliable scoring function which is a measure of binding affinity or inhibition potential of the drug-like compound. The major problem is that the number of compounds in the chemical spaces is huge, making the computational drug discovery very demanding. However, it is cheaper and less time-consuming when compared to experimental high-throughput screening. As the problem is to find the most stable (global) minima for numerous protein-ligand complexes (on the order of 106 to 1012), the parallel implementation of in silico virtual screening can be exploited to ensure drug discovery in affordable time. In this review, we discuss such implementations of parallelization algorithms in virtual screening programs. The nature of different scoring functions and search algorithms are discussed, together with a performance analysis of several docking softwares ported on high-performance computing architectures.
Language	English
Publishing date	2022-01-04
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2193542-7
ISSN	1424-8247
ISSN	1424-8247
DOI	10.3390/ph15010063
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Book ; Online: Legio

Rocco, Roberto / Gadioli, Davide / Palermo, Gianluca

Fault Resiliency for Embarrassingly Parallel MPI Applications

2021

Abstract: Due to the increasing size of HPC machines, the fault presence is becoming an eventuality that applications must face. Natively, MPI provides no support for the execution past the detection of a fault, and this is becoming more and more constraining. ... ...

Abstract	Due to the increasing size of HPC machines, the fault presence is becoming an eventuality that applications must face. Natively, MPI provides no support for the execution past the detection of a fault, and this is becoming more and more constraining. With the introduction of ULFM (User Level Fault Mitigation library), it has been provided with a possible way to overtake a fault during the application execution at the cost of code modifications. ULFM is intrusive in the application and requires also a deep understanding of its recovery procedures. In this paper we propose Legio, a framework that lowers the complexity of introducing resiliency in an embarrassingly parallel MPI application. By hiding ULFM behind the MPI calls, the library is capable to expose resiliency features to the application in a transparent manner thus removing any integration effort. Upon fault, the failed nodes are discarded and the execution continues only with the non-failed ones. A hierarchical implementation of the solution has been also proposed to reduce the overhead of the repair process when scaling towards a large number of nodes. We evaluated our solutions on the Marconi100 cluster at CINECA, showing that the overhead introduced by the library is negligible and it does not limit the scalability properties of MPI. Moreover, we also integrated the solution in real-world applications to further prove its robustness by injecting faults.
Keywords	Computer Science - Distributed ; Parallel ; and Cluster Computing ; Computer Science - Performance
Subject code	004
Publishing date	2021-04-29
Publishing country	us
Document type	Book ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Book ; Online: A Collaborative Filtering Approach for the Automatic Tuning of Compiler Optimisations

Cereda, Stefano / Palermo, Gianluca / Cremonesi, Paolo / Doni, Stefano

2020

Abstract: Selecting the right compiler optimisations has a severe impact on programs' performance. Still, the available optimisations keep increasing, and their effect depends on the specific program, making the task human intractable. Researchers proposed several ...

Abstract	Selecting the right compiler optimisations has a severe impact on programs' performance. Still, the available optimisations keep increasing, and their effect depends on the specific program, making the task human intractable. Researchers proposed several techniques to search in the space of compiler optimisations. Some approaches focus on finding better search algorithms, while others try to speed up the search by leveraging previously collected knowledge. The possibility to effectively reuse previous compilation results inspired us toward the investigation of techniques derived from the Recommender Systems field. The proposed approach exploits previously collected knowledge and improves its characterisation over time. Differently from current state-of-the-art solutions, our approach is not based on performance counters but relies on Reaction Matching, an algorithm able to characterise programs looking at how they react to different optimisation sets. The proposed approach has been validated using two widely used benchmark suites, cBench and PolyBench, including 54 different programs. Our solution, on average, extracted 90% of the available performance improvement 10 iterations before current state-of-the-art solutions, which corresponds to 40% fewer compilations and performance tests to perform. Comment: To be published in the 21st ACM SIGPLAN/SIGBED International Conference on Languages, Compilers, and Tools for Embedded Systems (LCTES 2020) PolyBench dataset available at: https://github.com/stefanocereda/polybench_data cBench dataset available at: https://github.com/amirjamez/COBAYN
Keywords	Computer Science - Distributed ; Parallel ; and Cluster Computing ; Computer Science - Performance
Subject code	006 ; 004
Publishing date	2020-05-06
Publishing country	us
Document type	Book ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Book ; Online: Improving computation efficiency using input and architecture features for a virtual screening application

Accordi, Gianmarco / Vitali, Emanuele / Gadioli, Davide / Crisci, Luigi / Cosenza, Biagio / Bisson, Mauro / Fatica, Massimiliano / Beccari, Andrea / Palermo, Gianluca

2023

Abstract: Virtual screening is an early stage of the drug discovery process that selects the most promising candidates. In the urgent computing scenario it is critical to find a solution in a short time frame. In this paper, we focus on a real-world virtual ... ...

