Hello,
I have a strange error where HDF5 files written with NetCDF4 and HDF5-1.8.4
on a big endian machine (Power6) could not be read on little endian and
vice versa. This isn't a NetCDF issue since pure HDF5 files written with
the attached program show the same behaviour. It turned out that the
"Fractal Heap ID for Managed Objects" in the "Version 2 B-tree, Type 8
Record Layout" isn't correctly written on big endian. The ID is constructed
from version, offset, and length with the macro
#define H5HF_MAN_ID_ENCODE(i, h, o, l) \
*(i) = H5HF_ID_VERS_CURR | H5HF_ID_TYPE_MAN;
\
(i)++;
\
UINT64ENCODE_VAR((i), (o), (h)->heap_off_size);
\
UINT64ENCODE_VAR((i), (l), (h)->heap_len_size)
so offset and length are already encoded. Prior to actually writing the ID,
it is encoded again, though:
In H5A_dense_btree2_name_encode():
UINT64ENCODE(raw, nrecord->id);
And this breaks on big endian. Just copying nrecord->id to raw works for me
but I don't know if this covers all use cases of
H5A_dense_btree2_name_encode().
Cheers,
Mathis
--
Mathis Rosenhauer
Application support
German Climate Computing Center
#include "hdf5.h"
int main (void)
{
hid_t file, dataset, fid, str_id, attribute, stype;
hsize_t dimsf[1];
herr_t ret;
float time[]={0.0};
hid_t fapl_id;
int i;
char string[6];
fapl_id = H5Pcreate(H5P_FILE_ACCESS);
/* only happens with V2 */
H5Pset_libver_bounds(fapl_id, H5F_LIBVER_LATEST, H5F_LIBVER_LATEST);
file = H5Fcreate("out.h5", H5F_ACC_TRUNC, H5P_DEFAULT, fapl_id);
dimsf[0] = 1;
fid = H5Screate_simple(1, dimsf, NULL);
dataset = H5Dcreate2(file, "data", H5T_NATIVE_FLOAT, fid, H5P_DEFAULT, H5P_DEFAULT,H5P_DEFAULT);
ret = H5Dwrite(dataset, H5T_NATIVE_FLOAT, H5S_ALL, H5S_ALL, H5P_DEFAULT, time);
/* We need at least 9 attributes to trigger the error */
for (i=0; i<9; i++)
{
str_id = H5Screate(H5S_SCALAR);
stype = H5Tcopy(H5T_C_S1);
H5Tset_size(stype, 4);
H5Tset_strpad(stype,H5T_STR_NULLTERM);
sprintf(string, "attr%i", i);
attribute = H5Acreate2(dataset, string, stype, str_id, H5P_DEFAULT, H5P_DEFAULT);
ret = H5Awrite(attribute, stype, "1234");
ret = H5Sclose(str_id);
ret = H5Aclose(attribute);
H5Tclose(stype);
}
H5Sclose(fid);
H5Dclose(dataset);
H5Fclose(file);
return 0;
}
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