[yt-users] Error saving clumps to the data file

[Andrew Myers]

Hi Matt,

Thanks! Using pickle with another file seems to work fine.

Best,
Andrew

On Mon, Jan 21, 2013 at 3:50 AM, Matthew Turk <matthewturk at gmail.com> wrote:

> Hi Andrew,
>
> This looks to me like the pickle for your objects has a null
> terminated string.  It's possible the newest h5py could fix this, or
> that you could specify a string length when pickling to h5py, but the
> easier solution might be to pickle the object to a file by itself:
>
> import cPickle
> cPIckle.dump(obj, open("my_file.cpkl", "wb"), protocol=-1)
>
> Let us know if that works!
>
> -Matt
>
> On Sun, Jan 20, 2013 at 12:48 PM, Andrew Myers <atmyers at berkeley.edu>
> wrote:
> > Dear yt users,
> >
> > I've generated some clumps, and would like to save them to look at later.
> > When I try
> >
> > pf.h.save_object(master_clump, 'Clumps')
> >
> > I get the following error, which looks like it's coming fron hdf5. Has
> > anybody seen this before?
> >
> > Thanks,
> > Andrew
> >
> >
> ---------------------------------------------------------------------------
> > ValueError                                Traceback (most recent call
> last)
> > <ipython-input-13-0bda0f3d0b42> in <module>()
> > ----> 1 pf.h.save_object(master_clump, 'Clumps')
> >
> > /indirect/o/atmyers/yt-x86_64/src/yt-hg/yt/data_objects/hierarchy.pyc in
> > save_object(self, obj, name)
> >     299         """
> >     300         s = cPickle.dumps(obj, protocol=-1)
> > --> 301         self.save_data(s, "/Objects", name, force = True)
> >     302
> >     303     def load_object(self, name):
> >
> > /indirect/o/atmyers/yt-x86_64/src/yt-hg/yt/data_objects/hierarchy.pyc in
> > _save_data(self, array, node, name, set_attr, force, passthrough)
> >     274         for q in node.split('/'):
> >     275             if q: myGroup = myGroup.require_group(q)
> > --> 276         arr = myGroup.create_dataset(name,data=array)
> >     277         if set_attr is not None:
> >     278             for i, j in set_attr.items(): arr.attrs[i] = j
> >
> > /o/atmyers/yt-x86_64/lib/python2.7/site-packages/h5py/_hl/group.pyc in
> > create_dataset(self, name, shape, dtype, data, **kwds)
> >      69         """
> >      70
> > ---> 71         dsid = dataset.make_new_dset(self, shape, dtype, data,
> > **kwds)
> >      72         dset = dataset.Dataset(dsid)
> >      73         if name is not None:
> >
> > /o/atmyers/yt-x86_64/lib/python2.7/site-packages/h5py/_hl/dataset.pyc in
> > make_new_dset(parent, shape, dtype, data, chunks, compression, shuffle,
> > fletcher32, maxshape, compression_opts, fillvalue)
> >      92
> >      93     if data is not None:
> > ---> 94         dset_id.write(h5s.ALL, h5s.ALL, data)
> >      95
> >      96     return dset_id
> >
> > /o/atmyers/yt-x86_64/lib/python2.7/site-packages/h5py/h5d.so in
> > h5py.h5d.DatasetID.write (h5py/h5d.c:2866)()
> >
> > /o/atmyers/yt-x86_64/lib/python2.7/site-packages/h5py/_proxy.so in
> > h5py._proxy.dset_rw (h5py/_proxy.c:1766)()
> >
> > /o/atmyers/yt-x86_64/lib/python2.7/site-packages/h5py/defs.so in
> > h5py.defs.H5Tconvert (h5py/defs.c:18439)()
> >
> > /o/atmyers/yt-x86_64/lib/python2.7/site-packages/h5py/_errors.so in
> > h5py._errors.set_exception (h5py/_errors.c:711)()
> >
> > /o/atmyers/yt-x86_64/lib/python2.7/site-packages/h5py/_conv.so in
> > h5py._conv.str2vlen (h5py/_conv.c:3382)()
> >
> > /o/atmyers/yt-x86_64/lib/python2.7/site-packages/h5py/_conv.so in
> > h5py._conv.generic_converter (h5py/_conv.c:1302)()
> >
> > /o/atmyers/yt-x86_64/lib/python2.7/site-packages/h5py/_conv.so in
> > h5py._conv.conv_str2vlen (h5py/_conv.c:2158)()
> >
> > ValueError: VLEN strings do not support embedded NULLs
> >
> >
> >
> >
> > _______________________________________________
> > yt-users mailing list
> > yt-users at lists.spacepope.org
> > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
> >
> _______________________________________________
> yt-users mailing list
> yt-users at lists.spacepope.org
> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/20130121/2e48cc79/attachment.htm>