Re: extensible datasets in every dimension?

• To: netcdf-hdf@xxxxxxxxxxxxxxxx
• Subject: Re: extensible datasets in every dimension?
• From: Quincey Koziol <koziol@xxxxxxxxxxxxx>
• Date: Mon, 3 Nov 2003 10:16:16 -0600 (CST)

Hi Ed,

> Greeting to HDF HQ!
> 
> Some questions:
> 
> 1 - If any dimension of a dataset is to be extensible, the dataset
> must be chunked, correct?
    Yes.

> 2 - If I have a dataset with one expendables dimension, and several
> fixed dimensions, I can create it using a space like this:
> 
>       if ((spaceid = H5Screate_simple(var->ndims, dimsize, maxdimsize)) < 0)
>        BAIL(NC_EHDFERR);
> 
> Where dimsize is an array of initial dimension sizes, and maxdimsize
> is an array of max dimension sizes, or -1 for an unlimited dimension.
> 
> The problem I have is this. If I try and create a space with one of
> the dimsizes as zero, and the corresponding maxdimsize as -1, HDF5
> hands when I try to close the defined dataset (this seems like a HDF
> bug, BTW).
> 
> So I can do it if I start with a dimsize of 1 instead of 0, but this
> is not the netcdf way. After defining such a dataset, when I get the
> number of records in it, using H5Sget_simple_extent_dims, I get a size
> of one along that dimension, even though I haven't written any data to
> it yet, because I have to define it as having length of at least one.
> 
> Any comment or help would be appreciated...
    Hmm, an initial size of 0 should work.  Can you send me some test code
that fails?  I'll address the bug immediately then.

    Quincey
>From owner-netcdf-hdf@xxxxxxxxxxxxxxxx 04 2003 Nov -0700 09:58:02 
Message-ID: <wrxwuagnk9x.fsf@xxxxxxxxxxxxxxxxxxxxxxx>
Date: 04 Nov 2003 09:58:02 -0700
From: Ed Hartnett <ed@xxxxxxxxxxxxxxxx>
To: netcdf-hdf@xxxxxxxxxxxxxxxx
Subject: HDF5 hangs...
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Quincey,

I am having a really weird problem. At a certain point in my code, the
following code hangs in the H5Dcreate call.

This code works a bunch of times, then, at some point (I'm doing lots
of other HDF stuff, but not with this file), it hangs.

I don't know what the deal is.

   {
      hid_t dsid = 0;
      hid_t typeid1 = H5Tcopy(H5T_NATIVE_CHAR);
      hid_t plistid1 = H5P_DEFAULT;
      hid_t spaceid1 = 0;
      hid_t hdfid = 0;
      if ((hdfid = H5Fcreate("ccc_test.h5", H5F_ACC_TRUNC, H5P_DEFAULT, 
H5P_DEFAULT)) < 0)
         return (-1);
      if ((spaceid1 = H5Screate(H5S_SCALAR)) < 0)
         return (-1);
      if ((dsid = H5Dcreate(hdfid, "scaley", 
                            H5T_NATIVE_CHAR, spaceid1, plistid1)) < 0)
         return (-1);
      if (spaceid1 > 0) H5Sclose(spaceid1);
      if (hdfid > 0) H5Fclose(hdfid);
      if (dsid > 0) H5Dclose(dsid);
      dsid = 0;
   }

When I use Cntl-C to interrupt the program, I get this message:

Program received signal SIGINT, Interrupt.
0x400c997a in malloc_consolidate () from /lib/i686/libc.so.6

Somehow there is some malloc issue in H5Dcreate. Are you checking all
your malloc returns to see that the memory you are using is really
being allocated?

I can't reproduce this in a short program (yet), but I'll keep
trying...

Ed