Parallelization of Atomic Image
Reconstruction from X-ray Fluorescence
Holograms with XcalableMP
Atsushi Kubota, Tomohiro Matsushita, and Naohisa Happo
Abstract X-ray fluorescence holography is a three-dimensional middle range local
structure analysis method, which can provide three-dimensional atomic images
around specific elements within a radius of a few nanometers. Three-dimensional
atomic images are reconstructed by applying discrete Fourier transform (DFT)
to hologram data. Presently, it takes long time to process this DFT. In this
study, the DFT program is parallelized by using a parallel programming language
XcalableMP. The DFT process, whose input is 21 holograms data of 179 × 360
points and output is a three-dimensional atomic image of 192 3 points, is executed
on PC cluster which consists of 8 nodes of Intel Xeon X5660 processors and 96
cores in total and we confirmed that the parallelized DFT execution is 94 times
faster than the sequential execution.
1 Introduction
X-ray fluorescence holography (XFH) is a three-dimensional middle range local
structure analysis method, which can prove 3D atomic images around specific
elements within a radius of a few nanometers[4]. Compared to other method such
as X-ray diffraction, which has been widely used for structure analysis of crystals
and other materials, XFH is more sensitive to atomic fluctuations, and therefore it is
useful for characterization of local lattice distortions.
In the XFH method, hologram data are obtained by experiments done at large
synchrotron facilities such as SPring-8 and KEK-PF. Three-dimensional atomic
images are reconstructed from the obtained holograms by Barton’s method[1, 2].
A. Kubota () · N. Happo
Hiroshima City University, Hiroshima, Japan
e-mail: kubota@hiroshima-cu.ac.jp; happo@hiroshima-cu.ac.jp
T. Matsushita
Nara Institute of Science and Technology, Ikoma, Nara, Japan
e-mail: t-matusita@ms.naist.jp
© The Author(s) 2021
M. Sato (ed.), XcalableMP PGAS Programming Language,
https://doi.org/10.1007/978-981-15-7683-6_8
205
Reconstruction from X-ray Fluorescence
Holograms with XcalableMP
Atsushi Kubota, Tomohiro Matsushita, and Naohisa Happo
Abstract X-ray fluorescence holography is a three-dimensional middle range local
structure analysis method, which can provide three-dimensional atomic images
around specific elements within a radius of a few nanometers. Three-dimensional
atomic images are reconstructed by applying discrete Fourier transform (DFT)
to hologram data. Presently, it takes long time to process this DFT. In this
study, the DFT program is parallelized by using a parallel programming language
XcalableMP. The DFT process, whose input is 21 holograms data of 179 × 360
points and output is a three-dimensional atomic image of 192 3 points, is executed
on PC cluster which consists of 8 nodes of Intel Xeon X5660 processors and 96
cores in total and we confirmed that the parallelized DFT execution is 94 times
faster than the sequential execution.
1 Introduction
X-ray fluorescence holography (XFH) is a three-dimensional middle range local
structure analysis method, which can prove 3D atomic images around specific
elements within a radius of a few nanometers[4]. Compared to other method such
as X-ray diffraction, which has been widely used for structure analysis of crystals
and other materials, XFH is more sensitive to atomic fluctuations, and therefore it is
useful for characterization of local lattice distortions.
In the XFH method, hologram data are obtained by experiments done at large
synchrotron facilities such as SPring-8 and KEK-PF. Three-dimensional atomic
images are reconstructed from the obtained holograms by Barton’s method[1, 2].
A. Kubota () · N. Happo
Hiroshima City University, Hiroshima, Japan
e-mail: kubota@hiroshima-cu.ac.jp; happo@hiroshima-cu.ac.jp
T. Matsushita
Nara Institute of Science and Technology, Ikoma, Nara, Japan
e-mail: t-matusita@ms.naist.jp
© The Author(s) 2021
M. Sato (ed.), XcalableMP PGAS Programming Language,
https://doi.org/10.1007/978-981-15-7683-6_8
205