Numerical Simulations of the Dynamical Behavior of the SK Model

We study the dynamical behavior of the Sherrington Kirkpatrick model. Thanks to the APE supercomputer we are able to analyze large lattice volumes, and to investigate the low $T$ region. We present a determination of the remnant magnetization and of its time decay exponent, of the energy time decay exponent, and we discuss aging phenomena in the model.Comment: 11 pages including 8 figures. Revised version with major restructurin

APEnet+: a 3D toroidal network enabling Petaflops scale Lattice QCD simulations on commodity clusters

Many scientific computations need multi-node parallelism for matching up both space (memory) and time (speed) ever-increasing requirements. The use of GPUs as accelerators introduces yet another level of complexity for the programmer and may potentially result in large overheads due to the complex memory hierarchy. Additionally, top-notch problems may easily employ more than a Petaflops of sustained computing power, requiring thousands of GPUs orchestrated with some parallel programming model. Here we describe APEnet+, the new generation of our interconnect, which scales up to tens of thousands of nodes with linear cost, thus improving the price/performance ratio on large clusters. The project target is the development of the Apelink+ host adapter featuring a low latency, high bandwidth direct network, state-of-the-art wire speeds on the links and a PCIe X8 gen2 host interface. It features hardware support for the RDMA programming model and experimental acceleration of GPU networking. A Linux kernel driver, a set of low-level RDMA APIs and an OpenMPI library driver are available, allowing for painless porting of standard applications. Finally, we give an insight of future work and intended developments

GPU peer-to-peer techniques applied to a cluster interconnect

Modern GPUs support special protocols to exchange data directly across the PCI Express bus. While these protocols could be used to reduce GPU data transmission times, basically by avoiding staging to host memory, they require specific hardware features which are not available on current generation network adapters. In this paper we describe the architectural modifications required to implement peer-to-peer access to NVIDIA Fermi- and Kepler-class GPUs on an FPGA-based cluster interconnect. Besides, the current software implementation, which integrates this feature by minimally extending the RDMA programming model, is discussed, as well as some issues raised while employing it in a higher level API like MPI. Finally, the current limits of the technique are studied by analyzing the performance improvements on low-level benchmarks and on two GPU-accelerated applications, showing when and how they seem to benefit from the GPU peer-to-peer method.Comment: paper accepted to CASS 201

NaNet:a low-latency NIC enabling GPU-based, real-time low level trigger systems

We implemented the NaNet FPGA-based PCI2 Gen2 GbE/APElink NIC, featuring GPUDirect RDMA capabilities and UDP protocol management offloading. NaNet is able to receive a UDP input data stream from its GbE interface and redirect it, without any intermediate buffering or CPU intervention, to the memory of a Fermi/Kepler GPU hosted on the same PCIe bus, provided that the two devices share the same upstream root complex. Synthetic benchmarks for latency and bandwidth are presented. We describe how NaNet can be employed in the prototype of the GPU-based RICH low-level trigger processor of the NA62 CERN experiment, to implement the data link between the TEL62 readout boards and the low level trigger processor. Results for the throughput and latency of the integrated system are presented and discussed.Comment: Proceedings for the 20th International Conference on Computing in High Energy and Nuclear Physics (CHEP

Anti-Vascular Endothelial Growth Factors Protect Retinal Pigment Epithelium Cells Against Oxidation by Modulating Nitric Oxide Release and Autophagy

Background/Aims: the anti-vascular endothelial growth factors (VEGF), Aflibercept and Ranibizumab, are used for the treatment of macular degeneration. Here we examined the involvement of nitric oxide (NO), mitochondria function and of apoptosis/autophagy in their antioxidant effects in human retinal pigment epithelium cells (RPE). Methods: RPE were exposed to Ranibizumab/Aflibercept in the absence or presence of NO synthase (NOS) inhibitor and of autophagy activator/blocker, rapamicyn/3-methyladenine. Specific kits were used for cell viability, NO and reactive oxygen species detection and mitochondrial membrane potential measurement, whereas Western Blot was performed for apoptosis/ autophagy markers and other kinases detection. Results: In RPE cultured in physiological conditions, Aflibercept/Ranibizumab increased NO release in a dose and time-dependent way. Opposite results were obtained in RPE pretreated with hydrogen peroxide. Moreover, both the anti-VEGF agents were able to prevent the fall of cell viability and of mitochondrial membrane potential. Those effects were reduced by the NOS inhibitor and 3-methyladenine and were potentiated by rapamycin. Finally, Aflibercept and Ranibizumab counteracted the changes of apoptosis/autophagy markers, NOS, Phosphatidylinositol-3-Kinase/Protein Kinase B and Extracellular signal–regulated kinases 1/2 caused by peroxidation. Conclusion: Aflibercept and Ranibizumab protect RPE against peroxidation through the modulation of NO release, apoptosis and autophagy

Three-dimensional facial morphometry in patients rehabilitated with implant-supported prostheses

The aim of the present study was to assess a low-cost, non-invasive facial morphometric digitizer to assist the practitioner in three-dimensional soft-tissue changes before and after oral rehabilitation. The method should provide quantitative data to support an objective assessment of the facial esthetic outcome [1]. Twenty-two patients aged 45-82 years, all with edentulous maxilla and mandible, were assessed both before and after receiving their definitive complete implant-supported prostheses (each received 4-11 implants in each dental arch; full-arch fixed prostheses were made). The three-dimensional coordinates of 50 soft-tissue facial landmarks were collected with a non-invasive digitizer; labial and facial areas, volumes, angles and distances were compared without/ with the prostheses [2]. Dental prostheses induced significant reductions in the nasolabial, mentolabial and interlabial angles, with increased labial prominence (p<0.05, Wilcoxon test). Lip vermilion area and volume significantly increased; significant increments were found in the vertical and anteroposterior labial dimensions. The presence of the dental prostheses significantly (p<0.001) modified the three-dimensional positions of several soft-tissue facial landmarks. The current approach enabled quantitative evaluation of the final soft-tissue results of oral rehabilitation with implant-supported prostheses, without submitting the patients to invasive procedures. The method could assess the three-dimensional appearance of the facial soft tissues of the patient while planning the provisional prosthetic restoration, providing quantitative information to prepare the best definitive prosthesis. Dote ricerca: FSE, Regione Lombardi