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      Just-In-Time 컴파일러를 이용한 파이썬 기반 지구동역학 코드 가속화 연구 = Boosting the Performance of Python-based Geodynamic Code using the Just-In-Time Compiler

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      https://www.riss.kr/link?id=A107745887

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      다국어 초록 (Multilingual Abstract)

      As the execution speed of Python is slower than those of other programming languages (e.g., C, C++, and FORTRAN), Python is not considered to be efficient for writing numerical geodynamic code that requires numerous iterations. Recently, many computational techniques, such as the Just-In-Time (JIT) compiler, have been developed to enhance the calculation speed of Python. Here, we developed two-dimensional (2D) numerical geodynamic code that was optimized for the JIT compiler, based on Python. Our code simulates mantle convection by combining the Particle-In-Cell (PIC) scheme and the finite element method (FEM), which are both commonly used in geodynamic modeling. We benchmarked well-known mantle convection problems to evaluate the reliability of our code, which confirmed that the root mean square velocity and Nusselt number obtained from our numerical modeling were consistent with those of the mantle convection problems. The matrix assembly and PIC processes in our code, when run with the JIT compiler, successfully achieved a speed-up 30× and 258× faster than without the JIT compiler, respectively. Our Python-based FEM-PIC code shows the high potential of Python for geodynamic modeling cases that require complex computations.
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      As the execution speed of Python is slower than those of other programming languages (e.g., C, C++, and FORTRAN), Python is not considered to be efficient for writing numerical geodynamic code that requires numerous iterations. Recently, many computat...

      As the execution speed of Python is slower than those of other programming languages (e.g., C, C++, and FORTRAN), Python is not considered to be efficient for writing numerical geodynamic code that requires numerous iterations. Recently, many computational techniques, such as the Just-In-Time (JIT) compiler, have been developed to enhance the calculation speed of Python. Here, we developed two-dimensional (2D) numerical geodynamic code that was optimized for the JIT compiler, based on Python. Our code simulates mantle convection by combining the Particle-In-Cell (PIC) scheme and the finite element method (FEM), which are both commonly used in geodynamic modeling. We benchmarked well-known mantle convection problems to evaluate the reliability of our code, which confirmed that the root mean square velocity and Nusselt number obtained from our numerical modeling were consistent with those of the mantle convection problems. The matrix assembly and PIC processes in our code, when run with the JIT compiler, successfully achieved a speed-up 30× and 258× faster than without the JIT compiler, respectively. Our Python-based FEM-PIC code shows the high potential of Python for geodynamic modeling cases that require complex computations.

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      참고문헌 (Reference)

      1 Wilbers, I. M., "Using cython to speed up numerical python programs" 9 : 495-512, 2009

      2 Mansour, "Underworld2: Python Geodynamics Modelling for Desktop" 5 (5): 1797-, 2020

      3 Van Der Walt, S., "The NumPy array: a structure for efficient numerical computation" 13 (13): 22-30, 2011

      4 Tackley, P. J., "Testing the tracer ratio method for modeling active compositional fields in mantle convection simulations" 4 (4): 8302-, 2003

      5 Gerya, T., "Tectonic overpressure and underpressure in lithospheric tectonics and metamorphism" 33 (33): 785-800, 2015

      6 Omelchenko, Y. A., "Self-adaptive time integration of flux-conservative equations with sources" 216 (216): 179-194, 2006

      7 Pedregosa, F., "Scikit-learn : Machine learning in Python" 12 : 2825-2830, 2011

      8 Virtanen, P., "SciPy 1.0: fundamental algorithms for scientific computing in Python" 17 : 261-272, 2020

      9 Srinath, K. R., "Python–the fastest growing programming language" 4 (4): 354-357, 2017

      10 Oliphant, T. E., "Python for scientific computing" 9 (9): 10-20, 2007

      1 Wilbers, I. M., "Using cython to speed up numerical python programs" 9 : 495-512, 2009

      2 Mansour, "Underworld2: Python Geodynamics Modelling for Desktop" 5 (5): 1797-, 2020

      3 Van Der Walt, S., "The NumPy array: a structure for efficient numerical computation" 13 (13): 22-30, 2011

      4 Tackley, P. J., "Testing the tracer ratio method for modeling active compositional fields in mantle convection simulations" 4 (4): 8302-, 2003

      5 Gerya, T., "Tectonic overpressure and underpressure in lithospheric tectonics and metamorphism" 33 (33): 785-800, 2015

      6 Omelchenko, Y. A., "Self-adaptive time integration of flux-conservative equations with sources" 216 (216): 179-194, 2006

      7 Pedregosa, F., "Scikit-learn : Machine learning in Python" 12 : 2825-2830, 2011

      8 Virtanen, P., "SciPy 1.0: fundamental algorithms for scientific computing in Python" 17 : 261-272, 2020

      9 Srinath, K. R., "Python–the fastest growing programming language" 4 (4): 354-357, 2017

      10 Oliphant, T. E., "Python for scientific computing" 9 (9): 10-20, 2007

      11 O'Boyle, N. M., "Pybel:a Python wrapper for the OpenBabel cheminformatics toolkit" 2 (2): 1-7, 2008

      12 Sun, Q., "PySCF: the Python based simulations of chemistry framework, Wiley Interdiscip" 8 : e1340-, 2018

      13 Dalcin, L. D., "Parallel distributed computing using Python" 34 (34): 1124-1139, 2011

      14 Schenk, O., "PARDISO : a high-performance serial and parallel sparse linear solver in semiconductor device simulation" 18 (18): 69-78, 2001

