A high-performance open-source framework for multiphysics simulation and adjoint-based shape and topology optimization

The first part of this thesis presents the advances made in the Open-Source software SU2, towards transforming it into a high-performance framework for design and optimization of multiphysics problems. Through this work, and in collaboration with other authors, a tenfold performance improvement was achieved for some problems. More importantly, problems that had previously been impossible to solve in SU2, can now be used in numerical optimization with shape or topology variables. Furthermore, it is now exponentially simpler to study new multiphysics applications, and to develop new numerical schemes taking advantage of modern high-performance-computing systems. In the second part of this thesis, these capabilities allowed the application of topology optimiza- tion to medium scale fluid-structure interaction problems, using high-fidelity models (nonlinear elasticity and Reynolds-averaged Navier-Stokes equations), which had not been done before in the literature. This showed that topology optimization can be used to target aerodynamic objectives, by tailoring the interaction between fluid and structure. However, it also made ev- ident the limitations of density-based methods for this type of problem, in particular, reliably converging to discrete solutions. This was overcome with new strategies to both guarantee and accelerate (i.e. reduce the overall computational cost) the convergence to discrete solutions in fluid-structure interaction problems.Open Acces

FSCL: Homogeneous programming, scheduling and execution on heterogeneous platforms

The last few years has seen activity towards programming models, languages and frameworks to address the increasingly wide range and broad availability of heterogeneous computing resources through raised programming abstraction and portability across different platforms. The effort spent in simplifying parallel programming across heterogeneous platforms is often outweighed by the need for low-level control over computation setup and execution and by performance opportunities that are missed due to the overhead introduced by the additional abstraction. Moreover, despite the ability to port parallel code across devices, each device is generally characterised by a restricted set of computations that it can execute outperforming the other devices in the system. The problem is therefore to schedule computations on increasingly popular multi-device heterogeneous platforms, helping to choose the best device among the available ones each time a computation has to execute. Our Ph.D. research investigates the possibilities to address the problem of programming and execution abstraction on heterogeneous platforms while helping to dynamically and transparently exploit the computing power of such platforms in a device-aware fashion

Piattaforme multicore e integrazione tri-dimensionale: analisi architetturale e ottimizzazione

Modern embedded systems embrace many-core shared-memory designs. Due to constrained power and area budgets, most of them feature software-managed scratchpad memories instead of data caches to increase the data locality. It is therefore programmers’ responsibility to explicitly manage the memory transfers, and this make programming these platform cumbersome. Moreover, complex modern applications must be adequately parallelized before they can the parallel potential of the platform into actual performance. To support this, programming languages were proposed, which work at a high level of abstraction, and rely on a runtime whose cost hinders performance, especially in embedded systems, where resources and power budget are constrained. This dissertation explores the applicability of the shared-memory paradigm on modern many-core systems, focusing on the ease-of-programming. It focuses on OpenMP, the de-facto standard for shared memory programming. In a first part, the cost of algorithms for synchronization and data partitioning are analyzed, and they are adapted to modern embedded many-cores. Then, the original design of an OpenMP runtime library is presented, which supports complex forms of parallelism such as multi-level and irregular parallelism. In the second part of the thesis, the focus is on heterogeneous systems, where hardware accelerators are coupled to (many-)cores to implement key functional kernels with orders-of-magnitude of speedup and energy efficiency compared to the “pure software” version. However, three main issues rise, namely i) platform design complexity, ii) architectural scalability and iii) programmability. To tackle them, a template for a generic hardware processing unit (HWPU) is proposed, which share the memory banks with cores, and the template for a scalable architecture is shown, which integrates them through the shared-memory system. Then, a full software stack and toolchain are developed to support platform design and to let programmers exploiting the accelerators of the platform. The OpenMP frontend is extended to interact with it.I sistemi integrati moderni sono architetture many-core, in cui spesso lo spazio di memoria è condiviso fra i processori. Per ridurre i consumi, molte di queste architetture sostituiscono le cache dati con memorie scratchpad gestite in software, per massimizzarne la località alle CPU e aumentare le performance. Questo significa che i dati devono essere spostati manualmente da parte del programmatore. Inoltre, tradurre in perfomance l’enorme parallelismo potenziale delle piattaforme many-core non è semplice. Per supportare la programmazione, diversi programming model sono stati proposti, e siccome lavorano ad un alto livello di astrazione, sfruttano delle librerie di runtime che forniscono servizi di base quali sincronizzazione, allocazione della memoria, threading. Queste librerie hanno un costo, che nei sistemi integrati è troppo elevato e ostacola il raggiungimento delle piene performance. Questa tesi analizza come un programming model ad alto livello di astrazione – OpenMP – possa essere efficientemente supportato, se il suo stack software viene adattato per sfruttare al meglio la piattaforma sottostante. In una prima parte, studio diversi meccanismi di sincronizzazione e comunicazione fra thread paralleli, portati sulle piattaforme many-core. In seguito, li utilizzo per scrivere un runtime di supporto a OpenMP che sia il più possibile efficente e “leggero” e che supporti paradigmi di parallelismo multi-livello e irregolare, spesso presenti nelle applicazioni moderne. Una seconda parte della tesi esplora le architetture eterogenee, ossia con acceleratori hardware. Queste architetture soffrono di problematiche sia i) per il processo di design della piattaforma, che ii) di scalabilità della piattaforma stessa (aumento del numero degli acceleratori e dei processori), che iii) di programmabilità. La tesi propone delle soluzioni a tutti e tre i problemi. Il linguaggio di programmazione usato è OpenMP, sia per la sua grande espressività a livello semantico, sia perché è lo standard de-facto per programmare sistemi a memoria condivisa

