Data placement in HPC architectures with heterogeneous off-chip memory

The performance of HPC applications is often bounded by the underlying memory system's performance. The trend of increasing the number of cores on a chip imposes even higher memory bandwidth and capacity requirements. The limitations of traditional memory technologies are pushing research in the direction of hybrid memory systems that, besides DRAM, include one or more modules based on some of the higher-density non-volatile memory technologies, where one of them will provide the required bandwidth, while the other will provide the required capacity for the application. This creates many challenges with data placement and migration policies between the modules of such hybrid memory system. In this paper, we propose an architecture with a hybrid memory design that places two technologically different memory modules in a flat address space. On such system, we evaluate several HPC workloads against different data placement and migration policies, compare their performance by means of execution time and the number of non-volatile memory writes, and consider how it can be applied to the future HPC architectures. Our results show that the hybrid memory system with dynamic page migration and limited DRAM capacity, can achieve performance that is comparable to a hypothetical, hard to implement, DRAM-only system.Postprint (published version

Main memory in HPC: do we need more, or could we live with less?

An important aspect of High-Performance Computing (HPC) system design is the choice of main memory capacity. This choice becomes increasingly important now that 3D-stacked memories are entering the market. Compared with conventional Dual In-line Memory Modules (DIMMs), 3D memory chiplets provide better performance and energy efficiency but lower memory capacities. Therefore, the adoption of 3D-stacked memories in the HPC domain depends on whether we can find use cases that require much less memory than is available now. This study analyzes the memory capacity requirements of important HPC benchmarks and applications. We find that the High-Performance Conjugate Gradients (HPCG) benchmark could be an important success story for 3D-stacked memories in HPC, but High-Performance Linpack (HPL) is likely to be constrained by 3D memory capacity. The study also emphasizes that the analysis of memory footprints of production HPC applications is complex and that it requires an understanding of application scalability and target category, i.e., whether the users target capability or capacity computing. The results show that most of the HPC applications under study have per-core memory footprints in the range of hundreds of megabytes, but we also detect applications and use cases that require gigabytes per core. Overall, the study identifies the HPC applications and use cases with memory footprints that could be provided by 3D-stacked memory chiplets, making a first step toward adoption of this novel technology in the HPC domain.This work was supported by the Collaboration Agreement between Samsung Electronics Co., Ltd. and BSC, Spanish Government through Severo Ochoa programme (SEV-2015-0493), by the Spanish Ministry of Science and Technology through TIN2015-65316-P project and by the Generalitat de Catalunya (contracts 2014-SGR-1051 and 2014-SGR-1272). This work has also received funding from the European Union’s Horizon 2020 research and innovation programme under ExaNoDe project (grant agreement No 671578). Darko Zivanovic holds the Severo Ochoa grant (SVP-2014-068501) of the Ministry of Economy and Competitiveness of Spain. The authors thank Harald Servat from BSC and Vladimir Marjanovi´c from High Performance Computing Center Stuttgart for their technical support.Postprint (published version

Influence of the COVID-19 pandemic on the incidence of tuberculosis and influenza

We examined whether the COVID-19 pandemic has affected the incidence of tuberculosis (TB) and influenza in Serbia, a Southeast European country with a low TB incidence rate and a mandatory BCG vaccination at birth. The first case of COVID-19 was registered on March 6, 2020. Despite the need for a sudden adaptation of the health care system, routines of mycobacterial laboratories have never stopped. In 2020, the number of newly diagnosed TB patients was significantly lower than expected (p = 0.04), but the number of patients with influenza increased when compared to 2019. Although many patients with influenza A H1N1 were observed before the beginning of the COVID-19 pandemic, the increment of cases could also be a consequence of cases of influenza with COVID-like symptoms detected thereafter. It may also be attributed to misclassification of clinical cases that were negative for SARS-CoV-2 and reported as influenza. Difficulties to seek medical attention because of the COVID-19 pandemic and possible underreporting are considered as reasons for the decline in the incidence rate of TB. On the other hand, individual and social measures to prevent the spread of SARS-CoV-2 such as wearing face masks, social distancing, lockdown, which were strictly applied to COVID-19 patients, health care staffs and most of the population, could have hindered TB infections more than the two viral diseases, which appear to be more contagious. The increased motivation of the population to protect their health during the COVID-19 pandemic provided an opportunity for their effective education. This is crucial in further combating TB as a preventable disease

