Asynchronous In Situ Processing with Gromacs: Taking Advantage of GPUs

International audienceNumerical simulations using supercomputers are producing an ever growing amount of data. Efficient production and analysis of these data are the key to future discoveries. The in situ paradigm is emerging as a promising solution to avoid the I/O bottleneck encountered in the file system for both the simulation and the analytics by treating the data as soon as they are produced in memory. Various strategies and implementations have been proposed in the last years to support in situ treatments with a low impact on the simulation performance. Yet, little efforts have been made when it comes to perform in situ analytics with hybrid simulations supporting accelerators like GPUs. In this article, we propose a study of the in situ strategies with Gromacs, a molecular dynamic simulation code supporting multi-GPUs, as our application target. We specifically focus on the computational resources usage of the machine by the simulation and the in situ analytics. We finally extend the usual in situ placement strategies to the case of in situ analytics running on a GPU and study their impact on both Gromacs performance and the resource usage of the machine. We show in particular that running in situ analytics on the GPU can be a more efficient solution than on the CPU especially when the CPU is the bottleneck of the simulation

The AIM2 inflammasome is critical for innate immunity to Francisella tularensis.

Francisella tularensis, the causative agent of tularemia, infects host macrophages, which triggers production of the proinflammatory cytokines interleukin 1beta (IL-1beta) and IL-18. We elucidate here how host macrophages recognize F. tularensis and elicit this proinflammatory response. Using mice deficient in the DNA-sensing inflammasome component AIM2, we demonstrate here that AIM2 is required for sensing F. tularensis. AIM2-deficient mice were extremely susceptible to F. tularensis infection, with greater mortality and bacterial burden than that of wild-type mice. Caspase-1 activation, IL-1beta secretion and cell death were absent in Aim2(-/-) macrophages in response to F. tularensis infection or the presence of cytoplasmic DNA. Our study identifies AIM2 as a crucial sensor of F. tularensis infection and provides genetic proof of its critical role in host innate immunity to intracellular pathogens

Toxicity of various silver nanoparticles compared to silver ions in the Ponto-Caspian amphipod Pontogammarus maeoticus (Sowinsky, 1894)

According to the increased probability of the presence of nanomaterials in the aquatic ecosystems, the present study examined the toxicity of three engineered silver nanoparticles (AgNPs) as well as silver ions in the Pontogammarus maeoticus, a brackish water benthic organism living in the littoral zone of the Caspian Sea. The animals were acutely exposed to different concentrations of two commercially prepared colloidal forms and a freshly prepared suspension of silver nanoparticles, plus AgNO3 during 48 hr. The number of mortalities was assessed and lethal concentration values were calculated using the EPA Probit Analysis Program. According to median lethal concentrations (LC50), the order of sensitivity of this amphipod to tested silver compounds was as: previously prepared AgNPs colloids > freshly prepared AgNPs suspension > AgNO3. Also the signs of nanoparticle accumulation were evident between the pereopods and pleopods of this gammarid; this accumulation could be one of the reasons for the higher toxicity of silver nanoparticles in comparison with silver ions in P. maeoticus. More acute and chronic studies are needed to understand the various aspects of nano-silver toxicity on amphipods in different salinities

Coherent quantum phase slip

A hundred years after discovery of superconductivity, one fundamental prediction of the theory, the coherent quantum phase slip (CQPS), has not been observed. CQPS is a phenomenon exactly dual to the Josephson effect: whilst the latter is a coherent transfer of charges between superconducting contacts, the former is a coherent transfer of vortices or fluxes across a superconducting wire. In contrast to previously reported observations of incoherent phase slip, the CQPS has been only a subject of theoretical study. Its experimental demonstration is made difficult by quasiparticle dissipation due to gapless excitations in nanowires or in vortex cores. This difficulty might be overcome by using certain strongly disordered superconductors in the vicinity of the superconductor-insulator transition (SIT). Here we report the first direct observation of the CQPS in a strongly disordered indium-oxide (InOx) superconducting wire inserted in a loop, which is manifested by the superposition of the quantum states with different number of fluxes. Similarly to the Josephson effect, our observation is expected to lead to novel applications in superconducting electronics and quantum metrology.Comment: 14 pages, 3 figure

