2,443 research outputs found
NaNet: a Low-Latency, Real-Time, Multi-Standard Network Interface Card with GPUDirect Features
While the GPGPU paradigm is widely recognized as an effective approach to
high performance computing, its adoption in low-latency, real-time systems is
still in its early stages.
Although GPUs typically show deterministic behaviour in terms of latency in
executing computational kernels as soon as data is available in their internal
memories, assessment of real-time features of a standard GPGPU system needs
careful characterization of all subsystems along data stream path.
The networking subsystem results in being the most critical one in terms of
absolute value and fluctuations of its response latency.
Our envisioned solution to this issue is NaNet, a FPGA-based PCIe Network
Interface Card (NIC) design featuring a configurable and extensible set of
network channels with direct access through GPUDirect to NVIDIA Fermi/Kepler
GPU memories.
NaNet design currently supports both standard - GbE (1000BASE-T) and 10GbE
(10Base-R) - and custom - 34~Gbps APElink and 2.5~Gbps deterministic latency
KM3link - channels, but its modularity allows for a straightforward inclusion
of other link technologies.
To avoid host OS intervention on data stream and remove a possible source of
jitter, the design includes a network/transport layer offload module with
cycle-accurate, upper-bound latency, supporting UDP, KM3link Time Division
Multiplexing and APElink protocols.
After NaNet architecture description and its latency/bandwidth
characterization for all supported links, two real world use cases will be
presented: the GPU-based low level trigger for the RICH detector in the NA62
experiment at CERN and the on-/off-shore data link for KM3 underwater neutrino
telescope
GPU-based Real-time Triggering in the NA62 Experiment
Over the last few years the GPGPU (General-Purpose computing on Graphics
Processing Units) paradigm represented a remarkable development in the world of
computing. Computing for High-Energy Physics is no exception: several works
have demonstrated the effectiveness of the integration of GPU-based systems in
high level trigger of different experiments. On the other hand the use of GPUs
in the low level trigger systems, characterized by stringent real-time
constraints, such as tight time budget and high throughput, poses several
challenges. In this paper we focus on the low level trigger in the CERN NA62
experiment, investigating the use of real-time computing on GPUs in this
synchronous system. Our approach aimed at harvesting the GPU computing power to
build in real-time refined physics-related trigger primitives for the RICH
detector, as the the knowledge of Cerenkov rings parameters allows to build
stringent conditions for data selection at trigger level. Latencies of all
components of the trigger chain have been analyzed, pointing out that
networking is the most critical one. To keep the latency of data transfer task
under control, we devised NaNet, an FPGA-based PCIe Network Interface Card
(NIC) with GPUDirect capabilities. For the processing task, we developed
specific multiple ring trigger algorithms to leverage the parallel architecture
of GPUs and increase the processing throughput to keep up with the high event
rate. Results obtained during the first months of 2016 NA62 run are presented
and discussed
ReconïŹgurable PCI Express cards for low-latency data transport in HEP experiments
State-of-the-art technology supports the High Energy Physics community in addressing the problem of managing an overwhelming amount of experimental data. From the point of view of communication between the detectorsâ readout system and computing nodes, the critical issues are the following: latency, moving data in a deterministic and low amount of time; bandwidth, guaranteeing the maximum capability of the link and communication protocol adopted; endpoint consolidation, tight aggregation of channels on a single board. This contribution describes the status and performances of the NaNet project, whose goal is the design of a family of FPGA-based PCIe network interface cards. The eïŹorts of the team are focused on implementing a low-latency, real-time data transport mechanism between the board network multi-channel system and CPU and GPU accelerators memories on the host. Several opportunities concerning technical solutions and scientiïŹc applications have been explored: NaNet-1 with a single GbE I/O interface, and NaNet-10, oïŹering four 10GbE ports, for activities related to the GPU-based real-time trigger of NA62 experiment at CERN; NaNet3, with four 2.5Gbit optical channels, developed for the KM3NeT-ITALIA underwater neutrino telescope