Performance impact of a slower main memory: a case study of STT-MRAM in HPC

In high-performance computing (HPC), significant effort is invested in research and development of novel memory technologies. One of them is Spin Transfer Torque Magnetic Random Access Memory (STT-MRAM) --- byte-addressable, high-endurance non-volatile memory with slightly higher access time than DRAM. In this study, we conduct a preliminary assessment of HPC system performance impact with STT-MRAM main memory with recent industry estimations. Reliable timing parameters of STT-MRAM devices are unavailable, so we also perform a sensitivity analysis that correlates overall system slowdown trend with respect to average device latency. Our results demonstrate that the overall system performance of large HPC clusters is not particularly sensitive to main-memory latency. Therefore, STT-MRAM, as well as any other emerging non-volatile memories with comparable density and access time, can be a viable option for future HPC memory system design.This work was supported by the Collaboration Agreement between Samsung Electronics Co., Ltd. and BSC, Spanish Government through Programa Severo Ochoa (SEV-2015-0493), by the Spanish Ministry of Science and Technology through TIN2015-65316-P project and by the Generalitat de Catalunya (contracts 2014-SGR-1051 and 2014-SGR-1272). This work has also received funding from the European Union's Horizon 2020 research and innovation programme under ExaNoDe project (grant agreement No 671578).Peer ReviewedPostprint (author's final draft

Stanje, mogućnosti i perspektive oplemenjivačkih progarma krastavaca (Cucumis Sativus L.) u Srbiji

Climatic conditions provide growing cucumbers Serbia as an open field and in greenhouses. Growing in greenhouses makes it possible to fruits of cucumber from domestic production on the market for almost the entire year. This capability dramatically increases the economic efficiency and thereby directly encouraged producers to cultivation of this plant species. Markets directly affected the characteristics of the fruit cucumbers that will be desired. This trend breeding companies must follow in order to offer farmers varieties that corresponds to preferences market. Also, farmers want high yield. The yield of cucumber is directly dependent on the expression of sex type plants.Klimatski uslovi Srbije omogućavaju gajenje krastavaca kako na otvorenom polju, tako i u zaštićenom prostoru. Gajenje u zaštićenom prostoru omogućava da se plodovi krastavca iz domaće proizvodnje mogu naći na tržištu skoro tokom celo godine. Ova mogućnost drastično povećava njegovu ekonomsku profitabilnost a time direktno podstiče prozvođače na gajenje ove biljne vrste. Tržišta direktno utiču na karakteristike krastavaca koje će bit cenjene. Ovaj trend oplemenjivačke kompanije morju pratiti kako bi proizvođačima ponudile sortiment koji odgovara željama kupaca. Takođe, proizvođači zahtevaju i visok prinos. Prinos kod krastavca direktno zavisi od tipa polne ekspresije biljaka

Antioxidant Capacities and Phenolic Levels of Different Varieties of Serbian White Wines

The biologically active compounds in wine, especially phenolics, are responsible for reduced risk of developing chronic diseases (cardiovascular disrease, cancer, diabetes, etc.), due to their antioxidant activities. We determined the contents of total phenolics (TP) and total flavonoids (TF) in selected Serbian white wines by colorimetric methods. Total antioxidant activity (TAA) of the white wines was analyzed using the 2,2-diphenyl-1-picrylhydrazyl (DPPH) radical scavenging capacity assay. Međaš beli had the highest content of TP, TF and TAA. The radical scavenging capacity (RSC) and total antioxidant activity (TAA) of white wines were 15.30% and 1.055 mM Trolox equivalent, respectively. Total phenolic (TP) and total flavonoid (TF) contents in white wines ranged from 238.3 to 420.6 mg gallic acid equivalent per L of wines and 42.64 to 81.32 mg catechin equivalent per L of wines, respectively. A high and significant correlation between antioxidant activity and total phenolic content was determined in wines (R2 = 0.968, p < 0.01). For the individual polyphenols determination we used a high performance liquid chromatography (HPLC)-diode array detection (DAD) technique. The majority of white wine polyphenols was represent by four hydroxycinnamic acids (HCAs)

