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.
The G5NR data files are generated using the NetCDF-4 library [link] which uses HDF-5 [link] as the underlying format.
Model config
Getting data
ftp
[NOTE: THIS IS FOR TRIAL2 DATA]
The ftp location for G5NR data is ftp://ftp.nccs.nasa.gov/c1440_NR-Trial2 To access G5NR data via ftp one can either
- browser - use a browser to connect to the ftp site. The data is
Download tool
opendap
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
Shmem example
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()
pygrads
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])
NCL
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'.