[yt-users] pHOP child halos

[Harinarayan Krishnan]

Hi all,

Nautilus should now have h5py version 1.3.1 for Yt. Please let me know if
anything is amiss.

Have a Happy Fourth of July!

Thanks,
Hari



On Mon, Jul 4, 2011 at 6:57 PM, Harinarayan Krishnan <hkrishnan at lbl.gov>wrote:

> 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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