      15 King, S. D., "On topography and geoid from 2‐D stagnant lid convection calculations" 10 (10): Q03002-, 2009

      16 Chaves, J. C., "Octave and Python: High-level scripting languages productivity and performance evaluation" 429-434, 2006

      17 Lam, S. K., "Numba: A llvm based python jit compiler" 1-6, 2015

      18 Yuen, D. A., "Normal modes of the viscoelastic earth" 69 (69): 495-526, 1982

      19 Glerum, A., "Nonlinear viscoplasticity in ASPECT : benchmarking and applications to subduction" 9 (9): 267-294, 2018

      20 Samuel, H., "Modeling advection in geophysical flows with particle level sets" 11 (11): Q08020-, 2010

      21 Gurnis, M., "Mixing in numerical models of mantle convection incorporating plate kinematics" 91 (91): 6375-6395, 1986

      22 Hunter, J. D., "Matplotlib : A 2D graphics environment" 9 (9): 90-95, 2007

      23 Dabrowski, M., "MILAMIN: MATLAB‐based finite element method solver for large problems" 9 (9): Q04030-, 2008

      24 Garel, F., "Interaction of subducted slabs with the mantle transition-zone : A regime diagram from 2-D thermo-mechanical models with a mobile trench and an overriding plate" 15 (15): 1739-1765, 2014

      25 Furuichi, M., "Implicit solution of the material transport in stokes flow simulation : Toward thermal convection simulation surrounded by free surface" 192 : 1-11, 2015

      26 Leng, W., "Implementation and application of adaptive mesh refinement for thermochemical mantle convection studies" 12 (12): Q04006-, 2011

      27 Akeret, J., "HOPE : A Python just-in-time compiler for astrophysical computations" 10 : 1-8, 2015

      28 Gassmöller, R., "Flexible and Scalable Particle-in-Cell Methods With Adaptive Mesh Refinement for Geodynamic Computations" 19 (19): 3596-3604, 2018

      29 Thieulot, C., "FANTOM: Two-and three-dimensional numerical modelling of creeping flows for the solution of geological problems" 188 (188): 47-68, 2011

      30 O’Neill, C., "Ellipsis 3D : A particle-in-cell finite-element hybrid code for modelling mantle convection and lithospheric deformation" 32 (32): 1769-1779, 2006

      31 Thieulot, C., "ELEFANT: a user-friendly multipurpose geodynamics code" 6 (6): 1949-2096, 2014

      32 Behnel, S., "Cython : The best of both worlds" 13 (13): 31-39, 2011

      33 Cock, P. J., "Biopython : freely available Python tools for computational molecular biology and bioinformatics" 25 (25): 1422-1423, 2009

      34 Wang, H., "Advantages of a conservative velocity interpolation(CVI)scheme for particle-in-cell methods with application in geodynamic modeling" 16 : 2015-2023, 2015

      35 Aagaard, B. T., "A domain decomposition approach to implementing fault slip in finite-element models of quasi-static and dynamic crustal deformation" 118 (118): 3059-3079, 2013

      36 Samuel, H., "A deformable particle-in-cell method for advective transport in geodynamic modelling" 214 (214): 1744-1773, 2018

      37 Van Keken, P. E., "A comparison of methods for the modeling of thermochemical convection" 102 (102): 22477-22495, 1997

      38 Blankenbach, B., "A benchmark comparison for mantle convection codes" 98 (98): 23-38, 1989

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      학술지 이력

      학술지 이력
      연월일 이력구분 이력상세 등재구분
      2026 평가예정 재인증평가 신청대상 (재인증)
      2020-01-01 평가 등재학술지 유지 (재인증) KCI등재
      2017-01-01 평가 등재학술지 유지 (계속평가) KCI등재
      2013-01-01 평가 등재 1차 FAIL (등재유지) KCI등재
      2010-01-01 평가 등재학술지 유지 (등재유지) KCI등재
      2008-12-23 학술지명변경 한글명 : 물리탐사 -> 지구물리와 물리탐사
      외국어명 : Geophysical Exploration -> Geophysics and Geophysical Exploration
      KCI등재
      2008-01-01 평가 등재학술지 유지 (등재유지) KCI등재
      2006-01-01 평가 등재학술지 선정 (등재후보2차) KCI등재
      2005-01-01 평가 등재후보 1차 PASS (등재후보1차) KCI등재후보
      2003-01-01 평가 등재후보학술지 선정 (신규평가) KCI등재후보
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      기준연도 WOS-KCI 통합IF(2년) KCIF(2년) KCIF(3년)
      2016 0.15 0.15 0.15
      KCIF(4년) KCIF(5년) 중심성지수(3년) 즉시성지수
      0.14 0.15 0.311 0.07
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