EuroEXA - D2.6: Final ported application software

This document describes the ported software of the EuroEXA applications to the single CRDB testbed and it discusses the experiences extracted from porting and optimization activities that should be actively taken into account in future redesign and optimization. This document accompanies the ported application software, found in the EuroEXA private repository (https://github.com/euroexa). In particular, this document describes the status of the software for each of the EuroEXA applications, sketches the redesign and optimization strategy for each application, discusses issues and difficulties faced during the porting activities and the relative lesson learned. A few preliminary evaluation results have been presented, however the full evaluation will be discussed in deliverable 2.8

Design and implementation of an FPGA-based convolutional neural network accelerator

A thesis submitted in fulfillment of the requirements for the DIPLOMA of Electrical and Computer Engineering in the School of Electrical and Computer Engineering.Περίληψη: Τα τελευταία χρόνια, τα Convolutional Neural Networks (CNNs) παρουσιάζουν εξαιρετική ανάπτυξη λόγω της αποτελεσματικότητάς τους σε σύνθετα προβλήματα αναγνώρισης εικόνων. Τα CNNs οδηγούνται στην επίλυση ενός συνεχώς μεγαλύτερου αριθμού προβλημάτων, από την αναγνώριση ομιλίας έως την κατάτμηση και την ταξινόμηση της εικόνας. Η συνεχώς αυξανόμενη ανάγκη για μεγαλύτερη υπολογιστική ισχύ που απαιτείται από τα CNN δίνει την δυνατότητα σε hardware υλοποιήσεις. Επιπλέον, το φόρτο εργασίας των CNN έχει ροή δεδομένων, κατάλληλη για αρχιτεκτονική σε επαναπρογραμματιζόμενο hardware, όπως οι FPGAs. O αριθμός των ερευνών για την Μηχανική Μάθηση και ειδικά για τα CNN (που υλοποιείται σε πλατφόρμες FPGA) μέσα στα τελευταία 4 χρόνια καταδεικνύει το τεράστιο βιομηχανικό και ακαδημαϊκό ενδιαφέρον. Αυτή η μελέτη παρουσιάζει έναν (Inference) επιταχυντή CNN βασισμένο σε τεχνολογίες FPGA. Το δίκτυο που επιδιώκουμε να επιταχύνουμε αναπτύχθηκε από τον Δρ. Τσαγκατάκη στο πλαίσιο του έργου DEDALE (Horizon 2020) για θέματα αστροφυσικής. Αφού πραγματοποιήθηκε Robustness Analysis, διαστασιολογήθηκε το υπολογιστικό φόρτο εργασίας και οι προσβάσεις στη μνήμη, καθώς εξετάστηκαν μέθοδοι συμπίεσης και αλγοριθμικές βελτιστοποιήσεις για την εκμετάλλευση του παραλληλισμού των FPGAs. Στο επίπεδο των νευρώνων, εξηγούνται και συγκρίνονται οι βελτιστοποιήσεις των Convolutional και Fully Connected Layers . Στο επίπεδο του δικτύου, οι προσεγγιστικές μέθοδοι βελτιστοποίησης υπολογισμών εξετάζονται έχοντας ως περιορισμό να μην μειωθεί αισθητά η ακρίβεια του δικτύου. Οι πλατφόρμες που χρησιμοποιήθηκαν είναι οι ZCU102 και QFDB (μια προσαρμοσμένη πλατφόρμα 4-FPGA που αναπτύχθηκε στο ΙΤΕ). Ο επιταχυντής που υλοποιήθηκε κατάφερε να επιτύχει 20x latency speedup, 2.17x throughput speedup και να είναι 11.9x πιο ενεργειακά αποδοτικός σε σύγκριση με την GPU NVIDIA-Quadro-K2200 στα πλαίσια του έργου EuroExa.Summarization: In recent years Convolutional Neural Networks (CNNs) have shown extremely growth due to their effectiveness at complex image recognition problems. They are currently adopted to solve an ever greater number of problems, ranging from speech recognition to image segmentation and classification. The continuing increasing amount of processing required by CNNs creates the field for hardware support methods. Moreover, CNN workloads have a streaming nature, well suited to reconfigurable hardware architectures such as FPGAs. The amount of research on the Machine Learning and especially on CNN (implemented on FPGA platforms) within the last 4 years demonstrates the tremendous industrial and academic interest. This study presents a CNN inference accelerator over FPGAs. The network we aim to accelerate was developed by Dr. Tsagatakis in the context of DEDALE project (Horizon 2020) for astrophysics subject. After carrying out Robustness Analysis computational workloads and memory accesses are analyzed, as well as compression methods and algorithmic optimizations to exploit FPGA parallelism. At the level of neurons, optimizations of the convolutional and fully connected layers are explained and compared. At the network level, approximate computing optimization methods are examined limited by not reducing the accuracy of the network. The platforms were used are ZCU102 and QFDB(a custom 4-FPGA platform developed at FORTH). The implemented accelerator was managed to achieve 20x latency speedup, 2.17x throughput speedup and 11.9x energy efficient over GPU NVIDIA-Quadro-K2200 in terms of EuroExa project

