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

Aerosol deposition of Ba0.8Sr0.2TiO3 thin films

In this work we optimized conditions for aerosol deposition of homogeneous, nanograined, smooth Ba0.8Sr0.2TiO3 thin films. Investigation involved optimization of deposition parameters, namely deposition time and temperature for different substrates. Solutions were prepared from titanium isopropoxide, strontium acetate and barium acetate. Films were deposited on Si (1 0 0) or Si covered by platinum (Pt (1 1 1) /Ti/SiO2/Si). Investigation showed that the best films were obtained at substrate temperature of 85ºC. After deposition films were slowly heated up to 650ºC, annealed for 30 min, and slowly cooled. Grain size of BST films deposited on Si substrate were in the range 40-70 nm, depending on deposition conditions, while the same films deposited on Pt substrates showed mean grain size in the range 35-50 nm. Films deposited under optimal conditions were very homogeneous, crackfree, and smooth with rms roughness lower than 4 nm for both substrates

The effect of sires on daily gain and fat thickness

The production characteristics of fatteners in this paper were examined in two farms of pigs in the Republic of Serbia. The research included 1166 pigs of both genders (female animals and male castrated heads) with various genotypes. Research examined influence of sire breed, sire within sire breed, gender of the pigs and the mass at the end of the fattening on the following characteristics of the fatteners: Daily gain of the warm carcass side mass (PTP), rump fat thickness (DSK), backfat thickness (DSL) and sum of the fat thickness rump+back (DSKL). The pigs in this research come from the following sires: Large White (LW), Swedish Landrace (SL), Duroc and Crossbreed H × D. Data processing was done using the Harvey computer program. It was determined that all the involved effects in the model show a different level of influence on the researched traits (P lt 0.05; P lt 0.01; P lt 0.001), whereas only one factor, sire within sire breed H ×. D does not influence the expression of the characteristic gain of the warm carcass side mass (P > 0.05)

Combined effect of GSTM1 gene deletion, GSTT1 gene deletion and MTHFR C677T mutation in male infertility

The aim of the study was to investigate the association between the GSTM1 and GSTT1 gene deletion and MTHFR C677T mutation and male infertility. The study has encompassed 52 infertile and 56 fertile males. Genotype distributions of GSTM1 and GSTT1 gene deletions and the MTHFR C677T mutation did not differ significantly among the analyzed groups, however, a difference in distribution of certain genotype combinations was observed. The obtained results indicate that carriers of double GSTM1/GSTT1 deletion and the MTHFR 677CC genotype are at higher risk of infertility than carriers of any other combination of genotypes (OR 3.5, 95%CI 0.68-18.30)

The Assessment of Breeding Value of First Farrowed Sows by the Method of Selection Indices

The goal of this research paper was to assess the breeding value of first farrowed Swedish Landrace sows by the means of selection indices method. The traits on the basis of which the breeding value of animals was assessed are following: daily liveweight gain, average thickness of collected back fat measured at five sites and number of liveborn piglets in the first litter. The liveweight gain and carcass quality traits determined at the end of performance test were corrected for the body mass of 100kg by the method of basic indexes and following mean values were determined: for corrected daily liveweight gain (KZDP) 499.92g/day and for corrected average collected backfat thickness (KSL) 20.01mm. The first farrowed sows on average produced 8.09 liveborn piglets in the litter. Studying the effect of the gilts` birth year and season on KZDP and KSL it was determined that the gilts` birth year and season had no statistically significant influence (P>0.05) on KZDP variation but they had a statistically significant effect on KSL (P lt 0.01). The year and the season of farrowing and the class of backfat thickness in performance test did not display any statistically significant effect (P>0.05) on BZPL, while the KZDP class and the age at first farrowing had a statistically significant effect on the variability of these trait (P lt 0.05; P lt 0.01). All studied traits varied statistically significantly (P lt 0.01) under the impact of the gilts` sire or dam. Heritability coefficients were: h2= 0.402 for KZDP, h2= 0.261 for KSL and h2= 0.177 for BZPL. The relation between KZDP and KSL was of a medium strength both at phenotype and genetic levels (rph=0.491; rg=0.411), while the relation of these traits with BZPL did not exist, except for the genetic relationship between KSL and KZDP which was of a medium strength (rg=0.252). Three equations for the selection indexes were constructed among which as the most optimal was chosen the one which includes all three traits (KZDP, KSL and BZPL) and whose correlation coefficent of selection index and aggregate genotype was rIAG = 0.5473

