G5NR Data Access Guide: Difference between revisions

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


== Background ==
== G5NR background ==
 
==== File spec ====
 
The G5NR data files are organized into ''collection''s 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.
 
==== Model config ====
 
== 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), collection name, year, month and day as follows:
 
|-resolution
|  |-type
|  |  |-collection
|  |  |  |-year
|  |  |  |  |-month
|  |  |  |  |  |-day
 
A web browser can be used to browse directories, read and retrieve files. To retrieve all files of collection inst01hr_2d_met1_Cx for the day 2006-09-18, one needs to point to
 
ftp://ftp.nccs.nasa.gov/c1440_NR_BETA9/DATA/0.5000_deg/inst/inst01hr_2d_met1_Cx/Y2006/M09/D16.
 
==== 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 <code>nc-config</code> (<code>nf-config</code> 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 =====


<nowiki>
The GEOS-5 Nature Run (Ganymed release) is a 2-year global, non-hydrostatic mesoscale simulation for the period 2005-2006. In addition to standard meteorological parameters (wind, temperature, moisture, surface pressure), this simulation includes 15 aerosol tracers (dust, seasalt, sulfate, black and organic carbon), O3, CO and CO2. This model simulation is driven by prescribed sea-surface temperature and sea-ice, daily volcanic and biomass burning emissions, as well as high-resolution inventories of anthropogenic sources.
#include<stdio.h>
#include<stdlib.h>
#include<netcdf.h>  // for reading NR files


/* Handle errors by printing an error message and exiting with a
GEOS-5 files are generated with the Network Common Data Form (NetCDF-4) library, which uses Hierarchical Data Format Version 5 (HDF-5) as the underlying format. NetCDF-4 is an open-source product of UCAR/Unidata (https://www.unidata.ucar.edu/software/netcdf/) and HDF-5 is developed by the HDF Group (http://www.hdfgroup.org/). One convenient method of reading GEOS-5 files is to use the netCDF library, but the HDF-5 library can also be used directly.
* 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
Each GEOS-5 file contains a '''collection''' of geophysical quantities that we will refer to as "fields" or "variables" as well as a set of coordinate variables that contain information about the grid coordinates. The variables as well as the complete structure of the file can be quickly listed using common utilities like <code>ncdump</code> or <code>h5dump</code>.
  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
For more details about File Spec, please see [[File:G5NR-Ganymed-7km_FileSpec-ON6-V1.0.pdf]].
  float minval, maxval;


  // misc counters
For model configuration, please see [[File:GMAO-OfficeNote-5-V1-22Oct2014.pdf]].
  int ctr;


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


  // read the data file
==== Global data ====
  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;
===== [[Recipe: Retrieve (global) data from FTP server|FTP]] =====
  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
===== [[Recipe: Retrieve (global) data from HTTPS server|HTTPS]] =====
  free(T);
 
  return 0;
}
</nowiki>


===== Fortran =====
==== Data subsets ====
===== [[Recipe: Retrieve data subsets using download tool|Download tool]] =====


<nowiki>
== Read downloaded data files ==
program g5nr_reader
==== [[Recipe: Fortran program to read data from downloaded file|Fortran program]] ====
==== [[Recipe: C program to read data from downloaded file|C program]] ====
==== [[Recipe: Python program to read data from downloaded file|Python script]] ====
==== [[Recipe: Matlab program to read data from downloaded file|Matlab script]] ====
==== [[Recipe: IDL program to read data from downloaded file|IDL script]] ====
==== [[Recipe: Visualize downloaded data using Panoply|Panoply]] ====


  use netcdf          ! for reading the NR files                                                                             
== OPeNDAP access ==


  implicit none
OPeNDAP is a data server architecture that allows users to use data files that are stored on remote computers with their favorite analysis and visualization tools. Opening an OPeNDAP file is as easy replacing the file name in the client software by an OPeNDAP URL. All G5NR collections that are provided by https/download-tool are also available on the OPeNDAP server


  ! File name                                                                                                               
  https://opendap.nccs.nasa.gov/dods/OSSE/G5NR/Ganymed/7km
  !  ---------                                                                                                               
  character(len=256) :: T_file


  !  Global, 4D array: (lon,lat,lev,time)                                                                                     
===== [[Recipe: Fortran program as OPeNDAP client|Fortran client]] =====
  !  ------------------------------------
===== [[Recipe: C program as OPeNDAP client|C client]] =====
  real, pointer :: T(:,:,:,:) => null()
===== [[Recipe: Python program as OPeNDAP client|Python client]] =====
 
