Efficient Process-to-Node Mapping Algorithms for Stencil Computations

Good process-to-compute-node mappings can be decisive for well performing HPC applications. A special, important class of process-to-node mapping problems is the problem of mapping processes that communicate in a sparse stencil pattern to Cartesian grids. By thoroughly exploiting the inherently present structure in this type of problem, we devise three novel distributed algorithms that are able to handle arbitrary stencil communication patterns effectively. We analyze the expected performance of our algorithms based on an abstract model of inter- and intra-node communication. An extensive experimental evaluation on several HPC machines shows that our algorithms are up to two orders of magnitude faster in running time than a (sequential) high-quality general graph mapping tool, while obtaining similar results in communication performance. Furthermore, our algorithms also achieve significantly better mapping quality compared to previous state-of-the-art Cartesian grid mapping algorithms. This results in up to a threefold performance improvement of an MPI_Neighbor_alltoall exchange operation. Our new algorithms can be used to implement the MPI_Cart_create functionality.Comment: 18 pages, 9 Figure

Sustainable Food System – Targeting Production Methods, Distribution or Food Basket Content?

Agriculture is the single most important contributor to the eutrophication of the Baltic Sea. Itis responsible for 59% of the anthropogenic nitrogen and 56% of the phosphorous emissions(HELCOM, 2005). A second important source of nutrient emissions is at the other end of thefood system – emissions from municipal waste-water treatment plants and from privatehouseholds. Addressing different aspects of the food system is thus crucial for the Baltic Seaenvironment. To tackle eutrophication both nitrogen and phosphorous loads should bereduced (MVB, 2005). This can be achieved if emissions from the food system are reduced,e.g. by closing the nutrient cycle from soil to crop and back to agricultural soil (Diaz andRosenberg, 2008). Granstedt (2000) finds that the high surplus and emissions of nitrate andphosphorous in Swedish agriculture is a consequence of specialized agriculture with itsseparation of crop and animal production. Similar findings are reported from different partsof Europe (Brower et al., 1995). About 80% of cropland in Sweden is used for fodderproduction but the animal production is concentrated to a limited number of specializedanimal farms. Manure, with its contents of nutrients from the whole agriculture area, istoday concentrated on only 20% of the Swedish arable land (Statistics Sweden, 2011). Thisresults in high nutrient surplus and load of nitrogen and phosphorus from these areas.Granstedt (2000) concludes that the emissions can be limited by combining best availableagricultural technology with increased recycling of nutrients within the agricultural systemtrough integration of crop and animal production - ecological recycling agriculture (ERA).This facilitates an efficient use of the plant nutrients in farm yard manure. Other studies ofnutrient balances comparing farming systems and lifecycle assessment report similarobservations (Halberg, 1999; Myrbeck, 1999; Steinshamn et al., 2004; Uusitalo, 2007). Thepotential of reduced nutrient emissions trough ERA was confirmed in case studies on localorganic farms around the Baltic Sea (Granstedt et al., 2008; Larsson and Granstedt, 2010).Carlsson-Kanyama (1999) found that greenhouse gas emissions could be reduced by localand organic food production due to shorter transportation. Similar results are reported in acompilation of studies (FiBL, 2006) and in studies of local production and processing inJärna, Sweden (Wallgren, 2008). According to Carlsson-Kanyama et al. (2004) the reductionsare not significant unless local distribution becomes more efficient.QC 20160524</p

Bridging immune activation with the kynurenine pathway : implications for psychosis