Clinical and biochemical characterization of the prothrombin Belgrade mutation in a large Serbian pedigree: new insights into the antithrombin resistance mechanism

Background: The recently reported c.1787G gt A mutation in the prothrombin gene leads to Arg596Gln replacement in the protein molecule (prothrombin Belgrade). This substitution impairs binding of antithrombin to thrombin and results in inherited thrombophilia, known as antithrombin resistance. Objectives: We aimed to elucidate the clinical and biochemical characteristics of thrombophilia associated with antithrombin resistance in a large Serbian family with the prothrombin Belgrade mutation. Patients and methods: Nineteen family members were investigated, among whom 10 were carriers of the c.1787G gt A mutation. In all subjects the clinical phenotype was determined and laboratory investigations of hemostatic parameters were performed. Results: Six out of the 10 mutation carriers developed thromboembolic events, mainly deep venous and mesenteric vein thrombosis. The median age of the first thrombotic event was 26.5 (12-41) years, whereas the incidence rate of first thrombosis was 2.2% per year. In all mutation carriers prothrombin activity was significantly decreased in comparison with non-carriers, clearly distinguishing each group. However, the presence of the mutation did not affect the prothrombin antigen level in plasma. The endogenous thrombin potential was significantly increased in all carriers in comparison with non-carriers, indicating the presence of blood hypercoagulability. Interestingly, levels of D-dimer and the F1+2 fragment were similar in both groups. Conclusions: Although rare, the prothrombin Belgrade mutation represents strong thrombophilia with early onset of thrombosis in the investigated family. According to our results, decreased prothrombin activity may be a simple screening test for detection of this mutation in thrombotic patients

Application of sos/umuc assay in eco/genotoxicology

Introduction. The SOS/umuC assay is used for assessment of water genotoxicity. Salmonella typhimurium TA1535/pSK1002 is used in this test, but the results can be extrapolated on higher eukaryotic organisms with the introduction of enzymatic S9 fraction in experimental procedure. The test is standardised for the determination of the genotoxic potential of water and wastewater (ISO/DIS 13829, 2000). Aim. Sensitivity of the assay was challenged by using parallel in situ and in vitro approach in evaluation of the genotoxic potential in the basins of significant tributaries of the Danube River: the Sava River and the Velika Morava River. Materials and methods. Within in vitro testing, native water samples were analysed by SOS/umuC test. DNA damage in situ was assessed in bleak (Alburnus alburnus) erythrocytes by the comet and micronucleus assays. The concentration of heavy metals in fish tissue and the data of the physico-chemical parameters measured in water were used as a measure of the pollution pressure at the sites. Results. Results showed that applied in vitro tests with native water samples are less sensitive in comparison with in situ tests. None of 20 investigated samples showed genotoxic potential in SOS/umuC assay while in situ analyses indicated variation of genotoxic potential among the investigated sites. Conclusions. The results of our study point towards low sensitivity of the SOS/umuC test when processing un-concentrated (native) water samples; the results of in vitro tests should be taken with precaution when making predictions on the status of the ecosystem

The emergence of non-secretory multiple myeloma during the non-cytotoxic treatment of essential thrombocythemia: A case report

