Transcript ESMPy - ESMF

ESMPy: The Python Interface to
the Earth System Modeling
Framework
Ryan O’Kuinghttons, Robert Oehmke
Cecelia DeLuca, Gerhard Theurich
Peggy Li, Joseph Jacob
Cooperative Institute for Research in Environmental Sciences
NOAA Environmental Software Infrastructure and Interoperability Project
American Meteorological Society Annual Meeting
Atlanta, Georgia
February 4, 2014
Introduction
• The Earth System Modeling Framework (ESMF) is open source software
for building modeling components, and coupling them together to
form weather prediction, climate, coastal, and other applications.
•
Supports a full Fortran and limited C and Python interfaces
• ESMF provides a mature high performance regridding package
• Transforms data from one grid to another by generating and applying
interpolation weights
• Supports structured and unstructured, global and regional, 2D
and 3D grids, with many options
• Fully parallel and highly scalable
• The Python interface to ESMF (ESMPy) offers
access to the regridding functionality and other
related features of ESMF.
vs.
ESMP
ESMPy
• Thin layer on top C interfaces to
ESMF regridding
ESMPYESMP
• Python package surrounding
ESMP and other related modules
• Grid objects created in memory
• Basic masking capability
• Grid objects created in memory
or from file
• Simple testing layer
• Field derived from MaskedArray
• Regrid testing framework
ESMPy
Contributed Package
Candidates:
Time Manager
ESMP
OCGIS
• Nose testing
What does ESMF gain
with a Python Interface?
• Enables ESMF regridding to be used with very little effort, in an object
oriented way:
• Regridding applied as a callable Python object
• Numpy array access to distributed data
• Grid creation from NetCDF files in standard formats
• Some users report computation times reduced from hours to minutes
• Enables ESMF regridding to be used in other scientific packages with
Python-based workflows – current users include:
• UV-CDAT (PCMDI) – Ultrascale Visualization Climate Data Analysis Tools
• PyFerret (NOAA) – Python based interactive visualization and analysis
environment
• Iris (Met Office) – Python library for visualizing meteorological and
oceanographic data sets.
• Community Surface Dynamics Modeling System (CU-Boulder) – tools for
hydrological and other surface modeling processes
Supported Grids and Methods
• Spherical coordinates – bilinear, higher order patch [1,2], or first order
conservative regridding with:
• Global or regional 2D logically rectangular grids
• 2D unstructured meshes composed of triangles or quadrilaterals
• Cartesian (x,y) coordinates:
• Bilinear, higher order patch or first order conservative regridding between
any pair of:
• 2D meshes composed of triangles and quadrilaterals
• 2D logically rectangular grids composed of a single patch
• Bilinear and first order conservative regridding between any pair of:
• 3D meshes composed of hexahedrons
• 3D logically rectangular grids composed of a single patch
2D Unstructured Mesh
From www.ngdc.noaa.gov
FIM Unstructured Grid
Regional Grid
ESMPy Classes
• Manager (esmpymanager module)
• Initialize and Finalize
• Logging
• Virtual Machine (parallel distribution)
• Grid
• Logically rectangular discretization object
• Mesh
• Unstructured mesh discretization object
• Field
• Grid or Mesh plus data, mask and metadata
• Derived type of the Numpy MaskedArray
• Regrid
• Callable object which operates on two Fields to compute and apply
interpolation weights
A Few Words on Data
Conventions…
The following data conventions makes it easier to use data and tools.
ESMPy grid files follow standard data file formats:
•Climate and Forecast (CF) grid conventions
• UGRID - candidate CF convention for unstructured grids[3]
• GRIDSPEC – accepted CF convention for logically rectangular grids [4]
•SCRIP – Spherical Coordinate Remapping and Interpolation Package [5]
• Legacy format for 2D logically rectangular or 2D unstructured grids
•ESMF
• Custom format for unstructured grids, more efficient storage than SCRIP
when used with ESMF codes
From-file Grid/Mesh creation
ESMPYESMP
MESH
GRID
• SCRIP format
• SCRIP (2D only)
• GRIDSPEC is not fully supported,
expected in a patch release by
the end of February 2014
• UGRID (2D and 3D)
• Examples:
• ESMFMESH (2D and 3D)
• Examples:
• Irregular cubed sphere
• Latitude longitude
• Icosahedral
• Gaussian
BOTH
• Regional and global
• Parallel implementation supported for basic
regridding - no masking or coordinate retrieval
Code – Grid
Create a Grid from a SCRIP formatted NetCDF file:
import ESMF
grid = ESMF.Grid(filename=“ll2.5deg_grid.nc”,
filetype=ESMF.FileFormat.SCRIP)
OPTIONS:
•is_sphere – set to False for a regional grid
•add_corner_stagger – set to True to add the corner stagger location defined
in the file, this is needed for conservative regridding
•add_user_area – set to True to read cell areas from the grid file, otherwise they
will be calculated by ESMF internally
•add_mask – set to True to generate missing value attribute in ‘varname’
•varname – missing value variable name for the mask
•**coord_names – two element array containing name of latitude and longitude
