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[netCDF #NUC-119714]: struggling with writing data to nc file

Laurens,

I think I see the problem, which I should have spotted earlier.

In subroutine write_nc_file, where you have

            cnt2d   = (/ 180,  360,              1 /)

it should be

            cnt2d   = (/ 360,  180,              1 /)

because the order in which you defined the shape of the netCDF "emis"
variable was (lon, lat, time), the Fortran order corresponding to the
reversed CDL/C order of the variable declaration

  float emis(time, lat, lon) ;

With the order you specified, you should have gotten a run-time error
message something like "Start+count exceeds dimension bound" corresponding
to error number NF_EEDGE (-57).

Please let me know if that doesn't fix the problem ...

--Russ

> Hi Russ, thanks for extensive feedback; I went through all your 
> comments/suggestions and got your points also on reading in the file. I 
> checked it out and realized that the code was apparently then 12 times 
> reading in the whole 4-D field (ilat, ilon, nlev, nmonths) and have 
> simplified the code getting the call to the reading outside the timeloop. I 
> also got your point on a problem assigning the output emission fields and 
> have modified this to be sure that the ilon and ilat loop indices were 
> properly used. Also using the start1d and cnt1d code works fine and the 
> script now properly writes the time array to the new nc file. However, you 
> said that it seems that then the actual writing of the 2-D emission field 
> inside this timeloop of 1,12 months was properly coded but that's exactly 
> where it still goes wrong. I went again through all your previous emails, the 
> manual that you suggested for the netcdf3.6.2 version including the use of 
> the functions nf_put_vara_real etc but don't
  get this last part solved (a frustrating experience now that I am so close 
but really want to completely get this since I will need to use this netcdf 
reading and writing code for many more applications). I know that I am asking a 
lot but have attached once more again the latest version including all these 
modifications; if you happen to have another glimpse at it to see if you see a 
remaining potential explanation for this problem I would really appreciate it.
> 
> Cheers, Laurens
> =======================================================================
> Dr. ir. Laurens Ganzeveld
> Assistant professor
> Department of Environmental Sciences, Chair group Earth System Sciences
> Wageningen University and Research Centre
> Lumen, room D.001, Droevendaalsesteeg 4, 6708 PB, Wageningen, Netherlands
> Phone: (+31) 317-486651 / 613066079, Fax: (+31) 317-419000,
> Being in in Colombia: +57 310 2979313
> E-mail: address@hidden
>  
> Affiliate of Universidad de Los Andes, Depart de Biología, Bogota, Colombia
> Affiliate of Max Planck Institute for Chemistry, Depart. of Atmospheric 
> Chemistry, Mainz, Germany,
> =======================================================================
> 
> 
> -----Original Message-----
> From: Unidata netCDF Support [mailto:address@hidden]
> Sent: dinsdag 15 oktober 2013 18:45
> To: Ganzeveld, Laurens
> Cc: address@hidden
> Subject: [netCDF #NUC-119714]: struggling with writing data to nc file
> 
> > Below is the header information of this input file that I read with
> > the script. But the reading seems to work all fine. The problems are
> > involved in then simply writing out the read data which I want to do
> > to be sure that I get the data for the proper location. I will also
> > check for these other locations to get the information on the
> > netcdf-3 F77 functions.
> 
> First, even though the reading "seems to work all fine", it's probably not 
> doing what you think it is.  In a loop with ii=1,12, you have
> 
> CALL read_nc_file(ii,ncid,emisid,emis)
> 
> but the code is just reading the entire 4D co_flux variable, including data 
> from all 12 times, each time through the loop, with the
> statement:
> 
> CALL nf(nf_get_var_real(ncid,emisid,emis)) ! emis.
> 
> in the read_nc_file subroutine.  If you really intended to read data from one 