Most Complex Non-Returning Regular Languages

A regular language $L$ is non-returning if in the minimal deterministic finite automaton accepting it there are no transitions into the initial state. Eom, Han and Jir\'askov\'a derived upper bounds on the state complexity of boolean operations and Kleene star, and proved that these bounds are tight using two different binary witnesses. They derived upper bounds for concatenation and reversal using three different ternary witnesses. These five witnesses use a total of six different transformations. We show that for each $n\ge 4$ there exists a ternary witness of state complexity $n$ that meets the bound for reversal and that at least three letters are needed to meet this bound. Moreover, the restrictions of this witness to binary alphabets meet the bounds for product, star, and boolean operations. We also derive tight upper bounds on the state complexity of binary operations that take arguments with different alphabets. We prove that the maximal syntactic semigroup of a non-returning language has $(n-1)^n$ elements and requires at least $\binom{n}{2}$ generators. We find the maximal state complexities of atoms of non-returning languages. Finally, we show that there exists a most complex non-returning language that meets the bounds for all these complexity measures.Comment: 22 pages, 6 figure

Podosome assembly is controlled by the GTPase ARF1 and its nucleotide exchange factor ARNO

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Complexity of Left-Ideal, Suffix-Closed and Suffix-Free Regular Languages

A language $L$ over an alphabet $\Sigma$ is suffix-convex if, for any words $x,y,z\in\Sigma^*$, whenever $z$ and $xyz$ are in $L$, then so is $yz$. Suffix-convex languages include three special cases: left-ideal, suffix-closed, and suffix-free languages. We examine complexity properties of these three special classes of suffix-convex regular languages. In particular, we study the quotient/state complexity of boolean operations, product (concatenation), star, and reversal on these languages, as well as the size of their syntactic semigroups, and the quotient complexity of their atoms.Comment: 20 pages, 11 figures, 1 table. arXiv admin note: text overlap with arXiv:1605.0669

Heat transport study of the spin liquid candidate 1T-TaS2

We present the ultra-low-temperature thermal conductivity measurements on single crystals of the prototypical charge-density-wave material 1$T$-TaS$_2$, which was recently argued to be a candidate for quantum spin liquid. Our experiments show that the residual linear term of thermal conductivity at zero field is essentially zero, within the experimental accuracy. Furthermore, the thermal conductivity is found to be insensitive to the magnetic field up to 9 T. These results clearly demonstrate the absence of itinerant magnetic excitations with fermionic statistics in bulk 1$T$-TaS$_2$ and, thus, put a strong constraint on the theories of the ground state of this material.Comment: 5 pages, 3 figure

Frustrated two-dimensional Josephson junction array near incommensurability

To study the properties of frustrated two-dimensional Josephson junction arrays near incommensurability, we examine the current-voltage characteristics of a square proximity-coupled Josephson junction array at a sequence of frustrations f=3/8, 8/21, 0.382 $(\approx (3-\sqrt{5})/2)$, 2/5, and 5/12. Detailed scaling analyses of the current-voltage characteristics reveal approximately universal scaling behaviors for f=3/8, 8/21, 0.382, and 2/5. The approximately universal scaling behaviors and high superconducting transition temperatures indicate that both the nature of the superconducting transition and the vortex configuration near the transition at the high-order rational frustrations f=3/8, 8/21, and 0.382 are similar to those at the nearby simple frustration f=2/5. This finding suggests that the behaviors of Josephson junction arrays in the wide range of frustrations might be understood from those of a few simple rational frustrations.Comment: RevTex4, 4 pages, 4 eps figures, to appear in Phys. Rev.

A screen-printed carbon electrode modified with a chitosan-based film for in situ heavy metal ions measurement

SEM images and FTIR data of the working electrode surface showed that Mn+ ions were adsorbed on chitosan (Chit) and crosslinked chitosan-carbon nanotube (Chit-CNT) films. XPS revealed that chelation of Mn+ ions with the –NH2/–OH groups from chitosan, –COOH group from carbon nanotubes, and aqua ligands represents a possible structure of the active Mn+ species in the Chit-based film. The electrochemical behaviors of the Chit-based film modified screen-printed carbon electrode (SPCE) were characterized for individual and simultaneous detection of Cu2+, Pb2+, Hg2+, Zn2+, Cd2+, and As3+ ions. For individual detection, the concentration range was 0.50–3.00 ppm with a detection limit of 0.4 ppm for Cu2+; 1.0–4.0 ppm with a detection limit of 0.5 ppm for Pb2+; 1.0–5.0 ppm with a detection limit of 0.8 ppm for Hg2+. For simultaneous detection, the lab chip sensor was successfully used to determine the concentrations of Pb2+, Cu2+, Hg2+, and As3+ ions simultaneously