Ed Hartnett wrote:
Jeff Whitaker <jswhit@xxxxxxxxxxx> writes:
Concerning packing of structs, one of us is very confused about how
HDF5 compound types work (and it's probably me). I thought that you
could specify arbitrary offsets that do not necessarily correspond to
the default alignment of your C compiler, and HDF5 would take care of
everything when you read the data back in.
No, sorry, this turns out not to be the case.
Otherwise, how would you
read a file created with HDF5 on a platform with a different default
alignment than the one it was written on? Isn't the whole point of
the HDF5 layer that you don't have worry about the default alignment
of structs for the C compiler?
HDF5 can handle it, but not if you change the alignment of your struct
with a compiler directive!
HDF5 figures out packing when it is built on your machine, in the HDF5
configure script. Using any other packing than the one HDF5 figured out
at its build time will result in confusion.
So if you want a different packing of your struct, you must specify the
packing options you want with compiler flags, and make sure you use
those flags when building HDF5 (and netCDF-4, and your own program).
I have forwarded your question to the HDF5 team to ensure that I am
telling you the correct answer, and to see if they can help explain this
any more clearly.
Thanks!
Ed
Ed: Attached is an HDF5 version of the netcdf program I sent before.
If you run this and look at the output with h5dump, you will see that
the output is the same whether the __packed__ attribute is set or not.
This is evidence that you should be able to align (i.e. pack) your
structs however you want, regardless of what packing HDF5 detected at
compile time. If this weren't the case, then why even require the user
to pass the offsets to nc_insert_compound?
It seems to me that somehow netcdf is not using the offsets the user
passed to nc_insert_compound correctly.
-Jeff
-Jeff
#include "hdf5.h"
int
main()
{
hid_t s1_tid; /* File datatype identifier */
hid_t file, dataset, space; /* Handles */
herr_t status;
hsize_t dim[] = {1}; /* Dataspace dimensions */
struct s1
{
short i;
long long j;
/*};*/
} __attribute__ ((__packed__));
struct s1 data[1];
/* Create some phony data. */
data[0].i = 20000;
data[0].j = 300000;
/*
* Create the data space.
*/
space = H5Screate_simple(1, dim, NULL);
/*
* Create the file.
*/
file = H5Fcreate("test.h5", H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
/*
* Create the memory datatype.
*/
s1_tid = H5Tcreate (H5T_COMPOUND, sizeof(struct s1));
H5Tinsert(s1_tid, "i", HOFFSET(struct s1, i), H5T_NATIVE_SHORT);
H5Tinsert(s1_tid, "j", HOFFSET(struct s1, j), H5T_NATIVE_LLONG);
/*
* Create the dataset.
*/
dataset = H5Dcreate (file, "phony_dataset", s1_tid, space, H5P_DEFAULT,
H5P_DEFAULT, H5P_DEFAULT);
/*
* Write data to the dataset;
*/
status = H5Dwrite (dataset, s1_tid, H5S_ALL, H5S_ALL, H5P_DEFAULT, data);
/*
* Release resources
*/
H5Tclose(s1_tid);
H5Sclose(space);
H5Dclose(dataset);
H5Fclose(file);
}
