nfmpi_put_var_char expected behavior?

[Wei-keng Liao]

I assume you are calling nfmpi_put_var_text. The "var" APIs are
intended for writing the entire variable, which in your case it writes
80 characters. PnetCDF (and netCDF) will not stop writing at the end
of the string (string length == 17 in your case). Instead, it writes
the whole 80 characters from the I/O buffer into the file.

Are you seeing those 0s from running ncmpidump, but not from ncdump?
Strangely, I got the same output from both ncmpidump and ncdump (4.1.3).
See below. Let me know if this program is same as your program is doing.

program main
    use pnetcdf
    implicit none
    include 'mpif.h'

    integer i, status, ncid, varid, dimid(1)
    integer(kind=MPI_OFFSET_KIND) :: len, count(1), offset(1)
    character*(80) buf, rbuf

    call MPI_Init(status)
    status = nfmpi_create(MPI_COMM_WORLD, 'testfile.nc', &
                          NF_CLOBBER, MPI_INFO_NULL, ncid)
    len = 80
    status = nfmpi_def_dim(ncid, "dim", len, dimid(1))
    status = nfmpi_def_var(ncid, "var", NF_CHAR, 1, dimid, varid)
    status = nfmpi_enddef(ncid)
    status = nfmpi_begin_indep_data(ncid)

    buf = "./none/foo.009.nc"
    status = nfmpi_put_var_text(ncid, varid, buf)
    status = nfmpi_end_indep_data(ncid)

    status = nfmpi_close(ncid)
    call MPI_Finalize(status)
end program

% ncmpidump testfile.nc
netcdf testfile {
// file format: CDF-1
dimensions:
	dim = 80 ;
variables:
	char var(dim) ;
data:

 var = "./none/foo.009.nc                                                               " ;
}

% 4.1.3/bin/ncdump testfile.nc
netcdf testfile {
dimensions:
	dim = 80 ;
variables:
	char var(dim) ;
data:

 var = "./none/foo.009.nc                                                               " ;
}


Wei-keng

On Aug 2, 2012, at 9:26 AM, Jim Edwards wrote:

> Hi Wei-keng,
> 
> In standard netcdf I set NC_NO_FILL when I open the file and I still get this behavior.   I think that you just need to null terminate the string when you pass it from fortran to c.    
> 
> Jim
> 
> On Wed, Aug 1, 2012 at 7:58 PM, Wei-keng Liao <wkliao at ece.northwestern.edu> wrote:
> Hi, Jim
> 
> NetCDF's default for fill mode is NC_FILL and the default fill value for char type
> is NC_FILL_CHAR == (char)0. See netCDF user guide below.
> http://www.unidata.ucar.edu/software/netcdf/docs/netcdf-c.html#nc_005fset_005ffill
> http://www.unidata.ucar.edu/software/netcdf/docs/netcdf-c.html#Fill-Values
> 
> In PnetCDF, only NC_NOFILL is implemented. So, for those spaces that were not
> written by the application, their contents are undefined.
> 
> 
> Wei-keng
> 
> On Aug 1, 2012, at 11:27 AM, Jim Edwards wrote:
> 
> > If I declare a character string variable with a length x and then write a string of length y<x using nfmpi_put_var_char
> > what is the expected behavior?     I think that what I am getting is incorrect (a bunch of garbage in the string from y:x )
> >
> > So for example I want to write string './none/foo.009.nc' into a variable of length 80.    In the file I am getting:
> >
> > './none/foo.009.nc 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0'
> >
> >
> > I think that this is a bug.
> >
> >
> > This is happening with the latest pnetcdf svn trunk code on jaguarpf compiled using:
> >
> > Currently Loaded Modulefiles:
> >   1) modules/3.2.6.6                      10) xpmem/0.1-2.0400.31280.3.1.gem       19) DefApps
> >   2) xtpe-network-gemini                  11) xe-sysroot/4.0.46                    20) altd/1.0
> >   3) pgi/12.5.0                           12) xt-asyncpe/5.11                      21) subversion/1.6.17
> >   4) xt-libsci/11.1.00                    13) atp/1.4.1                            22) szip/2.1
> >   5) udreg/2.3.2-1.0400.5038.0.0.gem      14) PrgEnv-pgi/4.0.46                    23) hdf5/1.8.7
> >   6) ugni/2.3-1.0400.4374.4.88.gem        15) xt-mpich2/5.5.0                      24) netcdf/4.1.3
> >   7) pmi/3.0.0-1.0000.8661.28.2807.gem    16) xtpe-interlagos                      25) esmf/5.2.0rp1
> >   8) dmapp/3.2.1-1.0400.4782.3.1.gem      17) eswrap/1.0.9
> >   9) gni-headers/2.1-1.0400.4351.3.1.gem  18) lustredu/1.0
> >
> > --
> > Jim Edwards
> >
> > CESM Software Engineering Group
> > National Center for Atmospheric Research
> > Boulder, CO
> > 303-497-1842
> >
> 
> 
> 
> 
> -- 
> Jim Edwards
> 
> 
>