[yt-users] Problem loading FLASH2.5 data
Alex Hill
ashill at haverford.edu
Tue Oct 18 08:48:23 PDT 2016
Hi John and Phillip,
I’m actively using yt with both Flash 4 and 2.5 data files now with up to date yt (3.3.1) on both my Mac laptop and NASA’s pleiades data analysis nodes, installed via pip; I have no trouble reading them or the test files Phillip uploaded. Maybe try installing with pip instead of conda?
This is the output I get for the _0015 test file:
yt : [INFO ] 2016-10-18 11:43:55,739 Parameters: current_time = 751000000000.0
yt : [INFO ] 2016-10-18 11:43:55,739 Parameters: domain_dimensions = [8 8 8]
yt : [INFO ] 2016-10-18 11:43:55,740 Parameters: domain_left_edge = [ -2.00000000e+18 -2.00000000e+18 -2.00000000e+18]
yt : [INFO ] 2016-10-18 11:43:55,741 Parameters: domain_right_edge = [ 2.00000000e+18 2.00000000e+18 2.00000000e+18]
yt : [INFO ] 2016-10-18 11:43:55,742 Parameters: cosmological_simulation = 0.0
Happy to help diagnose further.
-Alex
---------
Alex Hill
Postdoctoral Research Associate
Office: KINSC Link L106
Department of Astronomy, Haverford College
370 Lancaster Ave, Haverford, PA 19041 USA
phone: +1 484 297 2136
email/iMessage: ashill at haverford.edu
> On Oct 18, 2016, at 10:12, John ZuHone <jzuhone at gmail.com> wrote:
>
> Hi Nathan and Phillip,
>
> Since I am nominally the FLASH guy and used to run 2.5 I can check this one out.
>
>
> ================================
> John ZuHone, Chandra/ACIS Operations
> Harvard-Smithsonian Center for Astrophysics
>
> 60 Garden St., MS-67 (w) 617-496-1816
> Cambridge, MA 02138. (m) 781-708-5004
>
> john.zuhone at cfa.harvard.edu
> http://hea-www.cfa.harvard.edu/~jzuhone
> ================================
>
> On Oct 18, 2016, at 10:11 AM, Philipp <keule-phg at gmx.de> 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 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) at time 23.8 kyr. The block size is [8,8,8].
>>
>> With best regards,
>> Philipp
>>
>>
>>> 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. 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 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
>>>
>>> Nathan
>>>
>>> On Tuesday, October 18, 2016, Philipp Girichidis <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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