Re: [Pytables-users] HDF5 version

[Francesc A. <fa...@op...>]

Hello Berthold!,

A Divendres 22 Agost 2003 16:17, Berthold H=F6llmann va escriure:
> Hello,
>
> I have some problems with pytables 0.7.1. The file format seems to
> have changed. When I run an old h5dump on a new pytables generated
> file I get lots of
>
> h5dump error: unknown object "order"
>
> messages with different object names, with a 1.6 h5dump I get
>
> ...
>       DATASET "order" {
>          DATATYPE  H5T_STRING {
>                STRSIZE 1;
>                STRPAD H5T_STR_NULLTERM;
>                CSET H5T_CSET_ASCII;
>                CTYPE H5T_C_S1;
>             }
>          DATASPACE  SIMPLE { ( 9, 36 ) / ( 9, 36 ) }
> ...
>
> I can't see a difference to datasets accepted by the old h5dump, but
> theres the error message.

Well, it's perfectely possible that the internal format of the HDF5 have
changed from 1.4.x to 1.6.x. The important thing is, though, that new versi=
on
would be *backward* compatible with the old one. So, you can install the new
utilities from HDF5 1.6.x and hopefully you will be able to read *both*
formats.

>
> Another problem I'm still investigating is that HDF5 1.6.0 does not
> accept empty arrays as input. I get
>
> HDF5-DIAG: Error detected in HDF5 library version: 1.6.0 thread 0.  Back
> trace follows. #000: H5S.c line 1708 in H5Screate_simple(): zero sized
> dimension for non-unlimited dimension major(01): Function arguments
>     minor(05): Bad value
>
> when trying to save
>
> zeros((1, 0, 3), 'd')
>
> We had successfully written these arrays with pytables 0.3 or 0.4

Did you? I thought that zero sized arrays were only possible with chunked
arrays... Well, in any case this should be possible when chunked arrays will
be finally implemented, most probably in version 0.8 of PyTables.

> and I haven't found the time to upgrade until now. Unfortunately 0.7.1
> does not work with HDF5 1.4.4. There was a missing symbol when
> importing. Am I struck with pytables 0.3 or is there another solution?
>

Wait until chunked arrays would be implemented. I hope to be able to do this
real soon.

Cheers,

=2D-=20
=46rancesc Alted