Re: [netcdfgroup] NF90_GET_VAR from netcdf-fortran-4.4.3 release does not work with compound user defined type variable

On 04/25/2016 12:34 PM, Thompson, Matt (GSFC-610.1)[SCIENCE SYSTEMS AND APPLICATIONS INC] wrote: 
On 04/22/2016 10:37 AM, Arlindo Arriaga wrote:

Dear all


NASA has decided to change formats of MODIS data files with ocean biology
products from hdf4 to netcdf-4, and my software turned useless.  I was
asked
to change my Fortran executables from hdf4 to netcdf-4. After training
myself to get control on using netcdf-4 library functions of Fortran
interface, I hit on a road bloc: the function NF90_GET_VAR  to read
datasets
works well for arrays of single types (integers or reals) but NOT for
compound user defined types, like the structure sstdata

TYPE binSST
real(kind=4) :: sum
real(kind=4) :: sum2
end TYPE binSST

TYPE(binSST), allocatable, dimension(:) :: sstdata


In case someone has hit on a similar problem or has a suggestion, I would
kindly appreciate the help.
I work in Linux (Ubuntu) 64 bits, and the Fortran compiler is gfortran.


Arlindo,

Are you trying to use compound variables using nf90_def_compound, a la:

http://stackoverflow.com/questions/6924073/netcdf-and-fortran-structures

I've used these before and they seem to work well. If not, what does
your code look like?


Arlindo,
I'm beginning to think you are right. I grabbed a file that contains compound data (in a group, so even more fun), and I've been trying to figure out how to NF90_GET_VAR the data and I'm not sure I can. 

The nc4 file has:


group: level-3_binned_data {
  types:
    compound binListType {
      uint bin_num ;
      short nobs ;
      short nscenes ;
      float weights ;
      float time_rec ;
    }; // binListType
    compound binDataType {
      float sum ;
      float sum_squared ;
    }; // binDataType
    compound binIndexType {
      uint start_num ;
      uint begin ;
      uint extent ;
      uint max ;
    }; // binIndexType
  dimensions:
        binListDim = UNLIMITED ; // (4433821 currently)
        binDataDim = UNLIMITED ; // (4433821 currently)
        qualityDim = UNLIMITED ; // (4433821 currently)
        binIndexDim = UNLIMITED ; // (4320 currently)
  variables:
        binListType BinList(binListDim) ;
        binDataType sst(binDataDim) ;
        byte qual_l3(qualityDim) ;
        binIndexType BinIndex(binIndexDim) ;
For simplicities sake, I decided to focus on binDataType because that is easy and I don't have to mess with int(int16) and the like. I defined my own as: 


      type binDataType
         sequence
         real(real32)    :: sum
         real(real32)    :: sum_squared
      end type binDataType
      type(binDataType), allocatable, dimension(:) :: sst


I don't think sequence is needed, but couldn't hurt I guess.
Now I am definitely sure that "sst" is varids(2) thanks to a nf90_inq_varids on the group, but when I try to compile: 

  retval = nf90_get_var(grpid(1), varids(2), sst)

you get:


example_reader.F90(87): error #6284: There is no matching specific function for 
this generic function reference.   [NF90_GET_VAR]
      retval = nf90_get_var(grpid(1), varids(2), sst)
---------------^
compilation aborted for example_reader.F90 (code 1)
And, since I don't think the netcdf interfaces have a type(*) or class(*) variant, there is no interface that seems to work according to the compiler. But, the documentation says in 5.1: "Read data of user-defined type with NF90_GET_VAR (see NF90_GET_VAR)."
Does anyone know how to do this other than through the C or Python interfaces? 

Matt

--
Matt Thompson, SSAI, Sr Scientific Programmer/Analyst
NASA GSFC,    Global Modeling and Assimilation Office
Code 610.1,  8800 Greenbelt Rd,  Greenbelt,  MD 20771
Phone: 301-614-6712                 Fax: 301-614-6246
http://science.gsfc.nasa.gov/sed/bio/matthew.thompson