Integrated Grid workflow for mesoscale weather modeling

and visualizationZhizhin, M., A. Polyakov, D.

Medvedev, A. Poyda, S. BerezinSpace Research Institute of the Russian Academy of Sciences

Abstract• For the model input and output we use a scalable parallel storage and data mining

system called ActiveStorage. It can store different types of weather data, provided they are in the same Command Data Model (UNIDATA CDM): NCEP reanalysis, NCDC stations weather data, MM5 model output.

• The MM5 is a mesoscale weather forecast model. For the input boundary conditions the model takes basic parameters such as elevation, air pressure and temperature, etc. It can ingest reanalysis and direct observation data. As the output the model provides high-resolution regional weather grids.

• To make the MM5 input data and the modeling results accessible on the Grid to the Earth Science community, we have developed a set of grid services (resources and activities) inside the OGSA-DAI (both ver. 2 and 3) grid service container.

• To visualize the weather data we have developed a special plugin for the NASA World Wind which can read the data directly from the OGSA-DAI resources and plot it over the 3D globe in different ways, such as contour lines, filled areas and vector fields.

Active Storage, Modeling, Data Mining and Visualization Services

Active Storage

Common Data Model

Microsoft SQL Server Cluster

OGSA-DAI and Matlab API

Numerical Modeling

Parallel mesoscale meteorologial model MM5

Windows Compute Cluster + MPI parallelization

Data Analysis

Environmental Scenario Search Engine (ESSE)

Trend and change detection algorithms

Visaulization

Microsoft Virtual EarthNASA World Wind

EVL UIC Scalable Graphics Environment (SAGE+SAIL)

Derived products from satellite data

Weather observations and reanalysis time series

Geographical information: elevation, hydrology, ...

Raw data Input

Model output

Tim

e s

eri

es

Gri

ds

Tra

ject

ori

es

Trends and relations

Raw data

Numerical models

Geographical information

ActiveStorage• ActiveStorage is a generic storage for arrays of primitive

data types.

• Its data model is based on the Unidata’s Common Data Model, used in netCDF, HDF5 and OpenDAP.

• Basically, ActiveStorage is a SQL Server database with CLR stored procedures and a client library.

• The stored procedures and the client library provide an abstraction layer for data access.

• Large arrays are split into chunks and can be spread across several parallel database servers for better performance.

SQL Server 2005/2008 DBSQL Server 2005/2008 DB

ActiveStorage components

Metadata tables

Metadata tables

Data and directory

tables

Data and directory

tables

Stored proceduresClient library

Common Data Model

This is the Common Data Model (CDM) used in the recent versions of OpenDAP, netCDF and HDF5. Its purpose is the representation of multidimensional scientific data.

-name

Group

-name-value-dataType

Attribute

-name-shape-dataType

Variable

-name-length

Dimension-char-byte-short-int-long-float-double-String

DataType

-name

Dataset

How it works

SQL Server DB

SQL Server DBClient library

2. Issue commands to the database server

3. Select the requested data from several chunks

3. Return the data parts to the client library4. Assemble the data parts into

one multi-dimensional array

1. Pass multi-dimensional data request to the client library

ApplicationApplication

Parallel query processing

SQL Server DB 1

SQL Server DB 1

Client libraryApplicationApplication

SQL Server DB 2

SQL Server DB 2

Parallel query performance

1 database server

4 parallel database servers

NCEP/NCAR Weather Reanalysis• Continually updating gridded data set

• Incorporates observations and global climate model output

• 74 weather parameters

• 5000 netCDF files, 30 – 500 MB each

NCDC Integrated Surface Database

• 1901 – 2008 time coverage.

• 30 million sensors.

• 1.7 billion observations.

Fixed ground stations Ships Mobile stations Buoys

0189010020999992007022817004+80050+016250FM-12+000899999V0202201N008019999999N0090001N1+00631+00541098651ADDGA1031+003009999KA1120N+99999...

date time lat lon

Mandatory data section Additional data sectionSection markerControl data section

• 470 000 ASCII files packed with gzip.

• 50 GB packed; 400 GB unpacked.

When you’ve downloaded and unpacked the data...

import ru.wdcb.mdb.NcConnectorimport com.microsoft.sqlserver.jdbc.SQLServerDriver s = 'jdbc:sqlserver://localhost:1433;databaseName=NCEP_01;user=guest;password=guest';connector = NcConnector();ncid = connector.nc_open(s,0);varid = connector.nc_inq_varid(ncid,'air'); origin = [0 0 10 10];size = [80000 1 1 1];stride = [1 1 1 1];A = connector.nc_get_vars_short(ncid,varid,origin,size,stride); plot(A, 'DisplayName', 'A', 'YDataSource', 'A'); figure origin = [0 0 0 0];size = [1 1 73 144];stride = [1 1 1 1];B = connector.nc_get_vars_shortm(ncid,varid,origin,size,stride); B = reshape(B,[73 144]);imagesc (B); figure(gcf);

MATLAB script using ActiveStorage library

Environmental Data Service: OGSA-DAI plugin

NCEPdatabase

NWSdatabase

SPIDRdatabases

Tomcat

DAI

Clients

Dataexport

getMetadata

Metadata XML

getProperty: sources

sources list

getXMLData

data XML

getNetCDFData

URL to NetCDF file

NetC

DF

fileserialisation

User

NetCDF file

ActiveStorage

MM5weathermodel

MS Excel

Any client

Activities for data export• XML output stream

– We have plugin for NASA World Wind to visualize XML-formatted data

– Can easily be transformed using XSLT to web page or another XML document, e.g. MS Excel

– Can be used as input for ESSE fuzzy logic search engine

• NetCDF binary data file– Standard for scientific data storage in files– There are several visualization programs for NetCDF– Compatible with Unidata Common Data Model standard

Data flow management by OGSA-DAI

OGSA-DAI query fromsingle data source

OGSA-DAI query fromdistributed data sources

Parallel mesoscale weather model MM5

Same Source Parallel MM5• Source code for the parallel

MPI and the single process MM5 model are the same

• Automated parallel code generation from MM5 sources by ANL:

– FLIC compiler– RSL library for model domain

segmentation and message exchange

• We have ported MM5 code to the MS Windows Server 2008 HPC platform

MM5 model as a grid client

Visualizing data from ActiveStorage with NASA WorldWind

A NASA WorldWind plugin, developed at the Moscow State University allows to retrieve data from ActiveStorage via an OGSA-DAI service.

Several kinds of visualization are available:- isolines- color map- vector field

OGSA-DAI services can be used by other applications to retrieve data from ActiveStorage

NASA World Wind as a grid client

Using OGSA-DAI services and a special API plugin, the NASA World Wind can visualize both the MM5 input and output datasets