GEOS-5

Recipe: Fortran program as OPeNDAP client: Difference between revisions

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== Problem ==
== Problem ==


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 by accessing data via the OPeNDAP server.
By accessing the collection <code>inst01hr_3d_T_Cv</code> via the OPeNDAP server
https://opendap.nccs.nasa.gov/dods/OSSE/G5NR/Ganymed/7km
 
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.


== Solution ==
== Solution ==
 
First, we ensure that our NetCDF-4 library has been built with Fortran and OPeNDAP support. If both the queries
First, we ensure that out NetCDF-4 library has been built with Fortran, HDF5 and OPeNDAP support. All three queries
 
  > nc-config --has-f90
  > nc-config --has-f90
> nc-config --has-hdf5
  > nc-config --has-dap
  > nc-config --has-dap


should return yes.
return "yes", we have a compatible NetCDF-4 library. Here <code>nc-config</code> is a utility bundled with NetCDF-4 package.


== Read downloaded nc4 file ==
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


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 code below does the following
==== Code ====
* reads global temperature data and computes its max/min
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.
* reads a subset of the data and computes the subset's max/min


==== Code ====
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>
<syntaxhighlight lang="fortran" line>
program g5nr_reader
program g5nr_reader_dap


   use netcdf          ! for reading the NR files
   use netcdf          ! for reading the NR files
Line 36: Line 39:
   ! 4D array: (lon,lat,lev,time)
   ! 4D array: (lon,lat,lev,time)
   ! ------------------------------------
   ! ------------------------------------
   real, allocatable :: T(:,:,:,:)   ! global data
   real, allocatable :: T(:,:,:,:)
  real, allocatable :: Tsub(:,:,:,:) ! subset of global data


   ! Miscellaneous
   ! Miscellaneous
Line 43: Line 45:
   integer :: ierr
   integer :: ierr
   integer :: im, jm, lm
   integer :: im, jm, lm
  real :: minlat, minlon, maxlat, maxlon
  integer :: im_sub, jm_sub
  integer :: imin, imax, jmin, jmax
   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


   ! 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 = "c1440_NR.inst01hr_3d_T_Cv.20060918_0900z.nc4"


   ! Open file and get var id
   ! Open url and get var id
   ! ------------------------
   ! -----------------------
   call check(nf90_open(T_file,NF90_NOWRITE,ncid), "opening T file")
   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_inq_varid(ncid,"t",varid), "getting T varid")


   ! Read global temperature data
   ! Read temperature data
   ! ----------------------------
   ! ---------------------
   allocate(T(im,jm,lm,1))            ! global 4D array with 1 time level
   allocate(T(im,jm,lm,1))            ! global 4D array with 1 time level
   start = [1, 1, 1, 1]
   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
   count = [im, jm, lm, 1]            ! 1 time level, 3D (lon,lat,lev) array
   write(*,*) 'Reading global T...'
   write(*,*) 'Reading T...'
   call check(nf90_get_var(ncid,varid,T,start=start,count=count), "reading T")
   call check(nf90_get_var(ncid,varid,T,start=start,count=count), "reading T")
   write(*,*)'T: ', maxval(T),minval(T)
   write(*,*)'T: ', maxval(T),minval(T)
  ! Read temperature over US
  ! lons = -180:0.5:179.5
  ! lats = -90:0.5:90
  ! ------------------------
  write(*,*) 'Reading T over US'
  minlon = -130.
  maxlon = -65.
  minlat = 25.
  maxlat = 50.
  imin = nint((minlon + 180.)/0.5)
  imax = nint((maxlon + 180.)/0.5)
  jmin = nint((minlat +  90.)/0.5)
  jmax = nint((maxlat +  90.)/0.5)
  im_sub = imax-imin+1
  jm_sub = jmax-jmin+1
  allocate(Tsub(im_sub,jm_sub,lm,1)) ! global 4D array with 1 time level
  start = [1, 1, 1, 1]
  count = [im_sub, jm_sub, lm, 1]    ! 1 time level, 3D (lon,lat,lev) array
  call check(nf90_get_var(ncid,varid,Tsub,start=start,count=count), "reading Tsub")
  write(*,*)'Tsub: ', maxval(Tsub),minval(Tsub)


   ! close file, release memory
   ! close file, release memory
   call check(nf90_close(ncid), "closing T file")
   call check(nf90_close(ncid), "closing T file")
   deallocate(T)
   deallocate(T)
  deallocate(Tsub)


   ! All done
   ! All done
Line 113: Line 105:
   end subroutine check
   end subroutine check


end program g5nr_reader
end program g5nr_reader_dap
</syntaxhighlight>
</syntaxhighlight>


Line 120: Line 112:
We use the utility <code>nf-config</code> (included in the NetCDF-4 installation) to identify the linking rules
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.f90</code> can be compiled and linked to the NetCDF-4 library via
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.x `nf-config --fflags` g5nr_reader.f90 `nf-config --flibs`
  gfortran -o g5nr_reader_dap.x `nf-config --fflags` g5nr_reader_dap.f90 `nf-config --flibs`


creating the executable <code>g5nr_reader.x</code>.
creating the executable <code>g5nr_reader_dap.x</code>.


