Energy-efficiency evaluation of Intel KNL for HPC workloads

Energy consumption is increasingly becoming a limiting factor to the design of faster large-scale parallel systems, and development of energy-efficient and energy-aware applications is today a relevant issue for HPC code-developer communities. In this work we focus on energy performance of the Knights Landing (KNL) Xeon Phi, the latest many-core architecture processor introduced by Intel into the HPC market. We take into account the 64-core Xeon Phi 7230, and analyze its energy performance using both the on-chip MCDRAM and the regular DDR4 system memory as main storage for the application data-domain. As a benchmark application we use a Lattice Boltzmann code heavily optimized for this architecture and implemented using different memory data layouts to store its lattice. We assessthen the energy consumption using different memory data-layouts, kind of memory (DDR4 or MCDRAM) and number of threads per core

FER: A Benchmark for the Roofline Analysis of FPGA Based HPC Accelerators

Nowadays, the use of hardware accelerators to boost the performance of HPC applications is a consolidated practice, and among others, GPUs are by far the most widespread. More recently, some data centers have successfully deployed also FPGA accelerated systems, especially to boost machine learning inference algorithms. Given the growing use of machine learning methods in various computational fields, and the increasing interest towards reconfigurable architectures, we may expect that in the near future FPGA based accelerators will be more common in HPC systems, and that they could be exploited also to accelerate general purpose HPC workloads. In view of this, tools able to benchmark FPGAs in the context of HPC are necessary for code developers to estimate the performance of applications, as well as for computer architects to model that of systems at scale. To fulfill these needs, we have developed FER (FPGA Empirical Roofline), a benchmarking tool able to empirically measure the computing performance of FPGA based accelerators, as well as the bandwidth of their on-chip and off-chip memories. FER measurements enable to draw Roofline plots for FPGAs, allowing for performance comparisons with other processors, such as CPUs and GPUs, and to estimate at the same time the performance upper-bounds that applications could achieve on a target device. In this paper we describe the theoretical model on which FER relies, its implementation details, and the results measured on Xilinx Alveo accelerator cards

Using accelerators to speed up scientific and engineering codes: perspectives and problems

Accelerators are quickly emerging as the leading technology to further boost computing performances; their main feature is a massively parallel on-chip architecture. NVIDIA and AMD GPUs and the Intel Xeon-Phi are examples of accelerators available today. Accelerators are power-efficient and deliver up to one order of magnitude more peak performance than traditional CPUs. However, existing codes for traditional CPUs require substantial changes to run efficiently on accelerators, including rewriting with specific programming languages. In this contribution we present our experience in porting large codes to NVIDIA GPU and Intel Xeon-Phi accelerators. Our reference application is a CFD code based on the Lattice Boltzmann (LB) method. The regular structure of LB algorithms makes them suitable for processor architectures with a large degree of parallelism. However, the challenge of exploiting a large fraction of the theoretically available performance is not easy to met. We consider a state-of-the-art two-dimensional LB model based on 37 populations (a D2Q37 model), that accurately reproduces the thermo-hydrodynamics of a 2D-fluid obeying the equation-of-state of a perfect gas. We describe in details how we implement and optimize our LB code for Xeon-Phi and GPUs, and then analyze performances on single- and multi-accelerator systems. We finally compare results with those available on recent traditional multi-core CPUs

TOWARDS STEADY-STATE VISUALLY EVOKED POTENTIALS BRAIN-COMPUTER INTERFACES FOR VIRTUAL REALITY ENVIRONMENTS EXPLICIT AND IMPLICIT INTERACTION

