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D9.3.3: Report on prototypes evaluation

Lennart Johnsson, Gilbert Netzer
2013 Zenodo  
The objective of Work Package 9 task 3 is to assess and make recommendations to the PRACE RI for joint developments with industrial partners to develop highly energy efficient HPC components and systems, as well as power and cooling technologies. WP9 has carried out this task through evaluation of a number of prototypes targeting novel approaches to HPC server and system design with many prototypes having some degree of direct industry involvement or support. Prototype efforts assessed the use
more » ... f FPGAs for function acceleration, the use of CPUs for the mobile market and with a TDP about two orders of magnitude less than typical x86 CPUs for the HPC market, DSPs common for embedded systems and with a TDP about one order of magnitude less than x86 CPUs, the emerging heterogeneous CPUs integrating x86 and GPU cores, and traditional GPUs with a novel direct communication between GPUs via Infiniband between nodes. Two prototypes focused on novel approaches to scalability of I/O systems in support of Exascale systems and their energy efficiency. Technologies assessed included integration of I/O nodes into the MPP or cluster interconnect fabric, the use of flash technology, scalable disk systems and virtual tape libraries based on disk systems with spun down idle disks. Data management in file systems, in particular the management of large numbers of small files, was also addressed with the I/O-prototypes. One prototype evaluation assessed the issues and benefits of integrated cooling solutions for hot water cooling. The findings of the evaluations of prototypes looking at HPC server architectures is that 1) an optimized FPGA implementation of matrix-multiplication can offer a 5 – 10 times higher energy efficiency than an x86 software solution, 2) an optimized implementation of matrix multiplication on the DSP can yield about half the energy efficiency gain of an FPGA implementation, 3) the first and second generation x86+GPU CPUs are not competitive in regards to energy efficiency even with standard x86 CPUs fo [...]
doi:10.5281/zenodo.6553033 fatcat:nvxbrlq5jzdfhbkh5fde3kpl4e

D9.3.4: Final Report on Prototype Evaluation

Lennart Johnsson, Gilbert Netzer
2013 Zenodo  
This report supplements deliverable D9.3.3 and covers future technology prototype efforts from March 2013. Three prototype efforts not reported on in D9.3.3 are fully reported here: the ARM based NVidia Tegra3 with NVidia Kepler GPU acceleration prototype at BSC; the energy recovery prototype using immersive cooling techniques at PSNC; and the results from the Advanced Multi-level Fault Tolerant prototype. Additional results are provided for the x86+GPU prototype at CaSToRC, the DSP prototype
more » ... SNIC/KTH, and the energy recovery prototype at LRZ. The DSP results show that for the benchmarks that were well optimised the observed energy efficiency for the DSP was in line with the nominal energy efficiency that can be derived from specifications. Thus, the energy efficiency is comparable to that of GPUs and better than that of x86 CPUs. Furthermore, the DSP does not require a host processor. In fact, the 40 nm DSP used is, for the optimised benchmarks, more energy efficient than correspondingly optimised codes for the 22 nm Intel Ivy Bridge. ARM Coretx-A9 CPUs are not energy efficient for HPC workloads, but nodes using powerful and energy efficient acceleration, such as the NVidia Kepler, can form part of a viable HPC node. Due to late delivery of the relevant prototype only preliminary results are available at this time. The shared memory prototype is based on standard x86 servers and a node add-in card for cache coherency. This prototype clearly demonstrated that, though a very large shared memory address space is supported, it is a NUMA architecture and paying proper attention to the memory architecture is necessary for good performance. One of the lessons learnt in the project is that delivering energy efficiency advantages for architectures different from x86 architectures requires well-optimised codes also for the non- x86 architectures, i.e. for significant energy efficiency gains at the application level resource use [...]
doi:10.5281/zenodo.6553060 fatcat:psgnqsx7ovf6rijtocssmdavsm

BioExcel Deliverable D1.4 - Long-term hardware software assessment for pilot applications and general community