Kynurenic acid (KYNA), an endogenous N-Methyl-D-aspartic acid receptor (NMDAR) antagonist, is elevated in patients with schizophrenia. In addition, elevated levels of KYNA are associated with activation of the immune system, which also has been implicated in the development and maintenance of psychotic disorders, including schizophrenia. The aim of this thesis was to further investigate the role of KYNA in the pathophysiology of schizophrenia. Thus, patients with schizophrenia were examined with respect to cerebrospinal fluid (CSF) levels of interleukin (IL)-6, kynurenines, and the functional effects of G protein- coupled receptor kinase 3 (GRK3) expression. Mice administered lipopolysaccharide (LPS), amphetamine, or lacking the immune-regulating enzyme GRK3, were studied with respect to biochemical and functional aberrations associated with schizophrenia. The elevated CSF levels of IL-6 found in patients with schizophrenia were associated with increased CSF KYNA levels. Administration of IL-6 increased KYNA production in astrocytes and lower GRK3 expression in healthy individuals correlated to increased CSF KYNA levels. GRK3 was further found to be associated with psychosis in patients with bipolar disorder. Subchronic elevation of KYNA, or lack of GRK3 augmented the amphetamine response as verified by increased locomotor activity and dopamine release. Signs of amplified immune activity were evident in Grk3-/- mice by increases in astrocyte markers, IL-1β, kynurenine, and KYNA turnover. Intracerebroventricular (ICV) administration of IL-1β, and dual, bot not single injections of LPS increased brain KYNA. In addition, mice injected ICV with IL-1β or lacking GRK3 showed disrupted prepulse inhibition (PPI). Results presented here point to an intimate relationship between immune activation, the kynurenine pathway, and psychosis. Specifically, immune activation, present in patients with schizophrenia, was demonstrated to activate the kynurenine pathway. In addition, activation of the kynurenine pathway induced KYNA and lead to behavioral aberrations in rodents

Insiderinformation - analys och legalitetsaspekter

Legaldefinitionen av insiderinformation återfinns i 1 § 1 MmL. I den här uppsatsen analyseras den del av legaldefinitionen som lyder: ''information om en icke offentliggjord eller inte allmänt känd omständighet som är ägnad att påverka kursen''. Härvidlag fokuseras på de olika tolkningssvårigheter som finns och den försvagning av legalitetsprincipen samt de svårigheter för åklagare och domare som därmed blir följden. Först och främst uppstår svårigheter när det gäller att avgöra vad som kan utgöra en omständighet, till vilken sannolikhet en omständighet skall föreligga samt gränsdragningen mot ryktesspridning. I detta avseende analyseras de rättskällor som gör gällande att rykten samt köp- och säljrekommendationer inte kan utgöra insiderinformation. Slutsatsen i detta avseende är att även information om ett rykte och en köp- eller säljrekommendation skulle kunna utgöra insiderinformation. Vidare är formuleringen ''icke offentliggjord eller inte allmänt känd'' problematisk. Lagtexten ger sken av att det räcker med att informationen är antingen icke offentliggjord eller inte allmänt känd för att den skall kunna utgöra insiderinformation. I förarbeten, viss doktrin och domstolsavgöranden förutsätts att de båda uttrycken har samma innebörd. I uppsatsen intas ståndpunkten att det rör sig om två skilda begrepp med olika innebörd samt att det krävs att informationen är både icke offentliggjord och inte allmänt känd för att den skall kunna utgöra insiderinformation. Den fråga som har ägnats mest utrymme i förarbeten och doktrin är prispåverkanderekvisitet. I detta avseende analyseras förarbeten samt ett antal underinstansavgöranden. Analysen visar att innebörden av begreppet väsentlig prispåverkan är svårbestämt och varierar mellan olika instrument och marknader och att domstolar ofta tar hänsyn till faktiska kursrörelser, istället för att göra den erfarenhetsmässiga bedömning som följer av formuleringen ''ägnad att''. Därutöver uppmärksammas problemet med att särskilja en viss omständighets prispåverkan från prispåverkan av andra omständigheter, däribland rykten. Uppsatsens slutsats är att det är svårt att fastställa något så när tydliga gränser för det straffbara området avseende insiderinformation. Lagstiftningen är bristfällig på ett sätt som inte är acceptabelt inom straffrätten. Genomgående är att lagstiftaren och domstolarna visar stor osäkerhet och brist på precision vad gäller utformningen respektive tillämpningen av lagstiftningen. De olika delarna av begreppet insiderinformation är bristfälligt motiverade och tenderar att flyta samman. Lagstiftningens brister medför svårigheter både för åklagaren och för den tilltalade. Svårigheterna för åklagaren består i att försöka utröna exakt vad det är som skall bevisas, d.v.s. att med tillräcklig precision reda ut hur rekvisiten egentligen ser ut. Detta medför att både åtal och domskäl blir vaga och svepande, vilket i slutändan drabbar den tilltalade

Homocysteine and small vessel stroke: A mendelian randomization analysis.

