Expanding regridding capabilities of the earth system modeling framework
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Expanding Regridding Capabilities of the Earth System Modeling Framework. Andrew Scholbrock University of Colorado – Boulder Robert Oehmke NOAA/CIRES. Outline. Introduction Background Information Incorporating LibCF Regridding into ESMF Current Status Future Work. Introduction.

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Expanding Regridding Capabilities of the Earth System Modeling Framework

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Expanding regridding capabilities of the earth system modeling framework

Expanding Regridding Capabilities of the Earth System Modeling Framework

Andrew Scholbrock

University of Colorado – Boulder

Robert Oehmke

NOAA/CIRES


Outline

Outline

  • Introduction

  • Background Information

  • Incorporating LibCF Regridding into ESMF

  • Current Status

  • Future Work


Introduction

Introduction

  • This project aims to allow regridding software that follows a proposed metadata standard (Gridspec) to be used within the Earth System Modeling Framework (ESMF)

  • As new regridding capabilities are developed they will be automatically available through ESMF


Expanding regridding capabilities of the earth system modeling framework

ESMF

  • Framework developed by a multi-agency consortium [1]

  • Provides standard interfaces for model components

  • Provides standard structure for transferring data between model components

  • Provides a range of utilities to ease coupling

    • Data regridding

    • Data redistribution

    • Time management

    • Error handling


Gridspec

Gridspec

  • Metadata convention developed at NOAA GFDL [2]

  • Proposed for inclusion in the Climate and Forecast (CF) [3] conventions

  • Gridspec represents grids as mosaics and tiles

    • Mosaic files contain a list of tile files and how they are connected

    • Tile files contain actual grid coordinate information

http://www.gfdl.noaa.gov/~vb/gridstd/gridstdse2.html#x4-160002.7


Libcf

LibCF

  • Utility library developed at Unidata

  • Built on top of NetCDF [4] Climate and Forecast (CF) conventions

  • LibCF [3] includes the capability to:

    • Manipulate Gridspec metadata on a NetCDF file

    • Create Gridspec files

    • Regrid between different Gridspec files

  • LibCF is still in alpha release mode


Regridding overview

Regridding Overview

  • Climate and other models require coupling of modeling components (e.g. atmosphere, ocean)

  • Different modeling components may require different grids

    • e.g. different shapes or different resolutions

  • Regridding needs to be performed to move data between components on different grids

  • Steps involved in regridding:

    • Generate interpolation weights

    • Apply weights to interpolate field using a sparse matrix multiply


Esmf regridding

ESMF Regridding

  • Methods of accessing regridding:

    • Online

      • Subroutine calls which calculate weights during a model run

      • Can get weights or feed directly into ESMF sparse matrix multiply

    • Offline

      • Application which generates a netCDF interpolation weight file from two netCDF grid files

  • Computation of weights can be done in parallel

  • Supported grids:

    • 2D meshes composed of triangles or quadrilaterals

    • 3D meshes composed of hexahedra

    • 2D/3D logically rectangular grids

    • Cubed sphere

  • Supported interpolation methods:

    • Bilinear

    • Higher order finite element patch recovery [5][6]

    • Conservative (beta version)

  • Not all combinations of the above are supported


Libcf regridding

LibCF Regridding

  • LibCF takes Gridspec files and field data files as input to generate weights and interpolate data

    • If just Gridspec files are specified then only interpolation weights are generated

  • LibCF supports regridding between mosaics of logically rectangular grid tiles (e.g. cubed sphere, single tile logically rectangular)

  • Currently first order conservative interpolation methods are supported, and some specific bilinear cases


Combining esmf and libcf

Combining ESMF and LibCF

  • LibCF was introduced into the ESMF online regridding software.

  • This was somewhat awkward because LibCF requires Gridspec files as input, but ESMF online regridding holds grid descriptions in memory.

  • As a result, ESMF must convert its grid descriptions to Gridspec files and then have LibCF read them in.

  • This works, but more efficient connections could be made with regridding libraries that did not require file input.


Implementation steps getting interpolation weights

Implementation Steps:Getting Interpolation Weights

  • Write ESMF grids to NetCDF files

    • Take an existing ESMF grid and get the coordinate information out of it

    • Write out the coordinate information to a NetCDF file

      • Done using ESMF I/O functionality

    • Create mosaic files from the NetCDF grid

      • Done using LibCF’s make_mosaic function

  • Get interpolation weights from LibCF

    • Call LibCF’s regridding function through ESMF calls

    • Read in LibCF’s interpolation weights into ESMF

    • Convert interpolation data to a form that ESMF’s sparse matrix multiply can use


Implementation steps weight application

Implementation Steps:Weight Application

  • Apply LibCF interpolation weights to field data using the ESMF sparse matrix multiply call

  • Future regrid calls to updated field data can bypass the LibCF interpolation weight generation step

    • This holds as long as the grids involved remain the same


Libcf esmf regridding flow

LibCF/ESMF Regridding Flow

ESMF

Destination Grid

Source Grid

Weight Matrix

Create Mosaic

Write Tile

Create Weights

Read Weights

LibCF

Regrid

fregrid

Source Variable Data

Destination Variable Data

make_mosaic

File I/O

Legend:

NetCDF File

Destination Tile

Source Tile

Source Mosaic

Destination Mosaic

Remap File

API Call

ESMF Data


Esmf user interface for regridding with libcf

ESMF User Interface for Regridding with LibCF

  • Actual interface that users employ contains two steps:

    • ESMF_FieldRegridStore(): Provide source/destination grids and receive interpolation weights

    • ESMF_FieldRegrid(): Provide interpolation weights and source field data to receive interpolated field data corresponding to the destination grid

  • This is the same sequence of calls used for pure ESMF regridding


Current status

Current Status

  • Can read interpolation weight information generated by LibCF into ESMF sparse matrix representation and perform a regrid.

  • Can write ESMF grid structures to Gridspec files

  • ESMF restriction:

    • Writing Gridpsec files from ESMF is serial and thus restricts the scaling of the final code

  • Intersection of LibCF/ESMF capabilities:

    • Only supports single tile logically rectangular grids

  • LibCF restriction:

    • Only supports first order conservative remapping for this geometry


Future work

Future Work

  • Parallel I/O for writing Gridspec files

  • Switch to non-file based interface if LibCF develops one

  • Allow for regridding of more complicated grids including the cubed sphere


References

References

  • Hill, C., C. DeLuca, V. Balaji, M. Suarez, and A. da Silva (2004). Architecture of the Earth System Modeling Framework. Computing in Science and Engineering, Volume 6, Number 1, pp. 18-28.

  • Balaji, V., Liang, Z. Gridspec: A Standard for the Description of Grids Used in Earth System Models. http://www.gfdl.noaa.gov/~vb/gridstd/gridstd.html

  • The CF Library Users Guide. http://www.unidata.ucar.edu/software/libcf/docs/libcf.html

  • Hartnett, E. and Rew, R., Experience with an enhanced netCDF data model and interface for scientific data access, 88th AMS Annual Meeting, 24th Conference on IIPS, 2008.

  • Khoei S.A., Gharehbaghi A. R. The superconvergent patch recovery technique and data transfer operators in 3d plasticity problems. Finite Elements in Analysis and Design, 43(8), 2007.

  • Hung K.C, Gu H., Zong Z. A modified superconvergent patch recovery method and its application to large deformation problems. Finite Elements in Analysis and Design, 40(5-6), 2004.

    Questions?

    [email protected]


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