In the last two decades, Brain-Computer Interfaces (BCIs) have been investigated mainly for the purpose of implementing assistive technologies able to provide new channels for communication and control for people with severe disabilities. Nevertheless, more recently, thanks to technical and scientific advances in the different research fields involved, BCIs are gaining greater attention also for their adoption by healthy users, as new interaction devices. This thesis is dedicated to to the latter goal and in particular will deal with BCIs based on the Steady State Visual Evoked Potential (SSVEP), which in previous works demonstrated to be one of the most flexible and reliable approaches. SSVEP based BCIs could find applications in different contexts, but one which is particularly interesting for healthy users, is their adoption as new interaction devices for Virtual Reality (VR) environments and Computer Games. Although being investigated since several years, BCIs still poses several limitations in terms of speed, reliability and usability with respect to ordinary interaction devices. Despite of this, they may provide additional, more direct and intuitive, explicit interaction modalities, as well as implicit interaction modalities otherwise impossible with ordinary devices. This thesis, after a comprehensive review of the different research fields being the basis of a BCI exploiting the SSVEP modality, present a state-of-the-art open source implementation using a mix of pre-existing and custom software tools. The proposed implementation, mainly aimed to the interaction with VR environments and Computer Games, has then been used to perform several experiments which are hereby described as well. Initially performed experiments aim to stress the validity of the provided implementation, as well as to show its usability with a commodity bio-signal acquisition device, orders of magnitude less expensive than commonly used ones, representing a step forward in the direction of practical BCIs for end users applications. The proposed implementation, thanks to its flexibility, is used also to perform novel experiments aimed to investigate the exploitation of stereoscopic displays to overcome a known limitation of ordinary displays in the context of SSVEP based BCIs. Eventually, novel experiments are presented investigating the use of the SSVEP modality to provide also implicit interaction. In this context, a first proof of concept Passive BCI based on the SSVEP response is presented and demonstrated to provide information exploitable for prospective applications

Short-Term Bisphosphonate Therapy Could Ameliorate Osteonecrosis: A Complication in Childhood Hematologic Malignancies

Osteonecrosis (ON) is a critical complication in the treatment of childhood leukemia and lymphoma. It particularly affects survivors of acute lymphoblastic leukemia and non-Hodgkin lymphoma reflecting the cumulative exposure to glucocorticosteroid therapy. ON is often multiarticular and bilateral, specially affecting weight-bearing joints. A conventional approach suggests a surgical intervention even if pharmacological options have also recently been investigated. We reported two cases of long time steroid-treated patients who underwent Bone Marrow Transplantation (BMT) for hematological disease. Both patients developed femoral head osteonecrosis (ON) that was diagnosed by magnetic resonance imaging (MRI) and the ON was also accompanied with pain and a limp. Despite of the conventional strategies of therapy, we successfully started a short-term treatment with bisphosphonates in order to decrease the pain and the risk of fracture

Eliciting steady-state visual evoked potentials by means of stereoscopic displays

Brain-Computer Interfaces (BCIs) provide users communication and control capabilities by analyzing their brain activity. A technique to implement BCIs, used recently also in Virtual Reality (VR) environments, is based on the Steady State Visual Evoked Potentials (SSVEPs) detection. Exploiting the SSVEP response, BCIs could be implemented showing targets flickering at different frequencies and detecting which is gazed by the observer analyzing her/his electroencephalographic (EEG) signals. In this work, we evaluate the use of stereoscopic displays for the presentation of SSVEP eliciting stimuli, comparing their effectiveness between monoscopic and stereoscopic stimuli. Moreover we propose a novel method to elicit SSVEP responses exploiting the stereoscopic displays capability of presenting dichoptic stimuli. We have created an experimental scene to present flickering stimuli on an active stereoscopic display, obtaining reliable control of the targets' frequency independently for the two stereo views. Using an EEG acquisition device, we analyzed the SSVEP responses from a group of subjects. From the preliminary results, we got evidence that stereoscopic displays represent valid devices for the presentation of SSVEP stimuli. Moreover, the use of different flickering frequencies for the two views of a single stimulus proved to elicit non-linear interactions between the stimulation frequencies, clearly visible in the EEG signal. This suggests interesting applications for SSVEP-based BCIs in VR environments able to overcome some limitations imposed by the refresh frequency of standard displays, but also the use of commodity stereoscopic displays to implement binocular rivalry experiments

Quality of Life and psychopathology in adults who underwent Hematopoietic Stem Cell Transplantation (HSCT) in childhood: a qualitative and quantitative analysis.