Mark Abraham, Paul Bauer, Christian Blau, Erik Lindahl, Gilbert Netzer, Erwin Laure, Mikael Trellet, Adrien Melquiond, Emiliano Ippoliti, Vytautas Gapsys
2019 Zenodo  
Future software and hardware development will have a significant impact on all areas of scientific computing including the Life Sciences. Upcoming extreme-scale compute platforms will offer great opportunities for tackling important, large- scale scientific questions. In this document we update our previous analysis of the pre-exascale landscape from the perspective of biomolecular simulation software, including the pilot codes of BioExcel. These are largely unchanged from our previous
more » ... le 1.3 in this area, and so this report takes the form of an update to that report. Our findings are generally unchanged, and already well publicized among the European HPC stakeholders via several working groups which are involved in the development of EuroHPC, the newly updated PRACE Scientific Case, the ETP4HPC Strategic Research Agenda, and the EXDCI ( project in which BioExcel is leading the Life Science working group. Bio-molecular simulation scientists in industry and academe require effective and usable simulation software that runs well on the hardware resources they can access now. This software must be portable to emerging platforms, because we cannot afford to replace it to run well at the exascale. When we achieve this, we will be able to support the design of new drugs on scales impossible today, obtain better understanding of biochemical pathways, and open new doors for further innovation. This deliverable gives an overview of what we currently see as potential directions and then implementation plans for each of the pilot codes that will suit those directions.
doi:10.5281/zenodo.3563747 fatcat:k3ywsgsih5d6dkqnubzufabknu

Statins as anti-inflammatory agents: A potential therapeutic role in sight-threatening non-infectious uveitis

Rose Gilbert, Ahmed Al-Janabi, Oren Tomkins-Netzer, Sue Lightman
2017 Porto Biomedical Journal  
In addition to the known lipid-lowering effects, statins are now widely accepted to have anti-inflammatory and immunomodulatory effects. Adjunctive use of statins has proven beneficial in the context of a wide range of inflammatory diseases, including rheumatoid arthritis. Evidence also suggests that statins may also have utility in the management of uveitis, a form of sight threatening inflammation which occurs in the eye. In this article, we outline our rationale behind a clinical trial of
more » ... vastatin as a steroid-sparing agent in uveitis, to which patient recruitment started last year. Potential risks associated with the clinical use of statins, including putative effects on the eyes, are discussed.
doi:10.1016/j.pbj.2017.01.006 pmid:32258583 pmcid:PMC6806973 fatcat:poswmjpvxrgmvmzqihe2tnr7ou

Clinical Remission of Sight-Threatening Non-Infectious Uveitis Is Characterized by an Upregulation of Peripheral T-Regulatory Cell Polarized Towards T-bet and TIGIT

Rose M. Gilbert, Xiaozhe Zhang, Robert D. Sampson, Michael R. Ehrenstein, Dao X. Nguyen, Mahid Chaudhry, Charles Mein, Nadiya Mahmud, Grazyna Galatowicz, Oren Tomkins-Netzer, Virginia L. Calder, Sue Lightman
2018 Frontiers in Immunology  
Treg from patients in clinical remission demonstrated a 2 Gilbert et al.  ...  Peripheral blood TIGIT + Treg levels in the study population of patients with uveitis had a sensitivity of 92%, a specificity of 62%, a false positive rate 14 Gilbert et al.  ... 
doi:10.3389/fimmu.2018.00907 pmid:29774027 pmcid:PMC5943505 fatcat:giz3fmrdfzfmzpbbkrptgozoiu

Central Masses and Broad‐Line Region Sizes of Active Galactic Nuclei. II. A Homogeneous Analysis of a Large Reverberation‐Mapping Database

B. M. Peterson, L. Ferrarese, K. M. Gilbert, S. Kaspi, M. A. Malkan, D. Maoz, D. Merritt, H. Netzer, C. A. Onken, R. W. Pogge, M. Vestergaard, A. Wandel
2004 Astrophysical Journal  
This is done because the distributions of these values are rarely even approximately Gaussian ( Maoz & Netzer 1989) .  ...  However, observed SEDs suggest that a smaller ratio, e.g., L bol % 5kL k (Netzer 2003) , may be on average more appropriate.  ... 
doi:10.1086/423269 fatcat:odcwbor5bventnhl4sr2xdlrga

Page 23 of Australian Journal of Otolaryngology Vol. 6, Issue 1 [page]

2003 Australian Journal of Otolaryngology  
., NETZER A., JOACHIMS H.Z., WESTERMAN S.T., GILBERT L.M. VTs and persisting tympanic membrane perforations Otolaryngol Head and Neck Surg 1999; 120: 524-527 6. STRACHAN D., HOPE G., HUSSAIN M.  ... 