Abstract	Virtual screening is an early stage of the drug discovery process that selects the most promising candidates. In the urgent computing scenario it is critical to find a solution in a short time frame. In this paper, we focus on a real-world virtual screening application to evaluate out-of-kernel optimizations, that consider input and architecture features to improve the computation efficiency on GPU. Experiment results on a modern supercomputer node show that we can almost double the performance. Moreover, we implemented the optimization using SYCL and it provides a consistent benefit with the CUDA optimization. A virtual screening campaign can use this gain in performance to increase the number of evaluated candidates, improving the probability of finding a drug.
Keywords	Computer Science - Computational Engineering ; Finance ; and Science ; Computer Science - Hardware Architecture ; Computer Science - Distributed ; Parallel ; and Cluster Computing
Subject code	000
Publishing date	2023-03-09
Publishing country	us
Document type	Book ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Book ; Online: Low power networks-on-chip

Lajolo, Marcello / Palermo, Gianluca / Silvano, Cristina

2011

Abstract: In recent years, both Networks-on-Chip, as an architectural solution for high-speed interconnect, and power consumption, as a key design constraint, have continued to gain interest in the design and research communities, since power and energy issues ... ...

Author's details	Cristina Silvano, Marcello Lajolo, Gianluca Palermo, eds
Abstract	In recent years, both Networks-on-Chip, as an architectural solution for high-speed interconnect, and power consumption, as a key design constraint, have continued to gain interest in the design and research communities, since power and energy issues still represent one of the limiting factors in integrating multi- and many-cores on a single chip. This book covers power and energy aware design techniques from several perspectives and abstraction levels and offers a single-source reference to some of the most important design techniques proposed in the context of low-power design for networks-on-chip architectures. Describes the most important design techniques that were invented, proposed, and applied to reduce both dynamic power and static power dissipation in networks-on-chip based architectures, Applies state-of-the-art, low-power design techniques to the design of Networks-on-Chip, to demonstrate methodology for design of high-speed, low-power interconnect, Offers a single source reference to the latest research, otherwise available only in disparate journals and conference proceedings. In recent years, both Networks-on-Chip, as an architectural solution for high-speed interconnect, and power consumption, as a key design constraint, have continued to gain interest in the design and research communities. This book offers a single-source reference to some of the most important design techniques proposed in the context of low-power design for networks-on-chip architectures.
Keywords	Computer aided design ; Engineering ; Systems engineering ; Computer # CAD ; Technik / Wissen # Nachrichtentechnik
Language	English
Size	Online-Ressource
Publisher	Springer
Publishing place	New York u.a.
Document type	Book ; Online
Note	Includes bibliographical references and index ; Networks on a chip
ISBN	9781441969101 ; 9781441969118 ; 1441969101 ; 144196911X
DOI	10.1007/978-1-4419-6911-8
Database	Former special subject collection: coastal and deep sea fishing

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Book ; Online: Low power networks-on-chip

Lajolo, Marcello / Palermo, Gianluca / Silvano, Cristina

2011

Author's details	Cristina Silvano, Marcello Lajolo, Gianluca Palermo, eds
Abstract	In recent years, both Networks-on-Chip, as an architectural solution for high-speed interconnect, and power consumption, as a key design constraint, have continued to gain interest in the design and research communities, since power and energy issues still represent one of the limiting factors in integrating multi- and many-cores on a single chip. This book covers power and energy aware design techniques from several perspectives and abstraction levels and offers a single-source reference to some of the most important design techniques proposed in the context of low-power design for networks-on-chip architectures. Describes the most important design techniques that were invented, proposed, and applied to reduce both dynamic power and static power dissipation in networks-on-chip based architectures, Applies state-of-the-art, low-power design techniques to the design of Networks-on-Chip, to demonstrate methodology for design of high-speed, low-power interconnect, Offers a single source reference to the latest research, otherwise available only in disparate journals and conference proceedings. In recent years, both Networks-on-Chip, as an architectural solution for high-speed interconnect, and power consumption, as a key design constraint, have continued to gain interest in the design and research communities. This book offers a single-source reference to some of the most important design techniques proposed in the context of low-power design for networks-on-chip architectures.
Keywords	Computer aided design ; Engineering ; Systems engineering ; Computer CAD ; Technik / Wissen Nachrichtentechnik
Language	English
Size	Online-Ressource
Publisher	Springer
Publishing place	New York u.a.
Document type	Book ; Online
Note	Includes bibliographical references and index ; Networks on a chip
ISBN	9781441969101 ; 9781441969118 ; 1441969101 ; 144196911X
DOI	10.1007/978-1-4419-6911-8
Database	Library catalogue of the German National Library of Science and Technology (TIB), Hannover

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Article ; Online: MEDIATE - Molecular DockIng at homE: Turning collaborative simulations into therapeutic solutions.