variables in a GRIDSPEC file, for the case when multiple coordinates are defined
Code – Mesh
Create a Mesh from UGRID formatted NetCDF file:
import ESMF
mesh = ESMF.Mesh(filename=“FVCOM_grid2d_20120314.nc”,
filetype=ESMF.FileFormat.UGRID,
meshname=‘fvcom_mesh’)
OPTIONS:
•convert_to_dual – set to False to NOT calculate the dual mesh
•add_user_area – set to True to read cell areas from the file, otherwise they
will be calculated by ESMF internally
•meshname – name of the mesh metadata variable in a UGRID file
•add_mask – set to True to generate missing value attribute in ‘varname’
•varname – missing value variable name for the mask
Code - Regridding
Conservative regridding:
from ESMF import Regrid
r1to2 = Regrid(field1, field2,
regrid_method=ESMF.RegridMethod.CONSERVE)
destination_field = r1to2(source_field)
OPTIONS:
•src_mask_values – numpy array of values to use for a mask on the source field
•dst_mask_values – numpy array of values to use for a mask on the source field
•regrid_method – (RegridMethod.BILINEAR(default), PATCH, or CONSERVE)
•pole_method – specifies the type of artificial pole to construct on source grid
(PoleMethod.NONE
(default conserve), ALLAVG (default nonconserve), NPNTAVG, TEETH)
•regridPoleNPnts – number of points to use with PoleMethod.NPNTAVG
•unmapped_action – specifies which action to take if a destination point is found which does not map to
any source points (UnmappedAction.ERROR(default) or IGNORE)
•src_frac_field– returned numpy array with weights corresponding to fractions of each source field
value which contributes to the total mass of the source field
•dst_frac_field– returned numpy array with weights corresponding to fractions of each destination
field value which contributes to the total mass of the destination field
Regridding Results
r1to2 = Regrid(field1, field2, regrid_method=RegridMethod.CONSERVE)
where:
f(phi,theta) = 2 + cos(theta)**2 * cos(2*phi)
Source grid: fv1.9x2.5_050503.nc - 1.9x2.5 CAM finite volume grid
Destination grid: wr50a_090614.nc - Regional 205x275 grid
Mean relative error
=
Maximum relative error =
Conservation error
=
3.19E-03
1.93E-02
7.11E-15
Requirements, Supported
Platforms, Limitations, etc...
Requirements:
- Python 2.6, 2.7
- Numpy 1.6.1/2 (ctypes)
- ESMF installation (with NetCDF)
Testing:
- Regression tested nightly on 5 platforms
Supported Platforms:
- Linux, Darwin, and Cray
- Gfortran
- OpenMPI
Limitations:
- No object for collections of Fields
- No access to Field bounds
Installation:
-python setup.py build –ESMFMKFILE=<path_to_esmf.mk> install
Status and Future Work
• ESMPy is still in beta, production release expected later this year
• ESMP is in production and fully supported (fewer features)
• Later in 2014:
• Python layer functionality of Grid/Mesh created from file
• OpenClimateGIS
• Data type for observational data streams, and regridding to/from
• Time management, calendar
• Components?
OpenClimateGIS Overview
https://www.earthsystemcog.org/projects/openclimategis/
•
•
•
•
•
Developed by the NESII Group in association with the
NCPP Project under funding provided by the NOAA
Climate Program Office.
Python package designed to ease the “localization”
and accessibility of high-dimensional scientific
datasets
Primary Features: geospatial subsetting,
standardized calculation, bundling, and format
conversion
Could benefit from ESMPy conservative regridding
ESMPy could use subsetting capability and
access/conversion to/from GIS data formats
Will introduce a number of new dependencies:
•
GDAL, Shapely, Fiona, netCDF4-Python
https://www.earthsystemcog.org/projects/openclimategis/dependencies
https://github.com/NCPP/ocgis
Questions?
Please contact:
[email protected]
with questions or feature requests
Download:
http://earthsystemcog.org/proj
ects/ESMPy/releases
References:
1.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.
2.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.
3. UGRID wiki:
http://publicwiki.deltares.nl/display/NETCDF/Deltares+CF+proposal+for+Unstructured+Grid+data+model
4.GridSpec wiki: https://ice.txcorp.com/trac/modave/wiki/CFProposalGridspec
5.Jones, P.W. SCRIP: A Spherical Coordinate Remapping and Interpolation Package.
http://www.acl.lanl.gov/climate/software/SCRIP. Los Alamos National Laboratory Software Release LACC 98-45
ctypes bindings to ESMF
Interfacing with ctypes:
_ESMF.ESMC_GridGetCoord.restype = ctypes.POINTER(ctypes.c_void_p)
_ESMF.ESMC_GridGetCoord.argtypes = [ctypes.c_void_p, ctypes.c_int, ctypes.c_uint,
numpy.ctypeslib.ndpointer(dtype=numpy.int32),
numpy.ctypeslib.ndpointer(dtype=numpy.int32),
ctypes.POINTER(ctypes.c_int)]
gridCoordPtr = _ESMF.ESMC_GridGetCoord(grid.struct.ptr, coordDim, staggerloc,
exclusiveLBound, exclusiveUBound,
ctypes.byref(lrc))
# adjust bounds to be 0 based
exclusiveLBound = exclusiveLBound - 1
Allocating Numpy array buffers for memory allocated in ESMF:
buffer = numpy.core.multiarray.int_asbuffer(
ctypes.addressof(pointer.contents),
numpy.dtype(ESMF2PythonType[self.type]).itemsize*size)
array = numpy.frombuffer(buffer, ESMF2PythonType[self.type])
Switching between Fortran and C array striding:
array = numpy.reshape(array, self.size_local[stagger], order='F')