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Register a new userScaling and Acceleration of Three-dimensional Structure Determination for Single-Particle Imaging Experiments with SpiniFEL
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The Linac Coherent Light Source (LCLS) is an X- ray free electron laser (XFEL) facility enabling the study of the structure and dynamics of single macromolecules. A major upgrade will bring the repetition rate of the X-ray source from 120 to 1 million pulses per second. Exascale high performance computing (HPC) capabilities will be required to process the corresponding data rates. We present SpiniFEL, an application used for structure determination of proteins from single-particle imaging (SPI) experiments. An emerging technique for imaging individual proteins and other large molecular complexes by outrunning radiation damage, SPI breaks free from the need for crystallization (which is difficult for some proteins) and allows for imaging molecular dynamics at near ambient conditions. SpiniFEL is being developed to run on supercomputers in near real-time while an experiment is taking place, so that the feedback about the data can guide the data collection strategy. We describe here how we reformulated the mathematical framework for parallelizable implementation and accelerated the most compute intensive parts of the application. We also describe the use of Pygion, a Python interface for the Legion task-based programming model and compare to our existing MPI+GPU implementation.
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Single particle diffraction imaging experiments at free-electron lasers (FEL) have a great potential for structure determination of reproducible biological specimens that can not be crystallized. One of the challenges in processing the data from such an experiment is to determine correct orientation of each diffraction pattern from samples randomly injected in the FEL beam. We propose an algorithm (see also O. Yefanov et al., Photon Science - HASYLAB Annual Report 2010) that can solve this problem and can be applied to samples from tens of nanometers to microns in size, measured with sub-nanometer resolution in the presence of noise. This is achieved by the simultaneous analysis of a large number of diffraction patterns corresponding to different orientations of the particles. The algorithms efficiency is demonstrated for two biological samples, an artificial protein structure without any symmetry and a virus with icosahedral symmetry. Both structures are few tens of nanometers in size and consist of more than 100 000 non-hydrogen atoms. More than 10 000 diffraction patterns with Poisson noise were simulated and analyzed for each structure. Our simulations indicate the possibility to achieve resolution of about 3.3 {AA} at 3 {AA} wavelength and incoming flux of 10^{12} photons per pulse focused to 100times 100 nm^2.
In this paper, the OpenACC heterogeneous parallel programming model is successfully applied to modification and acceleration of the three-dimensional Tokamak magnetohydrodynamical code (CLTx). Through combination of OpenACC and MPI technologies, CLTx is further parallelized by using multiple-GPUs. Significant speedup ratios are achieved on NVIDIA TITAN Xp and TITAN V GPUs, respectively, with very few modifications of CLTx. Furthermore, the validity of the double precision calculations on the above-mentioned two graphics cards has also been strictly verified with m/n=2/1 resistive tearing mode instability in Tokamak.
Magnetic reconnection is invoked as one of the primary mechanisms to produce energetic particles. We employ large-scale three-dimensional (3D) particle-in-cell simulations of reconnection in magnetically-dominated ($sigma=10$) pair plasmas to study the energization physics of high-energy particles. We identify a novel acceleration mechanism that only operates in 3D. For weak guide fields, 3D plasmoids / flux ropes extend along the $z$ direction of the electric current for a length comparable to their cross-sectional radius. Unlike in 2D simulations, where particles are buried in plasmoids, in 3D we find that a fraction of particles with $gammagtrsim 3sigma$ can escape from plasmoids by moving along $z$, and so they can experience the large-scale fields in the upstream region. These free particles preferentially move in $z$ along Speiser-like orbits sampling both sides of the layer, and are accelerated linearly in time -- their Lorentz factor scales as $gammapropto t$, in contrast to $gammapropto sqrt{t}$ in 2D. The energy gain rate approaches $sim eE_{rm rec}c$, where $E_{rm rec}simeq 0.1 B_0$ is the reconnection electric field and $B_0$ the upstream magnetic field. The spectrum of free particles is hard, $dN_{rm free}/dgammapropto gamma^{-1.5}$, contains $sim 20%$ of the dissipated magnetic energy independently of domain size, and extends up to a cutoff energy scaling linearly with box size. Our results demonstrate that relativistic reconnection in GRB and AGN jets may be a promising mechanism for generating ultra-high-energy cosmic rays.
Light field microscopy methods together with three dimensional (3D) deconvolution can be used to obtain single shot 3D images of atomic clouds. We demonstrate the method using a test setup which extracts three dimensional images from a fluorescent $^{87}$Rb atomic vapor.
In the wake of the intense effort made for the experimental CILEX project, numerical simulation cam- paigns have been carried out in order to finalize the design of the facility and to identify optimal laser and plasma parameters. These simulations bring, of course, important insight into the fundamental physics at play. As a by-product, they also characterize the quality of our theoretical and numerical models. In this paper, we compare the results given by different codes and point out algorithmic lim- itations both in terms of physical accuracy and computational performances. These limitations are illu- strated in the context of electron laser wakefield acceleration (LWFA). The main limitation we identify in state-of-the-art Particle-In-Cell (PIC) codes is computational load imbalance. We propose an innovative algorithm to deal with this specific issue as well as milestones towards a modern, accurate high-per- formance PIC code for high energy particle acceleration.
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