[yt-users] Problem loading FLASH2.5 data
Dominik Derigs
derigs at ph1.uni-koeln.de
Wed Oct 19 09:57:18 PDT 2016
Hi again,
I can confirm that downgrading h5py from 2.6.0 to 2.5.0 fixed the issue for
me.
>>> ds = yt.load("DensTurbMag_hdf5_plt_cnt_0015")
> yt : [INFO ] 2016-10-19 18:56:40,998 Parameters: current_time
> = 751000000000.0
> yt : [INFO ] 2016-10-19 18:56:40,999 Parameters: domain_dimensions
> = [8 8 8]
> yt : [INFO ] 2016-10-19 18:56:40,999 Parameters: domain_left_edge
> = [ -2.00000000e+18 -2.00000000e+18 -2.00000000e+18]
> yt : [INFO ] 2016-10-19 18:56:40,999 Parameters: domain_right_edge
> = [ 2.00000000e+18 2.00000000e+18 2.00000000e+18]
> yt : [INFO ] 2016-10-19 18:56:40,999 Parameters:
> cosmological_simulation = 0.0
Best regards,
Dominik
2016-10-19 18:11 GMT+02:00 Nathan Goldbaum <nathan12343 at gmail.com>:
> So it turns out this is due to a regression in the h5py library:
>
> https://github.com/h5py/h5py/issues/764
>
> If you'd like a quick workaround without Kacper's pull request, you just
> need to forcibly downgrade h5py:
>
> $ conda uninstall h5py
> $ conda install h5py==2.5.0
>
> or if you use pip:
>
> $ pip uninstall h5py
> $ pip install h5py==2.5.0
>
> Hopefully Kacper's fix will be in by the time we release yt 3.3.2 and
> you'll be able to upgrade h5py once again and hopefully the h5py bug will
> be fixed by the time the next version fo h5py comes out.
>
> -Nathan
>
> On Wed, Oct 19, 2016 at 11:05 AM, Philipp <keule-phg at gmx.de> wrote:
>
>> Dear Kacper,
>>
>> sure you can add those files to the official testing suite!
>>
>>
>> Dear Alex,
>>
>> I installed yt on a “clean” machine using pip and I still get the error
>> that also Dominik confirmed.
>>
>> Thank you and best regards,
>> Philipp
>>
>>
>> > On 19 Oct 2016, at 17:33, Kacper Kowalik <xarthisius.kk at gmail.com>
>> wrote:
>> >
>> > On 10/18/2016 09:11 AM, Philipp wrote:
>> >> Hi Nathan,
>> >>
>> >> thank you for the fast reply. Sorry, I didn’t check the sample data
>> >> for F2.5 files. I uploaded a small test file here:
>> >> http://use.yt/upload/b895e885 <http://use.yt/upload/b895e885> which
>> >> is at time 0 (maybe not a very clever idea if the time is read
>> >> incorrectly) and another file (http://use.yt/upload/1106d6c4
>> >> <http://use.yt/upload/1106d6c4>) at time 23.8 kyr. The block size is
>> >> [8,8,8].
>> >>
>> >> With best regards,
>> >> Philipp
>> >
>> > Hi Phillip,
>> > can I add those datasets to yt's testing suite? That mandates having
>> > them publicly available at http://yt-project.org/data/
>> >
>> > I've also opened PR 2421 [1] that hopefully will fix the issue you're
>> > seeing.
>> >
>> > Cheers,
>> > Kacper
>> >
>> > [1] https://bitbucket.org/yt_analysis/yt/pull-requests/2421
>> >
>> >
>> >>> On 18 Oct 2016, at 15:37, Nathan Goldbaum <nathan12343 at gmail.com>
>> >>> wrote:
>> >>>
>> >>> Hi Phillip,
>> >>>
>> >>> I don't think we have any Flash2.5 test data on yt-project.org/data
>> >>> <http://yt-project.org/data>. We use the datasets there in our test
>> >>> suite, so if we don't have any such data that means that our
>> >>> support for a data format isn't tested and is subject to breakage.
>> >>>
>> >>> Would you be willing to share some test data that the yt project
>> >>> can use for debugging purposes? It should be relatively small,
>> >>> should trigger the error you're seeing, and should be ok to host
>> >>> publicly on yt-project.org/data <http://yt-project.org/data> and
>> >>> use in our test suite. If so, we can look into restoring support
>> >>> and making sure we don't regress again.