Background: Patients who undergo pediatric Hematopoietic Stem Cell Transplantation (HSCT) may experience long-term psychological sequelae and poor Quality of Life (QoL) in adulthood. This study aimed to investigate subjective illness experience, QoL, and psychopathology in young adults who have survived pediatric HSCT. Method: The study involved patients treated with HSCT in the Hematology-Oncology Department between 1984 and 2007. Psychopathology and QoL were investigated using the SCL-90-R and SF-36. Socio-demographic and medical information was also collected. Finally, participants were asked to write a brief composition about their experiences of illness and care. Qualitative analysis of the texts was performed using T-LAB, an instrument for text analysis that allows the user to highlight the occurrences and co-occurrences of lemma. Quantitative analyses were performed using non-parametric tests (Spearman correlations, Kruskal-Wallis and Mann-Whitney tests). Results: Twenty-one patients (9 males) participated in the study. No significant distress was found on the SCL-90 Global Severity Index, but it was found on specific scales. On the SF-36, lower scores were reported on scales referring to bodily pain, general health, and physical and social functioning. All the measures were significantly (p < 0.05) associated with specific socio-demographic and medical variables (gender, type of pathology, type of HSCT, time elapsed between communication of the need to transplant and effective transplantation, and days of hospitalization). With regard to the narrative analyses, males focused on expressions related to the body and medical therapies, while females focused on people they met during treatment, family members, and donors. Low general health and treatment with autologous HSCT were associated with memories about chemotherapy, radiotherapy, and the body parts involved, while high general health was associated with expressions focused on gratitude (V-Test \ub1 1.96). Conclusion: Pediatric HSCT survivors are more likely to experience psychological distress and low QoL in adulthood compared with the general population. These aspects, along with survivors' subjective illness experience, show differences according to specific medical and socio-demographic variables. Studies are needed in order to improve the care and long-term follow-up of these families

Genetic modifiers of Duchenne muscular dystrophy and dilated cardiomyopathy

OBJECTIVE: Dilated cardiomyopathy (DCM) is a major complication and leading cause of death in Duchenne muscular dystrophy (DMD). DCM onset is variable, suggesting modifier effects of genetic or environmental factors. We aimed to determine if polymorphisms previously associated with age at loss of independent ambulation (LoA) in DMD (rs28357094 in the SPP1 promoter, rs10880 and the VTTT/IAAM haplotype in LTBP4) also modify DCM onset. METHODS: A multicentric cohort of 178 DMD patients was genotyped by TaqMan assays. We performed a time-to-event analysis of DCM onset, with age as time variable, and finding of left ventricular ejection fraction 70 mL/m2 as event (confirmed by a previous normal exam < 12 months prior); DCM-free patients were censored at the age of last echocardiographic follow-up. RESULTS: Patients were followed up to an average age of 15.9 \ub1 6.7 years. Seventy-one/178 patients developed DCM, and median age at onset was 20.0 years. Glucocorticoid corticosteroid treatment (n = 88 untreated; n = 75 treated; n = 15 unknown) did not have a significant independent effect on DCM onset. Cardiological medications were not administered before DCM onset in this population. We observed trends towards a protective effect of the dominant G allele at SPP1 rs28357094 and recessive T allele at LTBP4 rs10880, which was statistically significant in steroid-treated patients for LTBP4 rs10880 (< 50% T/T patients developing DCM during follow-up [n = 13]; median DCM onset 17.6 years for C/C-C/T, log-rank p = 0.027). CONCLUSIONS: We report a putative protective effect of DMD genetic modifiers on the development of cardiac complications, that might aid in risk stratification if confirmed in independent cohorts

Matching microscopic and macroscopic responses in glasses

We first reproduce on the Janus and Janus II computers a milestone experiment that measures the spin-glass coherence length through the lowering of free-energy barriers induced by the Zeeman effect. Secondly we determine the scaling behavior that allows a quantitative analysis of a new experiment reported in the companion Letter [S. Guchhait and R. Orbach, Phys. Rev. Lett. 118, 157203 (2017)]. The value of the coherence length estimated through the analysis of microscopic correlation functions turns out to be quantitatively consistent with its measurement through macroscopic response functions. Further, non-linear susceptibilities, recently measured in glass-forming liquids, scale as powers of the same microscopic length.Comment: 6 pages, 4 figure