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[netCDF #JNH-860762]: Problems with CDL/vlen example

Lynton,

The problem has now been simplified to a small C program (attached) that 
creates a netCDF-4 file with one variable and gets an HDF5 error.  It's
not clear yet whether this is caused by a netCDF-4 bug or an HDF5 bug, but
we should be able to determine that by testing an equivalent HDF5 program
that doesn't use any netCDF-4 calls.  That has yet to be done ...

--Russ

> > New Client Reply: Problems with CDL/vlen example
> >
> > thanks Russ,
> > this is great news. I will need to schedule some time to get back to finish 
> > t
> > he work.I cannot do it right away but will get back to it as soon as I can.
> > Lynton
> >
> > -----Original Message-----
> > From: Unidata netCDF Support [mailto:address@hidden]
> > Sent: 29 August 2012 20:55
> > To: Appel, Lynton
> > Cc: address@hidden; address@hidden; Appel, Lynton; sa
> > address@hidden
> > Subject: [netCDF #JNH-860762]: Problems with CDL/vlen example
> >
> > Hi Lynton,
> >
> > > Dear Sylwester and Russ,
> > > thanks for the enquiry
> > > I spent a lot of time on developing an upgraded C++ API that could
> > > handle user-defined in a much better way.  The validation process has got
> > > somewhat stalled by a bug in the netCDF-C layer or HDF5-layer.
> > > Russ is there any news on this?
> >
> > Yes, there is as of this afternoon.  The bug that was holding things up
> > appears to have been fixed with changes to netCDF-4 or HDF5.  I say "or",
> > because at this point, it's difficult to determine whether the fix was in
> > the upgrade from HDF5 1.8.8 to 1.8.9 or the netCDF-4 upgrade from 4.1.3
> > to 4.2.0, but it works now with the combination netCDF-4 version 4.2.1.1
> > and HDF5 version 1.8.9.  The details are in this Jira issue description
> > and comments:
> >
> >   https://www.unidata.ucar.edu/jira/browse/NCF-155
> >
> > Please try compiling and linking against the new versions and verify whether
> > you agree that the bug that was blocking release of your new version of the
> > netCDF-4 C++ release is now fixed.  I'm hoping no new bugs affecting that
> > code have been introduced ...
> >
> > --Russ
> >
> >
> >
> > Russ Rew                                         UCAR Unidata Program
> > address@hidden                      http://www.unidata.ucar.edu
> >
> >
> >
> > Ticket Details
> > ===================
> > Ticket ID: JNH-860762
> > Department: Support netCDF
> > Priority: Critical
> > Status: Closed
> >
> >
> >
> > Ticket Details
> > ===================
> > Ticket ID: JNH-860762
> > Department: Support netCDF
> > Priority: Critical
> > Status: Open
> > Link:  
> > https://www.unidata.ucar.edu/esupport/staff/index.php?_m=tickets&_a=vi
> > ewticket&ticketid=19304
> 
> 

Russ Rew                                         UCAR Unidata Program
address@hidden                      http://www.unidata.ucar.edu



Ticket Details
===================
Ticket ID: JNH-860762
Department: Support netCDF
Priority: Critical
Status: Closed
#include <stdio.h>
#include <stdlib.h>
#include <netcdf.h>


typedef nc_vlen_t vl_t;
typedef struct cmp_t {
    vl_t strs[2];
} cmp_t;


void
check_err(const int stat, const int line, const char *file) {
    if (stat != NC_NOERR) {
        (void)fprintf(stderr,"line %d of %s: %s\n", line, file, 
nc_strerror(stat));
        fflush(stderr);
        exit(1);
    }
}

int
main() {/* create bugn.nc */

    int  stat;  /* return status */
    int  ncid;  /* netCDF id */

    /* group ids */
    int root_grp;

    /* type ids */
    int vl_t_typ;
    int cmp_t_typ;

    /* variable ids */
    int var_id;

    /* rank (number of dimensions) for each variable */
#   define RANK_var 0

    /* enter define mode */
    stat = nc_create("bugn.nc", NC_CLOBBER|NC_NETCDF4, &ncid);
    check_err(stat,__LINE__,__FILE__);
    root_grp = ncid;

    stat = nc_def_vlen(root_grp, "vl_t", NC_STRING, &vl_t_typ);              
    check_err(stat,__LINE__,__FILE__);

    stat = nc_def_compound(root_grp, sizeof(cmp_t), "cmp_t", &cmp_t_typ);    
    check_err(stat,__LINE__,__FILE__);
    {
    static int strs_dims[1] = {2};    
    stat = nc_insert_array_compound(root_grp, cmp_t_typ, "strs", 
NC_COMPOUND_OFFSET(cmp_t,strs), vl_t_typ, 1, strs_dims);    
    check_err(stat,__LINE__,__FILE__);
    }

    /* define variables */
    stat = nc_def_var(root_grp, "var", cmp_t_typ, RANK_var, 0, &var_id);
    check_err(stat,__LINE__,__FILE__);

    /* leave define mode */
    stat = nc_enddef (root_grp);
    check_err(stat,__LINE__,__FILE__);

    /* assign variable data */

    {
    static const char* vlen_3[] = {"ab", "cde", "fg"} ;
    static const char* vlen_4[] = {"hijk", "lm"} ;
    size_t zero = 0;
    static cmp_t var_data[1] = {{{{3, (void*)vlen_3}, {2, (void*)vlen_4}}}};
    stat = nc_put_var1(root_grp, var_id, &zero, var_data);
    check_err(stat,__LINE__,__FILE__);
    }

    stat = nc_close(root_grp);
    check_err(stat,__LINE__,__FILE__);
    return 0;
}