G5NR Data Access Guide

For questions or comments please send an email to g5nr at lists dot nasa dot gov.

Background

File spec

The G5NR data files are organized into collections with each collection containing a specific group of variables (geophysical quantities). Each collection, as its name suggests, contains either instantaneous or time-averaged products, but not both. For more details, see [link].

The G5NR data files are generated using the NetCDF-4 library [link] which uses HDF-5 [link] as the underlying format.

Getting data

ftp/http

[NOTE: THIS IS FOR BETA9 DATA]

The ftp location for G5NR data is ftp://ftp.nccs.nasa.gov/c1440_NR_BETA9/DATA. At this location, the data is organized by resolution (0.5000_deg/0.0625_deg), type (const/inst/tavg/tdav)

A web browser can be used to browse directories, read and retrieve files. The data is organized as follows:

under c1440_NR_BETA9/DATA/

 |-0.0625_deg
 |  |-inst
 |  |  |-inst30mn_2d_aer1_Nx
 |  |  |  |-Y2005
 |  |  |  |  |-M05
 |  |  |  |  |  |-D15
 |  |  |  |  |  |-D16
 |  |  |  |  |  |-D17

Client access

In the following, we read the field 'T' (air temperature) from collection http://opendap.nccs.nasa.gov:9090/dods/OSSE/GEOS-5.12/BETA9/0.5000_deg/inst/inst01hr_3d_T_Cv.

Programming

These are simple programs to read the air temperature and compute its min/max. These codes require an OPeNDAP enabled NetCDF-4 library. The utility nc-config (nf-config for Fortran) bundled with the NetCDF-4 installation can be used to determine the necessary compiler flags. Individually downloaded files can be read similarly.

C

#include<stdio.h>
#include<stdlib.h>
#include<netcdf.h>  // for reading NR files

/* Handle errors by printing an error message and exiting with a
 * non-zero status. */
#define ERRCODE 2
#define ERR(e) {printf("Error: %s\n", nc_strerror(e)); exit(ERRCODE);}

int main(void){
  // file name
  char* T_file = "http://opendap.nccs.nasa.gov:9090/dods/OSSE/GEOS-5.12/BETA9/0.5000_deg/inst/inst01hr_3d_T_Cv";
  
  // netCDF ID for the file and data variable
  int ncid, varid;
 
  // global 4D array: (time,lev,lat,lon), one time step
  const int IM = 720;
  const int JM = 361;
  const int LM = 72;
  const int asyz = 1*LM*JM*IM;
  float *T = NULL;

  // hypercube for reading one array for a given time
  size_t start[4] = {36, 0, 0, 0}; // time step 37
  size_t count[4] = {1, LM, JM, IM}; // 1 time step, 3D (lon,lat,lev) array

  // return code
  int rc;

  // min/max values
  float minval, maxval;

  // misc counters
  int ctr;

  // allocate memory for T
  T = malloc(asyz*sizeof(float));

  // read the data file
  printf("Reading T..."); fflush(stdout);
  if (rc = nc_open(T_file, NC_NOWRITE, &ncid)) ERR(rc);
  if (rc = nc_inq_varid(ncid, "t", &varid)) ERR(rc);
  if (rc = nc_get_vara_float(ncid, varid, start, count, T)) ERR(rc);
  printf("done.\n"); fflush(stdout);

  // min/max of T
  minval = 1.0e15;
  maxval = -1.0e15;
  for (ctr=0; ctr<asyz; ctr++){
    if (T[ctr]<minval){
      minval = T[ctr];
    }
    if (T[ctr]>maxval){
      maxval = T[ctr];
    }
  }
  printf("min(T): %f\n", minval);
  printf("max(T): %f\n", maxval);

  // free memory
  free(T);
  
  return 0;
}

Fortran

program g5nr_reader

  use netcdf           ! for reading the NR files                                                                               

  implicit none

  !  File name                                                                                                                 
  !  ---------                                                                                                                 
  character(len=256) :: T_file

  !  Global, 4D array: (lon,lat,lev,time)                                                                                      
  !  ------------------------------------ 
  real, pointer :: T(:,:,:,:) => null()

  !  Miscellaneous                                                                                                              
  !  -------------                                                                                                              
  integer :: ierr
  integer :: im, jm, lm
  integer :: ncid, varid
  integer :: start(4), count(4)

  !  For now hard code file name and dimensions                                                                                
  !  ------------------------------------------                                                                                
  im = 720
  jm = 361
  lm = 72
  T_file = "http://opendap.nccs.nasa.gov:9090/dods/OSSE/GEOS-5.12/BETA9/0.5000_deg/inst/inst01hr_3d_T_Cv"

  !  Allocate the Global 4-D array with only 1 time level                                                                      
  !  ----------------------------------------------------                                                                      
  allocate(T(im,jm,lm,1))

