[yt-users] Analyzing SPH data

Alankar Dutta dutta.alankar at gmail.com
Sat Mar 4 10:26:44 PST 2017


Thanks Nathan that works. Can you please suggest me a way to share with you
my entire 960 GB snapshot containing 1024 files? Then you can have a look
at them if you are interested in adding further support.

Alankar Dutta

On Sat, Mar 4, 2017 at 11:11 PM, Nathan Goldbaum <nathan12343 at gmail.com>
wrote:

> Oops, typo, should be https://bitbucket.org/ngoldbaum/yt
>
>
> On Sat, Mar 4, 2017 at 11:40 AM Alankar Dutta <dutta.alankar at gmail.com>
> wrote:
>
>> Hello,
>>
>>
>> $ hg pull -r f4c5c13 https://bitbucket.org/yt_analysis/yt
>> This is giving the following error:
>> pulling from https://bitbucket.org/yt_analysis/yt
>> abort: unknown revision 'f4c5c13'!
>>
>> Alankar Dutta
>>
>>
>> On Sat, Mar 4, 2017 at 10:46 PM, Nathan Goldbaum <nathan12343 at gmail.com>
>> wrote:
>>
>> To test my pull request you're going to want to build yt from a clone of
>> the mercurial repository after pulling in my changes.
>>
>> $ conda uninstall yt
>> $ hg clone https://bitbucket.org/yt_analysis/yt
>> $ cd yt
>> $ hg pull -r f4c5c13 https://bitbucket.org/yt_analysis/yt
>> $ hg update f4c5c13
>> $ python setup.py develop
>>
>> You'll need a compilation environment set up for that to succeed. If you
>> don't have compilers installed it will be less straightforward to test
>> this. I'd urge you *not* to hand-edit your installed version of yt from
>> conda, as that will create more headaches for you if you make a mistake and
>> forget to correct it.
>>
>>
>> On Sat, Mar 4, 2017 at 10:34 AM Alankar Dutta <dutta.alankar at gmail.com>
>> wrote:
>>
>> Hello,
>>
>> I have modified the yt files as given in the pull request. I get the
>> following error code:
>>
>> Traceback (most recent call last):
>>   File "dev.py", line 9, in <module>
>>     import yt
>>   File "/home/alankar/anaconda3/lib/python3.6/site-packages/yt/__init__.py",
>> line 133, in <module>
>>     frontends = _frontend_container()
>>   File "/home/alankar/anaconda3/lib/python3.6/site-packages/yt/frontends/api.py",
>> line 52, in __init__
>>     setattr(self, frontend, importlib.import_module(_mod))
>>   File "/home/alankar/anaconda3/lib/python3.6/importlib/__init__.py",
>> line 126, in import_module
>>     return _bootstrap._gcd_import(name[level:], package, level)
>>   File "/home/alankar/anaconda3/lib/python3.6/site-packages/yt/frontends/eagle/api.py",
>> line 17, in <module>
>>     from .data_structures import \
>>   File "/home/alankar/anaconda3/lib/python3.6/site-packages/yt/
>> frontends/eagle/data_structures.py", line 21, in <module>
>>     from yt.frontends.gadget.data_structures import \
>>   File "/home/alankar/anaconda3/lib/python3.6/site-packages/yt/
>> frontends/gadget/data_structures.py", line 28, in <module>
>>     from yt.frontends.sph.data_structures import \
>> ImportError: cannot import name 'SPHDataset'
>>
>> The following is my code:
>> import yt
>> ds = yt.load("snapshot_068.0")
>>
>> Alankar Dutta
>>
>> On Sat, Mar 4, 2017 at 3:13 PM, Alankar Dutta <dutta.alankar at gmail.com>
>> wrote:
>>
>> Oh I missed telling that the full dataset is around 950 GB
>>
>> On Sat, Mar 4, 2017 at 1:02 PM, Alankar Dutta <dutta.alankar at gmail.com>
>> wrote:
>>
>> Hello,
>>
>> This is only one part of the multipart snapshot of the simulation. I am
>> sending you the header information from the snapshot file:
>>
>> {'O0': 0.27500000000000002,
>>  'Ol': 0.72499999999999998,
>>  'boxsize': 100000.0,
>>  'flag_age': 1,
>>  'flag_cooling': 1,
>>  'flag_delaytime': 0,
>>  'flag_fb': 1,
>>  'flag_fh2': 0,
>>  'flag_metals': 1,
>>  'flag_potential': 3,
>>  'flag_sfr': 1,
>>  'flag_tmax': 0,
>>  'h': 0.70199999999999996,
>>  'massTable': array([ 0.        ,  0.00110449,  0.        ,  0.        ,  0.        ,  0.        ]),
>>  'nbndry': 76247,
>>  'nbulge': 0,
>>  'ndisk': 0,
>>  'ndm': 1459617792,
>>  'nfiles': 1024,
>>  'ngas': 1343721867,
>>  'npartThisFile': array([10045237, 10239661,        0,        0,   451148,       67], dtype=uint32),
