[yt-users] pHOP child halos

[Harinarayan Krishnan]

Hi Brian,

They already know :) I will get on it and update yt as soon as I get the
chance. Which will probably happen some time tomorrow.

Thanks,
Hari


On Mon, Jul 4, 2011 at 1:04 PM, Brian Crosby <crosby.bd at gmail.com> wrote:

> 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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