Karakteristike proizvodnje semena povrća u Srbiji

Seed production in the Republic of Serbia is a very important sector of agriculture. This production is taking place in public and private sector. Although seed production in Serbia can meet domestic demands, a certain amount of seed is being imported. Unfortunately, some vegetable producers (except for organic, dynamic or bio production) use a certain amount of vegetable seeds from their own mercantile production. Crops produced from such seed generate low yields due to poor seed quality (varietal impurity, low germination) and health. The study covered four years (2007-2010) and the surfaces under the vegetable crops aimed for seed production: 2007 (956 ha of seed produced in Serbia of which 64.9 ha produced by the Institute for Vegetable crops); 2008 (1152 in Serbia, 137 ha the Institute); 2009 (1219 ha in Serbia, 242.1 ha the Institute); 2010 (976 ha in Serbia, 198.7 the Institute).Proizvodnja semena je veoma bitna sa aspekta održivosti poljoprivrede jedne zemlje. U današnjoj eri sekvencioniranja, mapiranja i nadasve zaštite istraženih sekvenci, ovakve tendencije predstavljaju mogućnost za objektivnu zavisnost od istraživača (vlasnika) koji su odredili pojedine sekvence odgovorne za nasleđivanje pojedinih - traženih osobina novoselekcionisanih sorata. Posebno poglavlje ove problematike predstavljaju i GMO organizmi i njihova prezentacija širokoj proizvodnoj praksi kroz novonastale selekcije. U Republici Srbiji nije dozvoljena upotreba GMO selekcija ali smo svesni da se vrši pritisak na izmenu pozitivnih propisa i dozvolu širenja upotrebe ovih organizama. Semenarstvo Republike Srbije je veoma značajna grana poljoprivredne proizvodnje kojom se u državu slivaju velike količine novca od prodaje semena domaćih selekcija. Povrtarstvo je samo jedan mali segment ove proizvodnje, ali veoma bitan, kako za domaće proizvođače –farmere koji se sve podložniji svetskim trendovima nastupa na organizovanim tržištima a koji zahtevaju određene karakteristike gajenih sorti, tako i za konzumente povrća. Ovi zahtevi savremenog tržišta najčešće su u suprotnosti sa kvalitetom. Današnje semenarstvo Srbije se odvija u državnom i privatnom sektoru. Iako proizvodnja semena može podmiriti domaće potrebe, izvesna količina semena se nabavlja uvozom. Ovaj uvoz je postojao i u vreme zatvorenog tržišta SFRJ, te su smenske kompanije navikle na tržišnu utakmicu. Problem, a iskazala ga je i Evropska Unija svojim zakonima, jeste da jedan deo povrtara, osim za organsku (dinamičku, bio i dr proizvodnju), koriste određene količine semena povrća iz sopstvene merkantilne proizvodnje. Ovakvi usevi ostvaruju niske prinose kako zbog kvaliteta semena (sortna čistoća, klijavost), tako i zbog zdravstvene ispravnosti semena Sortiment povrća koji nastaje u Republici Srbiji stvaran je u agroekološkim uslovima Balkanskog poluostrva te je zato i našlo je tržište širom Balkana, a u poslednje vreme, i Evrope. Cilj ovog rada je da se iskaže učešće u proizvodnji pojedinih povrtarskih vrsta izraženo po površinama i u količinama Instituta za povrtarstvo d.o.o u semenarskoj proizvodnji Srbije. Istraživani ciklus je obuhvatao 4 godine i u njemu je proizvedeno seme povrća na 956 ha 2007 (64.9 ha), 1152 (137) 2008. godine, 1219 ha (242.1ha) 2009. godine i 976 ha (198.7 ha) 2010. godine

Phenolic compounds and biological activity of Capsicum annuum L.

The objective of this study was to evaluate antifungal and antioxidant activities of vegetable extracts (Capsicum annuum L. cv. Dora, cv. Strizanka, cv. Morava), grown in Serbia. Different experimental models have included the determination content of total phenolics, total flavonoids, antioxidant capacity and minimum inhibitory concentration of the extract. The phenolic composition of different extracts was determined by the high-performance liquid chromatography (HPLC) method. The highest amounts of phenols and highest antioxidant capacity were found in the cultivar Dora extracts. The highest phenolic content has been shown in cultivar Strizanka ethanol extract. All of the extracts showed strong antimicrobial activity. On the basis of the results obtained, the extracts were found to serve as a potential source of natural antioxidants and antimicrobial due to their marked activity. The obtained results may be useful in the evaluation of new dietary and food products.Key words: High-performance liquid chromatography (HPLC), phenolic components, antimicrobial activity, antioxidant activity