Bayesian statistical approach for protein residue-residue contact prediction

Despite continuous efforts in automating experimental structure determination and systematic target selection in structural genomics projects, the gap between the number of known amino acid sequences and solved 3D structures for proteins is constantly widening. While DNA sequencing technologies are advancing at an extraordinary pace, thereby constantly increasing throughput while at the same time reducing costs, protein structure determination is still labour intensive, time-consuming and expensive. This trend illustrates the essential importance of complementary computational approaches in order to bridge the so-called sequence-structure gap. About half of the protein families lack structural annotation and therefore are not amenable to techniques that infer protein structure from homologs. These protein families can be addressed by de novo structure prediction approaches that in practice are often limited by the immense computational costs required to search the conformational space for the lowest-energy conformation. Improved predictions of contacts between amino acid residues have been demonstrated to sufficiently constrain the overall protein fold and thereby extend the applicability of de novo methods to larger proteins. Residue-residue contact prediction is based on the idea that selection pressure on protein structure and function can lead to compensatory mutations between spatially close residues. This leaves an echo of correlation signatures that can be traced down from the evolutionary record. Despite the success of contact prediction methods, there are several challenges. The most evident limitation lies in the requirement of deep alignments, which excludes the majority of protein families without associated structural information that are the focus for contact guided de novo structure prediction. The heuristics applied by current contact prediction methods pose another challenge, since they omit available coevolutionary information. This work presents two different approaches for addressing the limitations of contact prediction methods. Instead of inferring evolutionary couplings by maximizing the pseudo-likelihood, I maximize the full likelihood of the statistical model for protein sequence families. This approach performed with comparable precision up to minor improvements over the pseudo-likelihood methods for protein families with few homologous sequences. A Bayesian statistical approach has been developed that provides posterior probability estimates for residue-residue contacts and eradicates the use of heuristics. The full information of coevolutionary signatures is exploited by explicitly modelling the distribution of statistical couplings that reflects the nature of residue-residue interactions. Surprisingly, the posterior probabilities do not directly translate into more precise predictions than obtained by pseudo-likelihood methods combined with prior knowledge. However, the Bayesian framework offers a statistically clean and theoretically solid treatment for the contact prediction problem. This flexible and transparent framework provides a convenient starting point for further developments, such as integrating more complex prior knowledge. The model can also easily be extended towards the Derivation of probability estimates for residue-residue distances to enhance the precision of predicted structures

Securing Critical Infrastructures

1noL'abstract è presente nell'allegato / the abstract is in the attachmentopen677. INGEGNERIA INFORMATInoopenCarelli, Albert

Bayesian statistical approach for protein residue-residue contact prediction

Despite continuous efforts in automating experimental structure determination and systematic target selection in structural genomics projects, the gap between the number of known amino acid sequences and solved 3D structures for proteins is constantly widening. While DNA sequencing technologies are advancing at an extraordinary pace, thereby constantly increasing throughput while at the same time reducing costs, protein structure determination is still labour intensive, time-consuming and expensive. This trend illustrates the essential importance of complementary computational approaches in order to bridge the so-called sequence-structure gap. About half of the protein families lack structural annotation and therefore are not amenable to techniques that infer protein structure from homologs. These protein families can be addressed by de novo structure prediction approaches that in practice are often limited by the immense computational costs required to search the conformational space for the lowest-energy conformation. Improved predictions of contacts between amino acid residues have been demonstrated to sufficiently constrain the overall protein fold and thereby extend the applicability of de novo methods to larger proteins. Residue-residue contact prediction is based on the idea that selection pressure on protein structure and function can lead to compensatory mutations between spatially close residues. This leaves an echo of correlation signatures that can be traced down from the evolutionary record. Despite the success of contact prediction methods, there are several challenges. The most evident limitation lies in the requirement of deep alignments, which excludes the majority of protein families without associated structural information that are the focus for contact guided de novo structure prediction. The heuristics applied by current contact prediction methods pose another challenge, since they omit available coevolutionary information. This work presents two different approaches for addressing the limitations of contact prediction methods. Instead of inferring evolutionary couplings by maximizing the pseudo-likelihood, I maximize the full likelihood of the statistical model for protein sequence families. This approach performed with comparable precision up to minor improvements over the pseudo-likelihood methods for protein families with few homologous sequences. A Bayesian statistical approach has been developed that provides posterior probability estimates for residue-residue contacts and eradicates the use of heuristics. The full information of coevolutionary signatures is exploited by explicitly modelling the distribution of statistical couplings that reflects the nature of residue-residue interactions. Surprisingly, the posterior probabilities do not directly translate into more precise predictions than obtained by pseudo-likelihood methods combined with prior knowledge. However, the Bayesian framework offers a statistically clean and theoretically solid treatment for the contact prediction problem. This flexible and transparent framework provides a convenient starting point for further developments, such as integrating more complex prior knowledge. The model can also easily be extended towards the Derivation of probability estimates for residue-residue distances to enhance the precision of predicted structures