Science AMA Series: Antarctic Peninsula Paleontology Project
Transcript of an online colloquium between members of the APPP expedition and readers of the online bulletin board Reddit
The Emerging Role of Ofatumumab in the Treatment of Chronic Lymphocytic Leukemia
The treatment of chronic lymphocytic leukemia (CLL) has evolved over the past decade. Our better understanding of disease biology and risk stratification has allowed delivering more effective therapies. In fact, front-line chemoimmunotherapy has demonstrated improvement in overall survival when compared to chemotherapy in randomized studies. Yet, treatment of relapsed CLL remains challenging and few agents are effective in that setting. Ofatumumab (Ofa) is a humanized monoclonal antibody targeted against CD20 with demonstrable activity in rituximab-resistant CLL cell lines. This agent was recently approved for the treatment of relapsed/refractory CLL patients who have failed fludarabine and alemtuzumab. In this review, we provide a historical perspective on approaches to CLL as front-line and in the relapsed setting. We further summarize novel anti-CD20 antibodies with specific emphasis on ofa. We review studies that led to ofatumumabâs approval including pre-clinical data, trials using ofa in combination therapies, and adverse events/toxicities reported with this agent
NectarCAM : a camera for the medium size telescopes of the Cherenkov Telescope Array
NectarCAM is a camera proposed for the medium-sized telescopes of the
Cherenkov Telescope Array (CTA) covering the central energy range of ~100 GeV
to ~30 TeV. It has a modular design and is based on the NECTAr chip, at the
heart of which is a GHz sampling Switched Capacitor Array and a 12-bit Analog
to Digital converter. The camera will be equipped with 265 7-photomultiplier
modules, covering a field of view of 8 degrees. Each module includes the
photomultiplier bases, high voltage supply, pre-amplifier, trigger, readout and
Ethernet transceiver. The recorded events last between a few nanoseconds and
tens of nanoseconds. The camera trigger will be flexible so as to minimize the
read-out dead-time of the NECTAr chips. NectarCAM is designed to sustain a data
rate of more than 4 kHz with less than 5\% dead time. The camera concept, the
design and tests of the various subcomponents and results of thermal and
electrical prototypes are presented. The design includes the mechanical
structure, cooling of the electronics, read-out, clock distribution, slow
control, data-acquisition, triggering, monitoring and services.Comment: In Proceedings of the 34th International Cosmic Ray Conference
(ICRC2015), The Hague, The Netherlands. All CTA contributions at
arXiv:1508.0589
Progress report on the online processing upgrade at the NA62 experiment
A new FPGA-based low-level trigger processor has been installed at the NA62 experiment. It is intended to extend the features of its predecessor due to a faster interconnection technology and additional logic resources available on the new platform. With the aim of improving trigger selectivity and exploring new architectures for complex trigger computation, a GPU system has been developed and a neural network on FPGA is in progress. They both process data streams from the ring imaging Cherenkov detector of the experiment to extract in real time high level features for the trigger logic. Description of the systems, latest developments and design flows are reported in this paper
The camera of the fifth H.E.S.S. telescope. Part I: System description
In July 2012, as the four ground-based gamma-ray telescopes of the H.E.S.S.
(High Energy Stereoscopic System) array reached their tenth year of operation
in Khomas Highlands, Namibia, a fifth telescope took its first data as part of
the system. This new Cherenkov detector, comprising a 614.5 m^2 reflector with
a highly pixelized camera in its focal plane, improves the sensitivity of the
current array by a factor two and extends its energy domain down to a few tens
of GeV.