OBJECTIVE: Trials of B vitamin therapy to lower blood total homocysteine (tHcy) levels for prevention of stroke are inconclusive. Secondary analyses of trial data and epidemiological studies suggest that tHcy levels may be particularly associated with small vessel stroke (SVS). We assessed whether circulating tHcy and B vitamin levels are selectively associated with SVS, but not other stroke subtypes, using Mendelian randomization. METHODS: We used summary statistics data for single-nucleotide polymorphisms (SNPs) associated with tHcy (n = 18), folate (n = 3), vitamin B6 (n = 1), and vitamin B12 (n = 14) levels, and the corresponding data for stroke from the MEGASTROKE consortium (n = 16,952 subtyped ischemic stroke cases and 404,630 noncases). RESULTS: Genetically predicted tHcy was associated with SVS, with an odds ratio of 1.34 (95% confidence interval [CI], 1.13-1.58; p = 6.7 × 10-4 ) per 1 standard deviation (SD) increase in genetically predicted tHcy levels, but was not associated with large artery or cardioembolic stroke. The association was mainly driven by SNPs at or near the MTHFR and MUT genes. The odds ratios of SVS per 1 SD increase in genetically predicted folate and vitamin B6 levels were 0.49 (95% CI, 0.34-0.71; p = 1.3 × 10-4 ) and 0.70 (95% CI, 0.52-0.94; p = 0.02), respectively. Genetically higher vitamin B12 levels were not associated with any stroke subtype. INTERPRETATION: These findings suggest that any effect of homocysteine-lowering treatment in preventing stroke will be confined to the SVS subtype. Whether genetic variants at or near the MTHFR and MUT genes influence SVS risk through pathways other than homocysteine levels and downstream effects require further investigation. Ann Neurol 2019;85:495-501

Circulating Vitamin K₁ Levels in Relation to Ischemic Stroke and Its Subtypes: A Mendelian Randomization Study.

Vitamin K plays a crucial role in blood coagulation, and hypercoagulability has been linked to atherosclerosis-related vascular disease. We used the Mendelian randomization study design to examine whether circulating vitamin K₁ (phylloquinone) levels are associated with ischemic stroke. Four single-nucleotide polymorphisms associated with vitamin K₁ levels were used as instrumental variables. Summary-level data for large artery atherosclerotic stroke (n = 4373 cases), small vessel stroke (n = 5386 cases), cardioembolic stroke (n = 7193 cases), and any ischemic stroke (n = 34,217 cases and 404,630 non-cases) were available from the MEGASTROKE consortium. Genetically-predicted circulating vitamin K₁ levels were associated with large artery atherosclerotic stroke but not with any other subtypes or ischemic stroke as a whole. The odds ratios per genetically predicted one nmol/L increase in natural log-transformed vitamin K₁ levels were 1.31 (95% confidence interval (CI) 1.12⁻1.53; p = 7.0 × 10-4) for large artery atherosclerotic stroke, 0.98 (95% CI 0.85⁻1.12; p = 0.73) for small vessel stroke, 1.01 (95% CI 0.90⁻1.14; p = 0.84) for cardioembolic stroke, and 1.05 (95% CI 0.99⁻1.11; p = 0.11) for any ischemic stroke. These findings indicate that genetic predisposition to higher circulating vitamin K₁ levels is associated with an increased risk of large artery atherosclerotic stroke