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@lists.nasa.gov.
== G5NR background ==


== 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.


==== File spec ====
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 <code>ncdump</code> or <code>h5dump</code>.


==== Model config ====
For more details about File Spec, please see [[File:G5NR-Ganymed-7km_FileSpec-ON6-V1.0.pdf]].


== Getting data ==
For model configuration, please see [[File:GMAO-OfficeNote-5-V1-22Oct2014.pdf]].


==== ftp, http ====
== Download data files ==


==== Download tool ====
==== Global data ====


==== opendap ====
<!--
===== [[Recipe: Retrieve (global) data from FTP server|FTP]] =====
-->


== Client access ==
===== [[Recipe: Retrieve (global) data from HTTPS server|HTTPS]] =====


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


==== Programming ====
== Read downloaded data files ==
==== [[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]] ====


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.
== OPeNDAP access ==


===== C =====
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


<code>
  https://opendap.nccs.nasa.gov/dods/OSSE/G5NR/Ganymed/7km
  #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;
}
</code>


===== Fortran =====
===== [[Recipe: Fortran program as OPeNDAP client|Fortran client]] =====
 
===== [[Recipe: C program as OPeNDAP client|C client]] =====
<code>
===== [[Recipe: Python program as OPeNDAP client|Python client]] =====
program g5nr_reader
===== [[Recipe: Matlab program as OPeNDAP client|Matlab client]] =====
===== [[Recipe: IDL program as OPeNDAP client|IDL client]] =====
  use netcdf          ! for reading the NR files                                                                             
===== [[Recipe: Visualize OPeNDAP data using Panoply|Panoply]] =====
<!--
  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
</code>


===== Shmem example =====
===== Shmem example =====


==== Free clients ====
===== R =====


===== Python =====
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.


====== netcdf4-python ======
<syntaxhighlight lang="rsplus">
 
> library(ncdf4)
If netcdf4-python module is available, the following script would read and compute the min/max value of air temperature for the specified time.
> library(rworldmap)
 
Loading required package: sp
<code>
### Welcome to rworldmap ###
#!/usr/bin/env python                                                                               
For a short introduction type : vignette('rworldmap')
> im <- 720
import sys
> jm <- 361
import numpy as np
> lm <- 72
import netCDF4 as nc4
> 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))
rootgrp = nc4.Dataset('http://opendap.nccs.nasa.gov:9090/dods/OSSE/GEOS-5.12/BETA9/0.5000_deg/inst/inst01hr_3d_T_Cv', 'r')
> str(t)
  num [1:720, 1:361, 1:72] 218 218 218 218 218 ...
# read air temperature                                                                               
> summary(t)
print 'Reading T for time=37...',; sys.stdout.flush()
  Min. 1st Qu. Median    Mean 3rd Qu.    Max.
  Ttime37 = rootgrp.variables['t'][36,:,:,:]
  179.7  220.9  241.7  243.4  265.3  316.7
print 'done.'; sys.stdout.flush()
> mapGriddedData(t[1:im,1:jm,71])
   
</syntaxhighlight>
# min/max                                                                                           
print 'min(T):', np.min(Ttime37)
print 'max(T):', np.max(Ttime37)
</code>
 
====== pygrads ======


===== NCL =====
===== NCL =====
Line 202: 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 212: 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
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