GEOS-5

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.


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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.
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 format and organization =====
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.
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-4 library, but the HDF-5 library can also be used directly. These files can be easily read by applications such as IDL, Matlab, GrADS, FERRET, NCL, Panoply as  
well in Python using the netCDF4, h5py or PyTables packages.
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>.


===== [[Recipe: File naming conventions|File naming conventions]] =====
For more details about File Spec, please see [[File:G5NR-Ganymed-7km_FileSpec-ON6-V1.0.pdf]].
===== [[Recipe: Read file metadata|Read file metadata]] =====
 
For model configuration, please see [[File:GMAO-OfficeNote-5-V1-22Oct2014.pdf]].


== Download data files ==
== Download data files ==


===== [[Recipe: Retrieve (global) data from FTP server|Retrieve (global) data from FTP server]] =====
==== Global data ====
===== [[Recipe: Retrieve data (global/subset) using download tool|Retrieve data (global/subset) using download tool]] =====


== Read downloaded data files ==
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==== [[Recipe: Fortran program to read data from downloaded file|Fortran program to read data from downloaded file]] ====
===== [[Recipe: Retrieve (global) data from FTP server|FTP]] =====
==== [[Recipe: Python program to read data from downloaded file|Python program to read data from downloaded file]] ====
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== OPeNDAP client access ==
===== [[Recipe: Retrieve (global) data from HTTPS server|HTTPS]] =====


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 ftp/download-tool are also available on the OPeNDAP server
==== Data subsets ====
===== [[Recipe: Retrieve data subsets using download tool|Download tool]] =====


http://opendap.nccs.nasa.gov/dods/OSSE/GEOS-5.12/BETA9.
== 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]] ====


===== [[Recipe: Fortran program as OPeNDAP client|Fortran program as OPeNDAP client]] =====
== OPeNDAP access ==
===== [[Recipe: C program as OPeNDAP client|C program as OPeNDAP client]] =====


<!--
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
== Client access ==
 
In the following, we read the field 'T' (air temperature) from collection ''inst01hr_3d_T_Cv'', compute its min/max and if applicable, plot it. We give an example for each of the two cases
 
# a file has been downloaded either via ftp or using the download tool
# using the OPenDAP server


For each case, we compute min/max for both
https://opendap.nccs.nasa.gov/dods/OSSE/G5NR/Ganymed/7km
# global temperature
# temperature over North America
 
==== Programming ====


===== [[Recipe: Fortran program as OPeNDAP client|Fortran client]] =====
===== [[Recipe: C program as OPeNDAP client|C client]] =====
===== [[Recipe: Python program as OPeNDAP client|Python client]] =====
===== [[Recipe: Matlab program as OPeNDAP client|Matlab client]] =====
===== [[Recipe: IDL program as OPeNDAP client|IDL client]] =====
===== [[Recipe: Visualize OPeNDAP data using Panoply|Panoply]] =====
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===== [[G5NR data access using C|C]] =====
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===== Fortran =====


For reading a downloaded file or accessing directly via OPeNDAP using Fortran, please see [[G5NR data access using Fortran|this]] page.
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===== Shmem example =====
===== Shmem example =====
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==== 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 =====
====== 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.


<syntaxhighlight lang="rsplus">
<syntaxhighlight lang="rsplus">
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> 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)
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===== 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
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* 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 =====
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