NOTE:
NOTE:
Line 132: Line 124:
Running the executable,
Running the executable,


  ./g5nr_reader.x
  ./g5nr_reader_dap.x


produces the output
produces the output
  Reading global T...
  Reading T (subset)...
T:    315.6512      180.3667   
T (subset):   305.6048      191.6956
Reading T over US
Tsub:    302.8958      183.1974
 
== Access data via OPeNDAP server ==
 
==== Code ====
 
The code to read data from the OPeNDAP server is a minor modification (4 lines) of the above program and is reproduced below
 
<syntaxhighlight lang="fortran" line>
program g5nr_reader_dap
 
  use netcdf          ! for reading the NR files
 
  implicit none
 
  ! File name
  ! ---------
  character(len=256) :: T_file
 
  ! 4D array: (lon,lat,lev,time)
  ! ------------------------------------
  real, allocatable :: T(:,:,:,:)    ! global data
  real, allocatable :: Tsub(:,:,:,:) ! subset of global data
 
  ! Miscellaneous
  ! -------------
  integer :: ierr
  integer :: im, jm, lm
  real :: minlat, minlon, maxlat, maxlon
  integer :: im_sub, jm_sub
  integer :: imin, imax, jmin, jmax
  integer :: ncid, varid
  integer :: start(4), count(4)
 
  ! 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"
 
  ! Open file and get var id
  ! ------------------------
  call check(nf90_open(T_file,NF90_NOWRITE,ncid), "opening T file")
  call check(nf90_inq_varid(ncid,"t",varid), "getting T varid")
 
  ! Read global temperature data
  ! ----------------------------
  allocate(T(im,jm,lm,1))            ! global 4D array with 1 time level
  start = [1, 1, 1, 11772]          ! time level 11772 corresponds to 2006/09/18, 9z
  count = [im, jm, lm, 1]            ! 1 time level, 3D (lon,lat,lev) array
  write(*,*) 'Reading global T...'
  call check(nf90_get_var(ncid,varid,T,start=start,count=count), "reading T")
  write(*,*)'T: ', maxval(T),minval(T)
 
  ! Read temperature over US
  ! lons = -180:0.5:179.5
  ! lats = -90:0.5:90
  ! ------------------------
  write(*,*) 'Reading T over US'
  minlon = -130.
  maxlon = -65.
  minlat = 25.
  maxlat = 50.
  imin = nint((minlon + 180.)/0.5)
  imax = nint((maxlon + 180.)/0.5)
  jmin = nint((minlat +  90.)/0.5)
  jmax = nint((maxlat +  90.)/0.5)
  im_sub = imax-imin+1
  jm_sub = jmax-jmin+1
  allocate(Tsub(im_sub,jm_sub,lm,1)) ! global 4D array with 1 time level
  start = [1, 1, 1, 11772]          ! time level 11772 corresponds to 2006/09/18, 9z
  count = [im_sub, jm_sub, lm, 1]    ! 1 time level, 3D (lon,lat,lev) array
  call check(nf90_get_var(ncid,varid,Tsub,start=start,count=count), "reading Tsub")
  write(*,*)'Tsub: ', maxval(Tsub),minval(Tsub)
 
  ! close file, release memory
  call check(nf90_close(ncid), "closing T file")
  deallocate(T)
  deallocate(Tsub)
 
  ! 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_dap
</syntaxhighlight>


===== Discussion =====
== Discussion ==


The four (4) differences from the case where an individual downloaded file was being read are
== See Also ==


# <code>Line 31</code>: Instead of reading a downloaded NetCDF-4 file, we read an OPeNDAP URL.
# File Spec: [[File:G5NR-Ganymed-7km FileSpec-ON6-V1.0.pdf]]
# <code>Line 36</code>: While in the downloaded file, the temperature variable appears in the uppercase (T), on the OPeNDAP server, this variable is in lowercase (see http://opendap.nccs.nasa.gov:9090/dods/OSSE/GEOS-5.12/BETA9/0.5000_deg/inst/inst01hr_3d_T_Cv). This is reflected in the call to <code>nf90_inq_varid</code>.
# [[Recipe: Fortran program to read data from downloaded file]]
# <code>Line 41</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> file.
# <code>Line 63</code>: Same as the difference above, but for retrieving a subset of data.


==== Compile and link ====
== No Warranty ==
 
We use the utility nf-config (included in the NetCDF-4 installation) to identify the linking rules
For a typical NetCDF-4 installation, the above code, g5nr_reader_dap.f90 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 gfortran.
# If the NetCDF-4 library was built with parallel I/O support, you will need to use mpif90 to link, even if your code does not use the MPI library.
 
===== Run =====
Running the executable,
./g5nr_reader_dap.x
 
produces the output


Reading global T...
== Copyright ==
T:    315.6512      180.3667   
Reading T over US
Tsub:    302.8958      183.1974
Retrieved from "https://geos5.org/wiki/index.php?title=Recipe:_Fortran_program_as_OPeNDAP_client"