>> >>>
>> >>> You can share the data using e.g. Dropbox, google drive, or by
>> >>> using the yt curldrop:
>> >>>
>> >>> https://docs.hub.yt/services.html#curldrop
>> >>> <https://docs.hub.yt/services.html#curldrop>
>> >>>
>> >>> Nathan
>> >>>
>> >>> On Tuesday, October 18, 2016, Philipp Girichidis <keule-phg at gmx.de
>> >>> <mailto:keule-phg at gmx.de>> wrote: Dear YT users,
>> >>>
>> >>> I upgraded my version of YT from an older version that still
>> >>> installed the libraries on its own (version downloaded 2016/06/21)
>> >>> to a more recent version using yt-conda. With the new version I
>> >>> cannot read old FLASH2.5 data any more. The previous version of yt
>> >>> gave me the correct output
>> >>>
>> >>> yt : [INFO ] 2016-09-09 16:37:59,285 Parameters: current_time
>> >>> = 1260000000.0 yt : [INFO ] 2016-09-09 16:37:59,286 Parameters:
>> >>> domain_dimensions = [8 8 8] yt : [INFO ] 2016-09-09
>> >>> 16:37:59,289 Parameters: domain_left_edge = [
>> >>> -4.00000000e+17 -4.00000000e+17 -4.00000000e+17] yt : [INFO ]
>> >>> 2016-09-09 16:37:59,290 Parameters: domain_right_edge = [
>> >>> 4.00000000e+17 4.00000000e+17 4.00000000e+17] yt : [INFO ]
>> >>> 2016-09-09 16:37:59,291 Parameters: cosmological_simulation =
>> >>> 0.0
>> >>>
>> >>> the new version does not read some of the numbers properly,
>> >>>
>> >>> yt : [INFO ] 2016-09-09 16:39:11,692 Parameters: current_time
>> >>> = 1.06099789548e-313 yt : [INFO ] 2016-09-09 16:39:11,692
>> >>> Parameters: domain_dimensions = [1104332420 0
>> >>> 1102957925] yt : [INFO ] 2016-09-09 16:39:11,693 Parameters:
>> >>> domain_left_edge = [ -4.00000000e+17 -4.00000000e+17
>> >>> -4.00000000e+17] yt : [INFO ] 2016-09-09 16:39:11,694
>> >>> Parameters: domain_right_edge = [ 4.00000000e+17
>> >>> 4.00000000e+17 4.00000000e+17] yt : [INFO ] 2016-09-09
>> >>> 16:39:11,695 Parameters: cosmological_simulation = 0.0
>> >>>
>> >>> The time value as well as the dimensions are messed up and thus yt
>> >>> crashes with a memory error at some point. To me it looks like a
>> >>> conversion problem between big and little endian or some similar
>> >>> conversion problem between single and double precision. I tried
>> >>> various combinations of MAC and linux and the problem does not seem
>> >>> to operating system dependent.
>> >>>
>> >>> Quite a few functions have changed in terms of reading particle
>> >>> data, but the simulation does not contain particles. I tried to
>> >>> find the part of the code that reads the domain_dimensions and
>> >>> looked at file
>> >>> yt-conda/lib/python2.7/site-packages/yt/frontends/flash/data
>> _structures.py
>> >>>
>> >>>
>> > where in line 99ff the block dimensions are read. But this part of the
>> > code is not executed (checked with print statements in iyt). Loading the
>> > hdf5 file with h5py and using the code in line 104 gives me the correct
>> > numbers, but I guess yt reads the data from somewhere else?
>> >>>
>> >>> Any hints on how the hierarchy of reading data is organized or
>> >>> where to search? I know FLASH2.5 is very old but we still have a
>> >>> lot of (quite expensive) F2.5 data.
>> >>>
>> >>> With best regards, Philipp Girichidis
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--
Dominik Derigs
I. Physikalisches Institut
Universität zu Köln
Zülpicher Straße 77
50937 Köln
GERMANY
https://hera.ph1.uni-koeln.de/~derigs/
Tel. (+49|0) 221 470-8352
Fax. (+49|0) 221 470-5162
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