[yt-users] Problem loading FLASH2.5 data
Dominik Derigs
derigs at ph1.uni-koeln.de
Wed Oct 19 01:56:57 PDT 2016
Hey all,
I can confirm the strange behavior with Phillips file for an up-to-date
version of yt installed from source (updated today) on Ubuntu (stock python
2.7, no pip, no conda):
>>> ds = yt.load("DensTurbMag_hdf5_plt_cnt_0015")
> yt : [INFO ] 2016-10-19 10:55:08,720 Parameters: current_time
> = 4.66839074012e-313
> yt : [INFO ] 2016-10-19 10:55:08,720 Parameters: domain_dimensions
> = [1113971554 -402653184 1108822134]
> yt : [INFO ] 2016-10-19 10:55:08,721 Parameters: domain_left_edge
> = [ -2.00000000e+18 -2.00000000e+18 -2.00000000e+18]
> yt : [INFO ] 2016-10-19 10:55:08,721 Parameters: domain_right_edge
> = [ 2.00000000e+18 2.00000000e+18 2.00000000e+18]
> yt : [INFO ] 2016-10-19 10:55:08,721 Parameters:
> cosmological_simulation = 0.0
Best regards,
Dominik
2016-10-18 17:48 GMT+02:00 Alex Hill <ashill at haverford.edu>:
> 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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--
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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