> time with each call, making use of the value of the "ii"
> parameter, you would instead have something like
> 
> start = (/ ii, 1, 1, 1 /)
> count = (/ 1, 6, 180, 360 /)
> CALL nf(nf_get_vara_real(ncid,emisid,start,count, &
> emis(ii, 1, 1, 1))) ! emis.
> 
> and each call would read in only the data for the ii-th time and store that 
> 3D slab of co_flux data in the right place in the 4D emis variable.
> 
> Second, I'll assume maybe you already knew all the above and really just want 
> to figure out what's wrong with the writing.
> 
> In your output_netcdf subroutine, the loop for setting the emis_output array, 
> declared emis_output(ilat,ilon), looks wrong:
> 
> FORALL (I=1:nlon, J=1:ngl)
> emis_output(I,J) = emis(ii,I,J)
> END FORALL
> 
> If the declaration is right, this should instead be
> 
> FORALL (I=1:ilon, J=1:ilat)
> emis_output(I,J) = emis(ii,I,J)
> END FORALL
> 
> unless you pass nlon and ngl as arguments to the subroutine.
> 
> In the write_nc_file subroutine, you first write the 1-dimensional variable 
> time using
> 
> start1d = (/ 1,           timestep /)
> cnt1d   = (/ 12,                 1 /)
> 
> status=nf_put_vara_int(ncid, timid, start1d, cnt1d,
> &     timestep)
> 
> Since you're only writing one value, you could instead use nf_put_var1_int 
> with fewer arguments, but to use nf_put_vara this should instead be
> 
> start1d = (/ timestep /)
> cnt1d   = (/ 1 /)
> 
> status=nf_put_vara_int(ncid, timid, start1d, cnt1d,
> &     timestep)
> ! instead could have used
> ! status=nf_put_var1_int(ncid, timid, (/ timestep /),
> timestep)
> 
> For writing the 2D emis data into the appropriate time slab of the 3D netCDF 
> variable identified by emisid, it looks to me like you've got it right!
> 
> start2d = (/ 1,    1,         timestep /)
> cnt2d   = (/ 180,  360,              1 /)
> 
> ! write 2d data: emissions
> CALL nf(nf_put_vara_double(ncid, emisid, start2d, cnt2d, emis)) ! emis.
> 
> Just as an aside, you don't need to pass netCDF constants such as nf_global, 
> nf_float, etc. to a subroutine.  Instead, just use the statement
> 
> include 'netcdf.inc'   ! for Fortran 77
> or
> use 'netcdf"           ! for Fortran 90
> 
> in the subroutine declarations, and all those parameter constants are 
> available from the appropriate include file or module file installed with 
> netCDF Fortran.
> 
> --Russ
> 
> > -----Original Message-----
> > From: Unidata netCDF Support [mailto:address@hidden]
> > Sent: maandag 14 oktober 2013 19:09
> > To: Ganzeveld, Laurens
> > Cc: address@hidden
> > Subject: [netCDF #NUC-119714]: struggling with writing data to nc file
> >
> > Laurens,
> >
> > In order to understand what your code is intended to do, we will need for 
> > you to send the output from running the following command:
> >
> > ncdump -h /data/ganzevl/inputdata/emissions/EDGARV3.2/co_2000.nc
> >
> > I suspect there might be a confusion of Fortran array order (first index 
> > varying fastest) with C and CDL array order (last index varying fastest).
> >
> > Also, since you are only using the netCDF-3 F77 functions, it might be
> > easier and less confusing for you to look at the older documentation
> > for that version of the F77 library, which is here (in HTML, or PDF,
> > or
> > ASCII):
> >
> > http://www.unidata.ucar.edu/software/netcdf/old_docs/docs_3_6_3/netcdf
> > -f77.html
> > http://www.unidata.ucar.edu/software/netcdf/old_docs/docs_3_6_3/netcdf
> > -f77.pdf
> > http://www.unidata.ucar.edu/software/netcdf/old_docs/docs_3_6_3/netcdf
> > -f77.txt
> >
> > That's the documentation I'll refer to in discussing how to use
> > nf_get_vara_real
> > from:
> >
> > http://www.unidata.ucar.edu/netcdf/old_docs/docs_3_6_3/netcdf-f77.html
> > #NF_005fGET_005fVARA_005f-type
> >
> > for example.
> >
> > --Russ
> >
> > > Dear Unidata employees,
> > >
> > > I hope that you are actually working at the moment and not affected
> > > by the government shutdown; I am already struggling now for some
> > > weeks with a simple script to read and write data to netcdf in a F77
> > > model code. I am able to read-in and then write some manipulated
> > > data in F90 version but the F77 version gives problems with the