>>  'npartTotal': array([1343721867, 1459617792,          0,          0,  503500456,
>>              76247], dtype=uint32),
>>  'npartTotalHW': array([1, 1, 0, 0, 0, 0], dtype=uint32),
>>  'nstar': 503500456,
>>  'redshift': 1.0000000010567627,
>>  'rhocrit': 2.707660428120944e-29,
>>  'time': 0.49999999973580939}
>>
>>
>>
>> I extracted this information using a different python program.
>>
>> Alankar Dutta
>>
>> On Sat, Mar 4, 2017 at 12:45 PM, Nathan Goldbaum <nathan12343 at gmail.com>
>> wrote:
>>
>>
>>
>> On Sat, Mar 4, 2017 at 12:25 AM, Nathan Goldbaum <nathan12343 at gmail.com>
>> wrote:
>>
>>
>>
>> On Sat, Mar 4, 2017 at 12:13 AM, Alankar Dutta <dutta.alankar at gmail.com>
>> wrote:
>>
>> Hello,
>>
>> Modifying the GADGET simulation isn't possible the moment because it has
>> already been developed by someone else who has a paper  published  on this
>> simulation and I want to use that simulation  snapshots to make mock xray
>> map from it.
>>
>>
>> I'm talking about modifying yt, not Gadget.
>>
>> Is the file you attached to your other e-mail just a single file in a
>> multi-file dataset? How large is the full dataset? Do you not have a way to
>> produce a full dataset in this output format that's not prohibitively large?
>>
>>
>> I've opened a pull request that allows me to do IO on the data you
>> attached: https://bitbucket.org/yt_analysis/yt/pull-requests/2537
>>
>> This allows me to read your data in, getting sensible values for e.g.
>> position. I suspect we're not using the correct field specification because
>> I see this warning:
>>
>> yt : [WARNING  ] 2017-03-04 01:06:09,109 Your Gadget-2 file may have
>> extra columns or different precision! (1814947576 file vs 1486279952
>> computed)
>>
>> yt supports a number of field specifications out of the box, see:
>>
>> https://bitbucket.org/yt_analysis/yt/src/3eca2ae80ab14a48b643d3055d7d3c
>> 0933fa77ae/yt/frontends/gadget/definitions.py?at=yt&
>> fileviewer=file-view-default#definitions.py-50
>>
>> Do you happen to know which fields are in your output file?
>>
>>
>>
>>
>>
>>
>> Alankar Dutta
>>
>> On Mar 4, 2017 11:38 AM, "Nathan Goldbaum" <nathan12343 at gmail.com> wrote:
>>
>> I think the most straightforward thing to do here is to fix the Gadget
>> frontend so it properly reads in gadget binary data with positions written
>> in double precision.
>>
>> Is there any chance you can generate a smallish test dataset in your
>> Gadget output format that we can use for debugging purposes? With that
>> available it should be straightforward to add support. You can share the
>> dataset using the yt curldrop (https://docs.hub.yt/services.html#curldrop)
>> or a cloud filesharing service like dropbox or google drive.
>>
>> Unfortunately there isn't a way to load SPH data without a full-fledged
>> frontend right now.
>>
>> We do have a load_particles function which allows creating a dataset from
>> particle data loaded as numpy arrays, but it's currently not possible to
>> use it to load SPH data.
>>
>> I'm currently actively working on improving support for SPH data in yt
>> and adding the ability to load SPH data with load_particles is one of the
>> things I've added in that branch of the code. Hopefully this work will be
>> stabilized sometime in the next few months.
>>
>>
>>
>> On Fri, Mar 3, 2017 at 11:45 PM, Alankar Dutta <dutta.alankar at gmail.com>
>> wrote:
>>
>> Hello yt-community,
>>
>> I am a beginner on yt. I have an array of data which I have read from a
>> Gadget simulation snapshot. It is not directly supported by yt at present
>> (I have ensured this by already discussing this issue in the community
>> before). The array has position,velocity, density, mass, internal energy
>> and smoothing length information on the gas particles. Now how can I use
>> this to make the slice plots or other useful visualizations?
>>
>> Alankar Dutta,
>> Third year Undergraduate,
>> Physics Department,
>> Presidency University, India
>>
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