Page 104 of Florida Bar Journal Vol. 32, Issue 7 [page]

1958 Florida Bar Journal  
Gelber, Seymour Genet, Martinf Genet, Saulf Gertler, Charles Gifford, Paul Edward Gilbert, George Gilbert, Robert R. Glaser, Leonard L. Glosser. William L. Godbold, Walter E.  ...  Nemser, Arthur M.f Netzer, William B. Newman, Godfrey K. Newman, Joel P. Oka, Kenneth Parker, Eugene Pearlman, Samuel B. Perkins, Julian Preston Gear Perlman, Clifford S.  ... 

Page 435 of Review of Educational Research Vol. 20, Issue 5 [page]

1950 Review of Educational Research  
Gilbert Mississippi Mitchell, Guy C. Phay, John E. Schmidt, Bernardine G. Segner, Esther F. Missouri Brown, Edwin J. Byerly, Carl L. Carpenter, W. W. Gilbert, Arthur W. Holland, Clement Johnson, B.  ...  Netzer, Royal F. Nifenecker, Eugene A. Norton, John K. Orleans, Jacob S. Pace, C. Robert Parke, Margaret B. Pastore, Nicholas Pease, Katharine Poruben, Adam, Jr. Powers, S. Ralph Rivlin, Harry N.  ... 

Page 271 of The American Economic Review Vol. 51, Issue 1 [page]

1961 The American Economic Review  
Milton Gilbert, Organisation for European Economic Co-operation, Paris: economic adviser, The Bank for International Settlements, Basle. Albert L.  ...  Dick Netzer, Federal Reserve Bank of Chicago: economic consultant, Regional Plan Association, Inc. Egon Neuberger : economist, The RAND Corporation.  ... 

Page 387 of The Journal of Educational Research Vol. 30, Issue 5 [page]

1937 The Journal of Educational Research  
Netzer, Royal Franklin. ‘‘ The Evalu- ation of a Technique for Measur- ing Improvement in Oral Composi- tion.’’ Iowa. Greene. 3.  ...  Gilbert. Morgan, John William, ‘‘ The Origin ind Distribution of the Graduates of the Negro Colleges of Geor- gia.’’ Columbia, Brunner.  ... 

Page 551 of Review of Educational Research Vol. 28, Issue 5 [page]

1958 Review of Educational Research  
Nesi, Carmella Netzer, Royal F. North, Robert D., Jr. Norton, John K. Oliverio, Mary Ellen Orshansky, Bernice Pace, C. Robert Parke, Margaret B. Passow, A. Harry Phillips, Murray G.  ...  Benz, Harry Betts, Gilbert L. Bollenbacher, Joan Buddemeyer, Guy W. Caskey, Helen Crossen Collings, Miller R. Edmiston, Robert W. Flesher, Mrs. Marie A. Flesher, William R. Garofalo, Marius P.  ... 

What the Optical Recombination Lines Can Tell Us about the Broad‐Line Regions of Active Galactic Nuclei

Kirk T. Korista, Michael R. Goad
2004 Astrophysical Journal  
, & Ferland (1989; see also Netzer 1975) .  ...  This is primarily due to the increasing populations and thus optical depths in the excited states of hydrogen and helium with increasing continuum flux (Netzer 1975; Netzer 1978; Ferland, Netzer, & Shields  ... 
doi:10.1086/383193 fatcat:txzyyyi4ezdl3pkyvfqgf6crzu

The difference with prokaryotes

Mary-Jane Gething
1997 Nature  
This is where the new work of Netzer and Hartl 1 comes in.  ...  Gilbert, G. K. US Geol. Surv. Prof. Pap. 105 (Gov. Print. Office, Washington DC, 1917). 9. Montgomery, D. R., Buffington, J. M., Smith, R., Schmidt, K. M. & Pess, G. Wat. Resour.  ... 
doi:10.1038/40979 pmid:9237748 fatcat:2lp2uccvsve23omdmwzdnkacia

Page 602 of Review of Educational Research Vol. 27, Issue 5 [page]

1957 Review of Educational Research  
Nesi, Carmella Netzer, Royal F. North, Robert D., Jr. Norton, John K. Oliverio, Mary Ellen Orshansky, Bernice Pace, C. Robert Parke, Margaret B. Passow, A. Harry Phillips, Murray G.  ...  Betts, Gilbert L. Bollenbacher, Joan Bonham, Samuel J., Jr. Buddemeyer, Guy W. Caskey, Helen Crossen Collings, Miller R. Conrad, M. J. 3 Dale, Edgar Edmiston, Robert W. Flesher, Mrs. Marie A.  ... 
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