GEOS-5

Recipe: Fortran program as OPeNDAP client: Difference between revisions

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{{rightTOC}}
Back to [[G5NR Data Access Guide]].


== Program to read downloaded nc4 file ==
== Problem ==


To read a downloaded file in Fortran we need a NetCDF-4 library that has been configured with HDF5 support. Availability of HDF5 support can be checked using the <code>nc-config</code> tool included in the NetCDF-4 package.
By accessing the collection <code>inst01hr_3d_T_Cv</code> via the OPeNDAP server
<code>
  https://opendap.nccs.nasa.gov/dods/OSSE/G5NR/Ganymed/7km
> nc_config --has-hdf5
</code>
should return the value <code>yes</code>.


For this example, we first download the collection inst01hr_3d_T_Cv for 2006-Sep-18/0900z as described [[G5NR Data Access Guide#ftp (global data)|here]]. The downloaded file is <code>c1440_NR.inst01hr_3d_T_Cv.20060918_0900z.nc4</code>. The program to read this file is
we want to read the surface temperature data inside the box bound by latitudes 25<sup>o</sup>N, 50<sup>o</sup>N and longitudes -130<sup>o</sup>W, -65<sup>o</sup>W for 2006/Sep/18, 9z and compute its min/max.


  <nowiki>
== Solution ==
program g5nr_reader
First, we ensure that our NetCDF-4 library has been built with Fortran and OPeNDAP support. If both the queries
  > nc-config --has-f90
> nc-config --has-dap


   use netcdf          ! for reading the NR files                                                                              
return "yes", we have a compatible NetCDF-4 library. Here <code>nc-config</code> is a utility bundled with NetCDF-4 package.
 
The metadata for the collection <code>inst01hr_3d_T_Cv</code> is available at
https://opendap.nccs.nasa.gov/dods/OSSE/G5NR/Ganymed/7km/0.5000_deg/inst/inst01hr_3d_T_Cv.info
 
==== Code ====
This code accesses the collection <code>inst01hr_3d_T_Cv</code> from the OPeNDAP server, reads a subset of the temperature data (all levels inside the bounding box specified above) and computes its max/min.
 
NOTE:
# Instead of reading a downloaded NetCDF-4 file, we read an OPeNDAP URL.
# While in the downloaded file, the temperature variable appears in the uppercase (T), on the OPeNDAP server, this variable is in lowercase. This is reflected in the call to <code>nf90_inq_varid</code>.
# Via the OPeNDAP URL, we now have access to all times for which data exists. The hourly <code>inst</code> files are available starting at 2005/15/15, 2200z. Our desired time, 2006/09/18, 0900z is then the 11772<sup>th</sup> step.
 
<syntaxhighlight lang="fortran" line>
program g5nr_reader_dap
 
   use netcdf          ! for reading the NR files


   implicit none
   implicit none


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


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


   ! Miscellaneous                                                                                                            
   ! Miscellaneous
   ! -------------                                                                                                            
   ! -------------
   integer :: ierr
   integer :: ierr
   integer :: im, jm, lm
   integer :: im, jm, lm
   integer :: ncid, varid
   integer :: ncid, varid
   integer :: start(4), count(4)
   integer :: start(4), count(4)
  integer :: imin, imax, jmin, jmax
  real :: minlat, minlon, maxlat, maxlon


   ! For now hard code file name and dimensions                                                                               
   ! We replace filename by opendal url
   ! ------------------------------------------                                                                              
   ! ----------------------------------
   im = 720
  T_file = "https://opendap.nccs.nasa.gov:9090/dods/OSSE/G5NR/Ganymed/7km/0.5000_deg/inst/inst01hr_3d_T_Cv"
   jm = 361
 
  ! file name and (subset) dimensions
  ! bounding box:
  !  lons = -130:0.5:-65
  !  lats =  25:0.5:50
  ! ---------------------------------
  ! array indices from the
  ! bounding lat/lon values
  imin = nint((-130. + 180.)/0.5)
  imax = nint(( -65. + 180.)/0.5)
  jmin = nint((  25 +  90.)/0.5)
  jmax = nint((  50 +  90.)/0.5)
  ! array sizes
   im = imax-imin+1
   jm = jmax-jmin+1
   lm = 72
   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                                                                     
   ! Open url and get var id
   ! ----------------------------------------------------                                                                     
   ! -----------------------
   allocate(T(im,jm,lm,1))
   call check(nf90_open(T_file,NF90_NOWRITE,ncid), "opening T file")
  call check(nf90_inq_varid(ncid,"t",varid), "getting T varid")


   ! Hypercube for reading one 1 array for a given time                                                                       
   ! Read temperature data
   ! -------------------------------------------------                                                                         
   ! ---------------------
   start = (/  1, 1, 1, 37 /)  ! time level 37                                                                               
  allocate(T(im,jm,lm,1))            ! global 4D array with 1 time level
   count = (/ im, jm, lm, 1 /)  ! 1 time level, 3D (lon,lat,lev) array                                                        
   start = [imin, jmin, 1, 11772]    ! time level 11772 corresponds to 2006/09/18, 9z
 
   count = [im, jm, lm, 1]            ! 1 time level, 3D (lon,lat,lev) array
  !  Read the data file                                                                                                       
   write(*,*) 'Reading T...'
  !  ------------------                                                                                                       
   call check(nf90_get_var(ncid,varid,T,start=start,count=count), "reading T")
   write(*,*)'Reading T'
   write(*,*)'T: ', maxval(T),minval(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                                                                                                   
   ! close file, release memory
   !  -----------------------                                                                                                   
   call check(nf90_close(ncid), "closing T file")
  write(*,*)'T: ', maxval(T),minval(T)
  deallocate(T)


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


contains
contains
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   end subroutine check
   end subroutine check


end program g5nr_reader
end program g5nr_reader_dap
</nowiki>
</syntaxhighlight>
 
==== Compile and link ====
 
We use the utility <code>nf-config</code> (included in the NetCDF-4 installation) to identify the linking rules
 
For a typical NetCDF-4 installation, the above code, <code>g5nr_reader_dap.f90</code> can be compiled and linked to the NetCDF-4 library via
gfortran -o g5nr_reader_dap.x `nf-config --fflags` g5nr_reader_dap.f90 `nf-config --flibs`
 
creating the executable <code>g5nr_reader_dap.x</code>.
 
NOTE:
# You can use your favorite Fortran compiler instead of <code>gfortran</code>.
# If the NetCDF-4 library was built with parallel I/O support, you will need to use <code>mpif90</code> to link, even if your code does not use the MPI library.
 
==== Run ====
Running the executable,
 
./g5nr_reader_dap.x
 
produces the output
Reading T (subset)...
T (subset):    305.6048      191.6956
 
== Discussion ==


==== Compile and run ====
== See Also ==
The above code, <code>g5nr_reader.f90</code> is compiled as


<nowiki>
# File Spec: [[File:G5NR-Ganymed-7km FileSpec-ON6-V1.0.pdf]]
gfortran
# [[Recipe: Fortran program to read data from downloaded file]]
</nowiki>


== Program to access data via OPeNDAP server ==
== No Warranty ==


==== Compile and run ====
== Copyright ==
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