[yt-users] pHOP child halos

[Brian Crosby]

Great, thanks Britton, I'll let them know.

-Brian

On Jul 4, 2011, at 2:03 PM, Britton Smith wrote:

> Hi Brian,
> 
> It's not the hdf5 library, but the version of h5py (the python module that depends on hdf5 libraries) which is the issue.  I would suggest contacting the Nautilus admins and asking them to upgrade the h5py install for the YT module.  If they update h5py to version 1.4, they will have to update the hdf5 libraries to version 1.8.x.  If they only update h5py to version 1.3, then the hdf5 1.6 libraries will be fine.
> 
> Britton
> 
> On Mon, Jul 4, 2011 at 11:59 PM, Brian Crosby <crosby.bd at gmail.com> wrote:
> This is a bit puzzling to me.  I'm using the yt/2.1 module that's installed on Nautilus, along with hdf5/1.6.10.  If the HDF5 version is the issue, does that mean that I cannot use the YT module on Nautilus, and should install it myself with HDF5 1.3?
> 
> Thanks,
> Brian
> 
> 
> On Jul 4, 2011, at 9:36 AM, Stephen Skory wrote:
> 
> > Brian and Britton,
> >
> >> It looks like this installation of yt is using h5py 1.2, which I believe has
> >> a bug that causes issues when using the same variable name to open multiple
> >> hdf5 files in sequence.  If this is the case, then the only solution is to
> >> upgrade the hdf5 version being used to version 1.3 or higher.  Stephen will
> >> know better than I if this is the issue.  Stephen, can you confirm this?
> >
> > I think Britton is correct. I just took a look at the code, and the
> > h5py file pointer is being closed, which is correct, and I think 1.3
> > fixes this issue.
> >
> > Actually, I think if the h5py pointer gets 'del'ed and perhaps
> > gc.collect() is called, this 1.2 bug can be circumvented. But,
> > overall, I think 1.3 is a better option that adding all that mess to
> > the code.
> >
> > Let us know if you run into trouble with installing or using 1.3!
> >
> > --
> > Stephen Skory
> > s at skory.us
> > http://stephenskory.com/
> > 510.621.3687 (google voice)
> > _______________________________________________
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> > yt-users at lists.spacepope.org
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> 
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