Vistoli, Giulio / Manelfi, Candida / Talarico, Carmine / Fava, Anna / Warshel, Arieh / Tetko, Igor V / Apostolov, Rossen / Ye, Yang / Latini, Chiara / Ficarelli, Federico / Palermo, Gianluca / Gadioli, Davide / Vitali, Emanuele / Varriale, Gaetano / Pisapia, Vincenzo / Scaturro, Marco / Coletti, Silvano / Gregori, Daniele / Gruffat, Daniel /

Leija, Edgardo / Hessenauer, Sam / Delbianco, Alberto / Allegretti, Marcello / Beccari, Andrea R

Expert opinion on drug discovery

2023 Volume 18, Issue 8, Page(s) 821–833

Abstract: Introduction: Collaborative computing has attracted great interest in the possibility of joining the efforts of researchers worldwide. Its relevance has further increased during the pandemic crisis since it allows for the strengthening of scientific ... ...

Abstract	Introduction: Collaborative computing has attracted great interest in the possibility of joining the efforts of researchers worldwide. Its relevance has further increased during the pandemic crisis since it allows for the strengthening of scientific collaborations while avoiding physical interactions. Thus, the E4C consortium presents the MEDIATE initiative which invited researchers to contribute via their virtual screening simulations that will be combined with AI-based consensus approaches to provide robust and method-independent predictions. The best compounds will be tested, and the biological results will be shared with the scientific community. Areas covered: In this paper, the MEDIATE initiative is described. This shares compounds' libraries and protein structures prepared to perform standardized virtual screenings. Preliminary analyses are also reported which provide encouraging results emphasizing the MEDIATE initiative's capacity to identify active compounds. Expert opinion: Structure-based virtual screening is well-suited for collaborative projects provided that the participating researchers work on the same input file. Until now, such a strategy was rarely pursued and most initiatives in the field were organized as challenges. The MEDIATE platform is focused on SARS-CoV-2 targets but can be seen as a prototype which can be utilized to perform collaborative virtual screening campaigns in any therapeutic field by sharing the appropriate input files.
MeSH term(s)	Humans ; Molecular Docking Simulation ; SARS-CoV-2 ; COVID-19 ; Proteins ; Antiviral Agents
Chemical Substances	Proteins ; Antiviral Agents
Language	English
Publishing date	2023-07-10
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2259618-5
ISSN	1746-045X ; 1746-0441
ISSN (online)	1746-045X
ISSN	1746-0441
DOI	10.1080/17460441.2023.2221025
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Book ; Online: EXSCALATE

Gadioli, Davide / Vitali, Emanuele / Ficarelli, Federico / Latini, Chiara / Manelfi, Candida / Talarico, Carmine / Silvano, Cristina / Cavazzoni, Carlo / Palermo, Gianluca / Beccari, Andrea Rosario

An extreme-scale in-silico virtual screening platform to evaluate 1 trillion compounds in 60 hours on 81 PFLOPS supercomputers

2021

Abstract: The social and economic impact of the COVID-19 pandemic demands the reduction of the time required to find a therapeutic cure. In the contest of urgent computing, we re-designed the Exscalate molecular docking platform to benefit from heterogeneous ... ...

Abstract	The social and economic impact of the COVID-19 pandemic demands the reduction of the time required to find a therapeutic cure. In the contest of urgent computing, we re-designed the Exscalate molecular docking platform to benefit from heterogeneous computation nodes and to avoid scaling issues. We deployed the Exscalate platform on two top European supercomputers (CINECA-Marconi100 and ENI-HPC5), with a combined computational power of 81 PFLOPS, to evaluate the interaction between 70 billions of small molecules and 15 binding-sites of 12 viral proteins of Sars-Cov2. The experiment lasted 60 hours and overall it performed a trillion of evaluations.
Keywords	Computer Science - Distributed ; Parallel ; and Cluster Computing ; Computer Science - Computational Engineering ; Finance ; and Science
Publishing date	2021-10-22
Publishing country	us
Document type	Book ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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