> > > writing; I have copied below the F90 version of the write_nc routine
> > > I used and that works with my installation of the netcdf software
> > > (3.6.2) on my
> > > Suse11.2 linux system. I have also copied a version of the F77
> > > subroutine that doesn't work; I am basically looking for the F77
> > > equivalent of some of the calls of the various nc functions where
> > > the help page has helped a lot but not to solve this remaining problem.
> > > Your feedback would be highly appreciated,
> > >
> > > Thanks, Laurens Ganzeveld
> > >
> > > F90:
> > >
> > > The subroutine is called in a timeloop over 12 months writing out
> > > the global emission field (emis3D), at a resolution of 1x1 degree
> > > for each month to a new netcdf file:
> > >
> > > SUBROUTINE write_nc_file
> > >
> > > ! write timestep
> > > CALL nf(nf90_inquire_dimension(ncid, tid, len=timestep)) timestep =
> > > timestep + 1
> > >
> > > print *,'write_nc: timestepping ',timestep read (*,*)
> > >
> > > CALL nf(nf90_put_var(ncid, tid, time, (/timestep/) ))
> > >
> > > ! syntax: nf90_put_var(ncid, varid, values, start, cnt) ! start:
> > > start in netcdf variable
> > > ! cnt:    number of netcdf variable points
> > > ! values: starting point of the fortran variable
> > > start1d = (/ 1,               timestep /)
> > > start2d = (/ 1,    1,         timestep /)
> > > start3d = (/ 1,    1,   1,    timestep /)
> > >
> > > CALL nf(nf90_put_var(ncid, emis3Did,      emis3D,   start3d, cnt3d)) ! 
> > > emis.
> > >
> > > END SUBROUTINE write_nc_file
> > >
> > >
> > > F77:
> > > Ncid, tid, emisid are all properly defined as well as the parameter
> > > emis
> > >
> > > SUBROUTINE write_nc_file(ii,time,ncid,tid,emisid,emis)
> > >
> > > integer :: ii,timestep,status,ncid,tid,dimtid,timelen,nrecs,
> > > &             emisid,start2d(3),cnt2d(3),j,k
> > > real    :: time,emis(180,360)
> > >
> > > character*(20) recnam
> > >
> > > ! write timestep
> > > timestep = ii
> > > print *,'timestep',timestep,time
> > >
> > > CALL nf(nf_put_var_double(ncid, tid, time, (/timestep/) )) read
> > > (*,*)
> > >
> > > ! syntax: nf90_put_var(ncid, varid, values, start, cnt) ! start:
> > > start in netcdf variable
> > > ! cnt:    number of netcdf variable points
> > > ! values: starting point of the fortran variable
> > > start2d = (/ 1,    1,         timestep /)
> > > cnt2d   = (/ 180,  360,              1 /)
> > >
> > > ! write 2d data
> > >
> > > CALL nf(nf_put_var_real(ncid, emisid, emis, start2d, cnt2d)) ! emis .
> > >
> > > END SUBROUTINE write_nc_file
> > >
> > > ====================================================================
> > > ==
> > > =
> > > Dr. ir. Laurens Ganzeveld
> > > Assistant professor
> > > Department of Environmental Sciences, Chair group Earth System
> > > Sciences Wageningen University and Research Centre Lumen, room
> > > D.001, Droevendaalsesteeg 4, 6708 PB, Wageningen, Netherlands
> > > Phone: (+31) 317-486651 / 613066079, Fax: (+31) 317-419000, Being in
> > > in Colombia: +57 310 2979313
> > > E-mail: address@hidden<mailto:address@hidden>
> > >
> > > Affiliate of Universidad de Los Andes, Depart de Biología, Bogota,
> > > Colombia Affiliate of Max Planck Institute for Chemistry, Depart. of
> > > Atmospheric Chemistry, Mainz, Germany,
> > > ====================================================================
> > > ==
> > > =
> > >
> > >
> > >
> > Russ Rew                                         UCAR Unidata Program
> > address@hidden                      http://www.unidata.ucar.edu
> >
> >
> >
> > Ticket Details
> > ===================
> > Ticket ID: NUC-119714
> > Department: Support netCDF
> > Priority: Normal
> > Status: Closed
> >
> >
> >
> 
> Russ Rew                                         UCAR Unidata Program
> address@hidden                      http://www.unidata.ucar.edu
> 
> 
> 
> Ticket Details
> ===================
> Ticket ID: NUC-119714
> Department: Support netCDF
> Priority: Normal
> Status: Closed
> 
> 
> 
Russ Rew                                         UCAR Unidata Program
address@hidden                      http://www.unidata.ucar.edu



Ticket Details
===================
Ticket ID: NUC-119714
Department: Support netCDF
Priority: Normal
Status: Closed