Routine histopathology of septal myectomy for hypertrophic obstructive cardiomyopathy in a greek cohort

Hypertrophic cardiomyopathy (HCM) is a diverse inherited disease affecting 1 in 500 individuals irrespective of gender and ethnicity. A fraction of HCM patients will eventually develop drug refractory dynamic obstruction of the left ventricular outflow tract. For such patients, septal myectomy is the procedure of choice to alleviate their symptoms and improve their quality of life. The current histopathological study, the first from the Greek region, aims to examine the hallmark histopathological characteristics of Hypertrophic Obstructive Cardiomyopathy in a population of patients undergoing septal myectomy at a single center over a ten year period. Medical records and histopathology specimens of thirty nine (n=39) patients were evaluated. The sample comprised 22 males (56.4%) and 17 females (43.6%). Mean patient age at myectomy was 53.9±16.7 years, ranging from 12 to 79 years. Maximal IVS thickness on echocardiography was available for 35 patients with a median value of 2.08cm. Peak resting LVOT Pressure Gradient was available for 33 patients with a mean value of 104.88±44.20 mmHg. Central tendency of each histopathological attribute expressed as the median value was: moderate for myocyte hypertrophy, mild for cytoplasmic vacuolization, moderate for subendocardial fibrosis, moderate for interstitial fibrosis, mild for replacement fibrosis, moderate for myofibrillar disarray and mild for capillary stenosis. Myocyte hypertrophy, present in all specimens, was positively correlated with maximal IVS thickness (tau-b=0.43, p=0.002). Replacement fibrosis was positively correlated with the grade of microvascular stenosis (tau-b=0.45, p=0.004). LVEF was negatively correlated with the grade of interstitial fibrosis (taub=−0.43, p=0.035) and with the extent of myocardial fiber disarray (tau-b=−0.42, p=0.034). Histopathological attributes were not correlated with patient gender or age thus proving that HCM has a histological phenotype unique to each patient, mainly depending on each specific sarcomeric mutatio

Epidemiology and management of chronic thromboembolic pulmonary hypertension: experience from two expert centers

Objectives: Chronic thromboembolic pulmonary hypertension (CTEPH) is a rare, distinct pulmonary vascular disease, and therefore, there is a lack of data regarding its clinical presentation, diagnosis, and management at a national basis. We aimed to describe the demographics and management of patients with CTEPH in Northern Greece. Methods: We conducted a retrospective, observational study by a joint collaboration between two pulmonary hypertension expert centers in Greece, and the study included patients diagnosed with CTEPH. The patient population was divided into two groups depending on their operability. Results: Overall, 27 consecutive patients were included (59% female, mean age 59.3±15.1 years). Dyspnea and fatigue were the most common presenting symptoms. History of pulmonary embolism was present in 82%. Of patients, 18 (67%) were assessed as operable, of whom 10 (55%) finally underwent pulmonary endarterectomy (PEA). There were no differences in symptoms, WHO functional class, 6-min walking test distance, and hemodynamics between the operable and nonoperable groups. At the end of follow-up, all non-operable and operable patients who did not receive surgical treatment were treated with at least one pulmonary hypertension-specific drug. Conclusion: This is the first report that presents data of patients diagnosed with CTEPH in Greece. The percentage of patients who underwent surgical treatment is lower but approaches the reported rates in large registries. Considering that PEA is a relatively safe and potentially curative surgical procedure, we emphasize the need for establishing a designated PEA center in Greece. Keywords: Chronic thromboembolic pulmonary hypertension, pulmonary endarterectomy, registry, riocigua

Epidemiology and management of chronic thromboembolic pulmonary hypertension: experience from two expert centers

Objectives: Chronic thromboembolic pulmonary hypertension (CTEPH) is a rare, distinct pulmonary vascular disease, and therefore, there is a lack of data regarding its clinical presentation, diagnosis, and management at a national basis. We aimed to describe the demographics and management of patients with CTEPH in Northern Greece. Methods: We conducted a retrospective, observational study by a joint collaboration between two pulmonary hypertension expert centers in Greece, and the study included patients diagnosed with CTEPH. The patient population was divided into two groups depending on their operability. Results: Overall, 27 consecutive patients were included (59% female, mean age 59.3±15.1 years). Dyspnea and fatigue were the most common presenting symptoms. History of pulmonary embolism was present in 82%. Of patients, 18 (67%) were assessed as operable, of whom 10 (55%) finally underwent pulmonary endarterectomy (PEA). There were no differences in symptoms, WHO functional class, 6-min walking test distance, and hemodynamics between the operable and nonoperable groups. At the end of follow-up, all non-operable and operable patients who did not receive surgical treatment were treated with at least one pulmonary hypertension-specific drug. Conclusion: This is the first report that presents data of patients diagnosed with CTEPH in Greece. The percentage of patients who underwent surgical treatment is lower but approaches the reported rates in large registries. Considering that PEA is a relatively safe and potentially curative surgical procedure, we emphasize the need for establishing a designated PEA center in Greece. Keywords: Chronic thromboembolic pulmonary hypertension, pulmonary endarterectomy, registry, riociguat