===== [[Recipe: Matlab program as OPeNDAP client|Matlab client]] =====
  !  Miscellaneous                                                                                                             
===== [[Recipe: IDL program as OPeNDAP client|IDL client]] =====
  !  -------------                                                                                                             
===== [[Recipe: Visualize OPeNDAP data using Panoply|Panoply]] =====
  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
</nowiki>


===== Shmem example =====
===== 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.
<nowiki>
#!/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()                                                                                           
</nowiki>
====== pygrads ======


===== R =====
===== R =====


This example requires the [http://cran.r-project.org/web/packages/ncdf4/index.html ncdf4] and [http://cran.r-project.org/web/packages/rworldmap/index.html rworldmap] packages.
This example requires the [https://cran.r-project.org/web/packages/ncdf4/index.html ncdf4] and [https://cran.r-project.org/web/packages/rworldmap/index.html rworldmap] packages.


<nowiki>
<syntaxhighlight lang="rsplus">
> library(ncdf4)
> library(ncdf4)
> library(rworldmap)
> library(rworldmap)
Line 253: Line 64:
> jm <- 361
> jm <- 361
> lm <- 72
> 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")
> nc <- nc_open("https://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))
< t <- ncvar_get(nc,"t",start=c(1,1,1,37),count=c(im,jm,lm,1))
> str(t)
> str(t)
Line 261: Line 72:
   179.7  220.9  241.7  243.4  265.3  316.7  
   179.7  220.9  241.7  243.4  265.3  316.7  
> mapGriddedData(t[1:im,1:jm,71])
> mapGriddedData(t[1:im,1:jm,71])
</nowiki>
</syntaxhighlight>


===== NCL =====
===== NCL =====
Line 267: Line 78:
===== IDV =====
===== IDV =====


[http://www.unidata.ucar.edu/software/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.
[https://www.unidata.ucar.edu/software/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.
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 https://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
From the 'Dashboard' panel
Line 277: Line 88:
* 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'.
* 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'.


==== Proprietary clients ====
===== Matlab =====


===== IDL =====
-->

Latest revision as of 11:17, 10 April 2019

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

G5NR background

The GEOS-5 Nature Run (Ganymed release) is a 2-year global, non-hydrostatic mesoscale simulation for the period 2005-2006. In addition to standard meteorological parameters (wind, temperature, moisture, surface pressure), this simulation includes 15 aerosol tracers (dust, seasalt, sulfate, black and organic carbon), O3, CO and CO2. This model simulation is driven by prescribed sea-surface temperature and sea-ice, daily volcanic and biomass burning emissions, as well as high-resolution inventories of anthropogenic sources.

GEOS-5 files are generated with the Network Common Data Form (NetCDF-4) library, which uses Hierarchical Data Format Version 5 (HDF-5) as the underlying format. NetCDF-4 is an open-source product of UCAR/Unidata (https://www.unidata.ucar.edu/software/netcdf/) and HDF-5 is developed by the HDF Group (http://www.hdfgroup.org/). One convenient method of reading GEOS-5 files is to use the netCDF library, but the HDF-5 library can also be used directly.

Each GEOS-5 file contains a collection of geophysical quantities that we will refer to as "fields" or "variables" as well as a set of coordinate variables that contain information about the grid coordinates. The variables as well as the complete structure of the file can be quickly listed using common utilities like ncdump or h5dump.

For more details about File Spec, please see File:G5NR-Ganymed-7km FileSpec-ON6-V1.0.pdf.

For model configuration, please see File:GMAO-OfficeNote-5-V1-22Oct2014.pdf.

Download data files

Global data

HTTPS

Data subsets

Download tool

Read downloaded data files

Fortran program

C program

Python script

Matlab script

IDL script

Panoply

OPeNDAP access

OPeNDAP is a data server architecture that allows users to use data files that are stored on remote computers with their favorite analysis and visualization tools. Opening an OPeNDAP file is as easy replacing the file name in the client software by an OPeNDAP URL. All G5NR collections that are provided by https/download-tool are also available on the OPeNDAP server 

https://opendap.nccs.nasa.gov/dods/OSSE/G5NR/Ganymed/7km
Fortran client
C client
Python client
Matlab client
IDL client
Panoply
Retrieved from "https://geos5.org/wiki/index.php?title=G5NR_Data_Access_Guide&oldid=4307"