Re: question about vlens and the size of their base type...

Hi Ed,

Welcome to 64-bit world :-)

I believe that the sizes of size_t and integer pointer are 8 on your new machine


At 04:26 PM 8/29/2005, Ed Hartnett wrote:

Howdy HDF5 Folk!

I have a HDF5 question.

I just switched to a new, faster, computer, and when I compile my
usual set of HDF5 "tests," I get some new behavior.

(I have tests in quotes because I'm not really trying to test HDF5,
just exercising it in a way similar to that which netCDF-4 does -
more of a sanity check than a set of tests).

Anyway, the program is appended below. What happens is that I create a
VLEN of base type NC_INT. Then I check the size of the VLEN type, and
it has been, until today, 8. (Is this 4 bytes each for the two fields
in hvl_t?)

Now, when I run this program, I get a size of 16 instead of 8.

What's up with that, I wonder?

Here's my new system name info, in case it helps:
Linux 2.6.12-1.1398_FC4smp #1 SMP Fri Jul 15
01:05:24 EDT 2005 x86_64 x86_64 x86_64 GNU/Linux

It does seem to imply some 64-bit stuff going on...

Any thoughts or suggestions would be most welcome.


   hid_t fileid, grpid, spaceid, typeid, attid;
   hsize_t dims[1] = {DIM1_LEN};
   hvl_t data[DIM1_LEN];
   int *phoney;
   int i, j;
   size_t size;

   /* Create some phoney data, an array of struct s1, which holds a
    * pointer to a variable length array of int. */
   for (i=0; i<DIM1_LEN; i++)
      if (!(phoney = malloc(sizeof(int) * i+1)))
        return NC_ENOMEM;
      for (j=0; j<i+1; j++)
        phoney[j] = -99;
      data[i].p = phoney;
      data[i].len = i+1;

   printf("*** Checking simple HDF5 variable length types...");

   /* Open file. */
   if ((fileid = H5Fcreate(FILE_NAME, H5F_ACC_TRUNC, H5P_DEFAULT,
                           H5P_DEFAULT)) < 0) ERR;
   if ((grpid = H5Gcreate(fileid, "grp1", 0)) < 0) ERR;

   /* Create VLEN type. */
   if ((typeid =  H5Tvlen_create(H5T_NATIVE_INT)) < 0) ERR;

   /* Although it's a vlen of ints, the size is rouned up to 8. */
   if (!(size = H5Tget_size(typeid))) ERR;
   if (size != 8) ERR;

   /* Write an attribute of this vlen type. */
   if ((spaceid = H5Screate_simple(1, dims, NULL)) < 0) ERR;
   if ((attid = H5Acreate(grpid, ATT_NAME, typeid, spaceid,
                          H5P_DEFAULT)) < 0) ERR;
   if (H5Awrite(attid, typeid, data) < 0) ERR;
   if (H5Aclose(attid) < 0) ERR;
   if (H5Tclose(typeid) < 0) ERR;
   if (H5Gclose(grpid) < 0) ERR;
   if (H5Fclose(fileid) < 0) ERR;


   /* Print out our number of errors, if any, and exit badly. */
   if (total_err)
      printf("%d errors detected! Sorry!\n", total_err);
      return 2;

   printf("*** Tests successful!\n");
   return 0;

Ed Hartnett  -- ed@xxxxxxxxxxxxxxxx

Elena Pourmal, HDF QA, Maintenance and Support Team Leader
NCSA University of Illinois at Urbana-Champaign
605 E. Springfield Ave.
Champaign, IL 61820

(217)333-0238 (office)
(217)244-1987 (fax)