Introduction. The emergence of multiple myeloma as a second malignancy in patients with essential thrombocythemia is extremely rare. Several cases have been published so far, pointing out the impact of a cytotoxic effect during treatment of essential thrombocythemia on the development of multiple myeloma. Case presentation. We report the case of a 52-year-old Caucasian man who presented to our hospital because of leukocytosis, a slightly decreased hemoglobin level and thrombocytosis. After a complete hematological work-up, essential thrombocythemia was diagnosed. The patient was included in a multicenter clinical study, treated with anagrelide and his platelet counts were maintained in the normal range for more than 3 years. A sudden drop in his hemoglobin level with normal leukocyte and platelet count occurred at the same time as a back pain. Magnetic resonance imaging of his spine revealed the existence of a pathological fracture of Th4, the collapse of the upper edge of Th7 and osteolytic lesions of multiple thoracic vertebrae. Repeated hematological examinations, including bone biopsy with immunohistochemistry, disclosed diagnosis of multiple myeloma of the non-secretory type. Conclusions: To the best of our knowledge this is the first published case in which multiple myeloma developed during the treatment of essential thrombocythemia with the non-cytotoxic drug anagrelide. Our attempts to find a common origin for the coexistence of multiple myeloma and essential thrombocythemia have not confirmed the genetic basis of their appearance. Further studies are needed to determine the biological impact of this coexistence

Application of sos/umuc assay in eco/genotoxicology

Introduction. The SOS/umuC assay is used for assessment of water genotoxicity. Salmonella typhimurium TA1535/pSK1002 is used in this test, but the results can be extrapolated on higher eukaryotic organisms with the introduction of enzymatic S9 fraction in experimental procedure. The test is standardised for the determination of the genotoxic potential of water and wastewater (ISO/DIS 13829, 2000). Aim. Sensitivity of the assay was challenged by using parallel in situ and in vitro approach in evaluation of the genotoxic potential in the basins of significant tributaries of the Danube River: the Sava River and the Velika Morava River. Materials and methods. Within in vitro testing, native water samples were analysed by SOS/umuC test. DNA damage in situ was assessed in bleak (Alburnus alburnus) erythrocytes by the comet and micronucleus assays. The concentration of heavy metals in fish tissue and the data of the physico-chemical parameters measured in water were used as a measure of the pollution pressure at the sites. Results. Results showed that applied in vitro tests with native water samples are less sensitive in comparison with in situ tests. None of 20 investigated samples showed genotoxic potential in SOS/umuC assay while in situ analyses indicated variation of genotoxic potential among the investigated sites. Conclusions. The results of our study point towards low sensitivity of the SOS/umuC test when processing un-concentrated (native) water samples; the results of in vitro tests should be taken with precaution when making predictions on the status of the ecosystem

Risky Travel? Subjective vs. Objective Perceived Risks in Travel Behaviour—Influence of Hydro-Meteorological Hazards in South-Eastern Europe on Serbian Tourists

In terms of climate related security risks, the region of South-Eastern Europe (SEE) can be identified as one of the world’s hot spots. As weather-related hazards continue to increase in num-bers and spatial distribution, risk perception in the tourism industry becomes even more important. Additionally, people’s perception of natural hazards is one of the key elements in their decision-making process when choosing a travel destination. Although a vast number of studies have exam-ined aspects of risk perception, an integrated approach which considers both objective and subjec-tive factors related to the tourism industry and hydro-meteorological hazards remains relatively scarce. This pioneering study inspects the causality between objective perceived risks, as well as subjective risk factors. A methodological approach and the obtained results present a certain nov-elty since the previous conceptualized Psychological Preparedness for Disaster Threat Scale (PPDTS) was applied for the first time in the tourism industry. The obtained results reveal the pres-ence of a statistically significant relationship between objective risks and certain subjective risk fac-tors (gender, age, education, prior experience, anticipation, and awareness). Therefore, this study may offer a conceptual platform for both theoretical and practical implications for enhanced ap-proaches oriented toward more qualitative risk management at a given travel destination, in regions prone to hydro-meteorological hazards