206
A. Kubota et al.
In Barton’s method, it takes long time to reconstruct the atomic images from the
obtained holograms.
In distributed-memory computing environment such as PC clusters and supercomputers, hybrid parallelization is widely used by describing inter- and intra- node
parallelism with Message-Passing Interface (MPI) [6] and OpenMP [7], respectively. However, it is pointed out that MPI programs tend to be complicated and
error-prone. Therefore, in order to improve productivity of parallel programming, a
variety of parallel programming languages, language extensions, and libraries have
been proposed. Some examples of them are High Performance Fortran (HPF) [5],
CoArray adopted in Fortran2008, UPC [9], which is based on C language, and
XcalableMP [10], in which distribution of data and parallelization of loops are
specified by directives. New parallel programming languages such as X10 [8] and
Chapel [3] are also proposed.
We adopted a hybrid parallel programming approach, in which inter- and intranode parallelism are described in XcalableMP and OpenMP, respectively, to parallelize the existing atomic image reconstruction program by Barton’s method written
in C language because it can be parallelized with small amount of modification.
In the rest of this chapter, X-ray fluorescence holography and reconstruction of
atomic images are explained in Sect. 2. Parallelization of atomic image reconstruction is explained in Sect. 3 and its performance results are shown in Sect. 4. Finally,
concluding remarks are given in Sect. 5
2 X-ray Fluorescence Holography
There are two modes in XFH, namely the normal mode and the inverse mode. In
this chapter, we focus on the inverse mode because it is mainly used in experiments
of XFH recently. Please refer to the literatures such as [4] in details.
In the inverse mode, the angle of a sample material to the incident X-ray is varied
as shown in Fig. 1 and intensity of X-ray fluorescence emitted from atoms in the
sample is measured by the detector.
As shown in Fig. 2, the incident X-ray approaching atom A and another incident
X-ray also approaching atom A after scattered by atom B form a constant wave of Xray around atom A. The pattern of the constant wave from atom A varies according
to the angle of the incident X-ray and resulted in the variation of the intensity of
the X-ray fluorescence from atom A. Experimental data obtained by measuring the
intensity of X-ray fluorescence make a hologram of the atomic image.
Incident X-ray wave approaching atom A directly corresponds to reference wave
of ordinary hologram and incident X-ray wave approaching atom A after scattered
by atom B corresponds to object wave.
A. Kubota et al.
In Barton’s method, it takes long time to reconstruct the atomic images from the
obtained holograms.
In distributed-memory computing environment such as PC clusters and supercomputers, hybrid parallelization is widely used by describing inter- and intra- node
parallelism with Message-Passing Interface (MPI) [6] and OpenMP [7], respectively. However, it is pointed out that MPI programs tend to be complicated and
error-prone. Therefore, in order to improve productivity of parallel programming, a
variety of parallel programming languages, language extensions, and libraries have
been proposed. Some examples of them are High Performance Fortran (HPF) [5],
CoArray adopted in Fortran2008, UPC [9], which is based on C language, and
XcalableMP [10], in which distribution of data and parallelization of loops are
specified by directives. New parallel programming languages such as X10 [8] and
Chapel [3] are also proposed.
We adopted a hybrid parallel programming approach, in which inter- and intranode parallelism are described in XcalableMP and OpenMP, respectively, to parallelize the existing atomic image reconstruction program by Barton’s method written
in C language because it can be parallelized with small amount of modification.
In the rest of this chapter, X-ray fluorescence holography and reconstruction of
atomic images are explained in Sect. 2. Parallelization of atomic image reconstruction is explained in Sect. 3 and its performance results are shown in Sect. 4. Finally,
concluding remarks are given in Sect. 5
2 X-ray Fluorescence Holography
There are two modes in XFH, namely the normal mode and the inverse mode. In
this chapter, we focus on the inverse mode because it is mainly used in experiments
of XFH recently. Please refer to the literatures such as [4] in details.
In the inverse mode, the angle of a sample material to the incident X-ray is varied
as shown in Fig. 1 and intensity of X-ray fluorescence emitted from atoms in the
sample is measured by the detector.
As shown in Fig. 2, the incident X-ray approaching atom A and another incident
X-ray also approaching atom A after scattered by atom B form a constant wave of Xray around atom A. The pattern of the constant wave from atom A varies according
to the angle of the incident X-ray and resulted in the variation of the intensity of
the X-ray fluorescence from atom A. Experimental data obtained by measuring the
intensity of X-ray fluorescence make a hologram of the atomic image.
Incident X-ray wave approaching atom A directly corresponds to reference wave
of ordinary hologram and incident X-ray wave approaching atom A after scattered
by atom B corresponds to object wave.