  !  Hypercube for reading one 1 array for a given time                                                                         
  !  -------------------------------------------------                                                                          
  start = (/  1,  1,  1, 37 /)   ! time level 37                                                                                
  count = (/ im, jm, lm, 1  /)   ! 1 time level, 3D (lon,lat,lev) array                                                         

  !  Read the data file                                                                                                         
  !  ------------------                                                                                                         
  write(*,*)'Reading T'
  call check( nf90_open(T_file,NF90_NOWRITE,ncid), "opening T file")
  call check( nf90_inq_varid(ncid,"t",varid), "getting T varid")
  call check( nf90_get_var(ncid,varid,T,start=start,count=count), "reading T")
  call check( nf90_close(ncid), "closing T file")

  !  Orint min/max of arrays                                                                                                    
  !  -----------------------                                                                                                    
  write(*,*)'T: ', maxval(T),minval(T)

  !  All done                                                                                                                   
  !  --------                                                                                                                   

contains

  subroutine check(status, loc)

    integer, intent(in) :: status
    character(len=*), intent(in) :: loc

    if(status /= NF90_NOERR) then
       write (*,*) "Error at ", loc
       write (*,*) NF90_STRERROR(status)
    end if

  end subroutine check

end program g5nr_reader

Free clients

In this section we read air temperature, compute it min/max (as with the 'programming' examples) and display the surface air temperature.

Python

netcdf4-python

If netcdf4-python module is available, the following script would read air temperature for the specified time, compute its min and max values and plot it.

#!/usr/bin/env python                                                                                 

import sys
import numpy as np
import netCDF4 as nc4
import matplotlib.pyplot as plt                                                                       
                                                                                                      
from mpl_toolkits.basemap import Basemap                                                              

rootgrp = nc4.Dataset('http://opendap.nccs.nasa.gov:9090/dods/OSSE/GEOS-5.12/BETA9/0.5000_deg/inst/inst01hr_3d_T_Cv', 'r')

# read air temperature                                                                                
print 'Reading T for time=37...',; sys.stdout.flush()
Ttime37 = rootgrp.variables['t'][36,:,:,:]
print 'done.'; sys.stdout.flush()

# min/max                                                                                             
print 'min(T):', np.min(Ttime37)
print 'max(T):', np.max(Ttime37)

# set up cylindrical map                                                                              
m = Basemap(                                                                                          
    projection='cyl',                                                                                 
    llcrnrlat=-90, urcrnrlat=90,                                                                      
    llcrnrlon=-180, urcrnrlon=180,                                                                    
    resolution='c'                                                                                    
    )                                                                                                 
m.drawcoastlines(linewidth=0.5)                                                                       
m.drawmapboundary()                                                                                   
                                                                                                      
# plot contour                                                                                        
level = 71                                                                                            
X = np.arange(-180.0, 180.0, .5)                                                                      
Y = np.arange(-90.0, 90.1, .5) # 90 is the last element                                               
cp = plt.contour(X, Y, T[0,level,:,:], 20, zorder=2)                                                  
plt.clabel(cp, inline=1, fontsize=9)                                                                  
plt.title('Air temperature at the surface')                                                           
plt.show()                                                                                            

R

This example requires the ncdf4 and rworldmap packages.

> library(ncdf4)
> library(rworldmap)
Loading required package: sp
### Welcome to rworldmap ###
For a short introduction type : 	 vignette('rworldmap')
> im <- 720
> jm <- 361
> lm <- 72
> nc <- nc_open("http://opendap.nccs.nasa.gov:9090/dods/OSSE/GEOS-5.12/BETA9/0.5000_deg/inst/inst01hr_3d_T_Cv")
< t <- ncvar_get(nc,"t",start=c(1,1,1,37),count=c(im,jm,lm,1))
> str(t)
 num [1:720, 1:361, 1:72] 218 218 218 218 218 ...
> summary(t)
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
  179.7   220.9   241.7   243.4   265.3   316.7 
> mapGriddedData(t[1:im,1:jm,71])

IDV

IDV is an OPeNDAP tool that can access and display the nature run data. In our OPenDAP server, all files are time aggregated, so they appear as a single dataset for each location.

This is an example to open and display the field 'T' (air temperature) from the collection 'inst01hr_3d_T_Cv'. The OPenDAP URL for this dataset is http://opendap.nccs.nasa.gov:80/dods/OSSE/GEOS-5.12/BETA9/0.5000_deg/inst/inst01hr_3d_T_Cv. The following steps are valid for IDV version 5.0u1 running on a Linux desktop.

From the 'Dashboard' panel

• Select Data Choosers -> URLS.In the URL field, enter the above OPenDAP URL and click on 'Add Source'

• Select Field Selector and choose the 3D field'air_temperature'. The 'Times' tab lists all the available levels and times for this data. At this point, one can select specific times, level and regions (subsetting) from the 'Times' and 'Level' and 'Region' tabs. Click on 'Create Display'.