The present part I of the paper gives a detailed description of the fifth
H.E.S.S. telescope's camera, presenting the details of both the hardware and
the software, emphasizing the main improvements as compared to previous
H.E.S.S. camera technology.Comment: 16 pages, 13 figures, accepted for publication in NIM
Glycomics Analysis of Mammalian Heparan Sulfates Modified by the Human Extracellular Sulfatase HSulf2
The Sulfs are a family of endosulfatases that selectively modify the 6O-sulfation state of cell-surface heparan sulfate (HS) molecules. Sulfs serve as modulators of cell-signaling events because the changes they induce alter the cell surface co-receptor functions of HS chains. A variety of studies have been aimed at understanding how Sulfs modify HS structure, and many of these studies utilize Sulf knockout cell lines as the source for the HS used in the experiments. However, genetic manipulation of Sulfs has been shown to alter the expression levels of HS biosynthetic enzymes, and in these cases an assessment of the fine structural changes induced solely by Sulf enzymatic activity is not possible. Therefore, the present work aims to extend the understanding of substrate specificities of HSulf2 using in vitro experiments to compare HSulf2 activities on HS from different organ tissues.To further the understanding of Sulf enzymatic activity, we conducted in vitro experiments where a variety of mammalian HS substrates were modified by recombinant human Sulf2 (HSulf2). Subsequent to treatment with HSulf2, the HS samples were exhaustively depolymerized and analyzed using size-exclusion liquid chromatography-mass spectrometry (SEC-LC/MS). We found that HSulf2 activity was highly dependent on the structural features of the HS substrate. Additionally, we characterized, for the first time, the activity of HSulf2 on the non-reducing end (NRE) of HS chains. The results indicate that the action pattern of HSulf2 at the NRE is different compared to internally within the HS chain.The results of the present study indicate that the activity of Sulfs is dependent on the unique structural features of the HS populations that they edit. The activity of HSulf2 at HS NREs implicates the Sulfs as key regulators of this region of the chains, and concomitantly, the protein-binding events that occur there
Active surveillance in renal transplant patients with prostate cancer: a multicentre analysis
Introduction: Due to medical improvements leading to increased life expectancy after renal transplantation and widened eligibility criteria allowing older patients to be transplanted, incidence of (low-risk) prostate cancer (PCa) is increasing among renal transplant recipients (RTR). It remains to be established whether active surveillance (AS) for PCa represents a safe treatment option in this setting. Therefore, we aim to compare AS discontinuation and oncological outcomes of AS for PCa of RTR vs. non-transplant patients. Methods: Multicentre study including RTR diagnosed with PCa between 2008 and 2018 in whom AS was initiated. A subgroup of non-RTR from the St. Antonius hospital AS cohort was used as a control group. Comparison of RTR vs. non-RTR was performed by 2:1 propensity score matched survival analysis. Outcome measures included tumour progression-free survival, treatment-free survival, metastasis rates, biochemical recurrence rates and overall survival. Patients were matched based on age, year of diagnosis, PSA, biopsy ISUP grade group, relative number of positive biopsy cores and clinical stage. Results: A total of 628 patients under AS were evaluated, including 17 RTRs and 611 non-RTRs. A total of 13 RTR cases were matched with 24 non-RTR cases. Median overall follow-up for the RTR and non-RTR matched cases was, respectively, 5.1 (IQR 3.2â8.7) years and 5.7 (IQR 4.8â8.1) years. There were no events of metastasis and biochemical recurrence among matched cases. The matched-pair analysis results in a 1-year and 5-year survival of the RTR and non-RTR patients were, respectively, 100 vs. 92%, and 39 vs. 76% for tumour progression, 100 vs. 91% and 59 vs. 76% for treatment-free survival and, respectively, 100 vs. 100% and 88 vs. 100% for overall survival. No significant differences in tumour progression-free survival (p = 0.07) and treatment-free survival were observed (p = 0.3). However, there was a significant difference in overall survival comparing both groups (p = 0.046). Conclusions: AS may be carefully considered in RTR with low-risk PCa. In our preliminary analysis, no major differences were present in AS outcomes between RTR and non-RTR. Overall mortality was significantly higher in the RTR subgroup
- âŠ