<div><div dir="auto">Sorry, I'm confused.</div><div dir="auto"><br></div><div dir="auto">In your first email you said you were having issues with the dark skies simulation, but it seems you're trying to load it using the Gadget frontend somehow? Or is this a different Gadget dataset?</div><div dir="auto"><br></div><div dir="auto">As far as I'm aware, Dark Skies is available in the SDF output format, or streaming over HTTP via thingking.</div><div dir="auto"><br></div><div dir="auto">If it's just a big Gadget dataset, the issue is that it's too big to load given the memory available on your machine. Right now you need enough memory to store the Morton indices for all the particles (one int64 per particle). We are actively working on improving this situation by making yt use compressed bitmaps to store the Morton indices, but that work won't be done for several months at least.</div><div dir="auto"><br></div><div dir="auto">You should be able to stream the dark skies data over HTTP though without having a ton of memory, there were some clever tricks applied to get around the memory limit I described above.</div><div dir="auto"><br></div><div dir="auto">The reason I was asking about the field_list for dark skies is because I'd like to see what fields are available. The error message you saw indicates that one or more of the fields necessary to calculate the radial velocity is not available (or yt is not aware of an alias from a field name on disk to yt's internal field name).</div><br><div class="gmail_quote"><div>On Sat, Jul 1, 2017 at 6:46 PM ALEXANDROS TSOUROS <<a href="mailto:ph4602@edu.physics.uoc.gr">ph4602@edu.physics.uoc.gr</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Thanks for your prompt reply!<br>
<br>
So this is another problem. I'm using a 64-bit python installation, yet<br>
the output of 'print ds.file_list' is<br>
<br>
"<br>
(...)<br>
Traceback (most recent call last):<br>
File "ds.py", line 5, in <module><br>
print ds.field_list<br>
File<br>
"/home/atsouros/gadget2/yt/yt-conda/src/yt-git/yt/data_objects/static_output.py",<br>
line 545, in field_list<br>
return self.index.field_list<br>
File<br>
"/home/atsouros/gadget2/yt/yt-conda/src/yt-git/yt/data_objects/static_output.py",<br>
line 503, in index<br>
self, dataset_type=self.dataset_type)<br>
File<br>
"/home/atsouros/gadget2/yt/yt-conda/src/yt-git/yt/geometry/particle_geometry_handler.py",<br>
line 39, in __init__<br>
super(ParticleIndex, self).__init__(ds, dataset_type)<br>
File<br>
"/home/atsouros/gadget2/yt/yt-conda/src/yt-git/yt/geometry/geometry_handler.py",<br>
line 50, in __init__<br>
self._setup_geometry()<br>
File<br>
"/home/atsouros/gadget2/yt/yt-conda/src/yt-git/yt/geometry/particle_geometry_handler.py",<br>
line 50, in _setup_geometry<br>
self._initialize_particle_handler()<br>
File<br>
"/home/atsouros/gadget2/yt/yt-conda/src/yt-git/yt/geometry/particle_geometry_handler.py",<br>
line 104, in _initialize_particle_handler<br>
self._initialize_indices()<br>
File<br>
"/home/atsouros/gadget2/yt/yt-conda/src/yt-git/yt/geometry/particle_geometry_handler.py",<br>
line 126, in _initialize_indices<br>
morton = np.empty(self.total_particles, dtype="uint64")<br>
MemoryError<br>
"<br>
<br>
I would assume that the problem is that it's running out of ram. In<br>
general, I am able to produce the examples provided by Dark Sky, so I<br>
can in general load data from the dataset. But I cannot use 'print<br>
ds.field_list'.<br>
<br>
TL;DR<br>
<br>
The output is 'MemoryError'.<br>
<br>
<br>
<br>
On 2017-07-02 01:34, Nathan Goldbaum wrote:<br>
> What's the output of "print(ds.field_list)" with the loaded dataset?<br>
><br>
> On Sat, Jul 1, 2017 at 4:21 PM ALEXANDROS TSOUROS<br>
> <<a href="mailto:ph4602@edu.physics.uoc.gr" target="_blank">ph4602@edu.physics.uoc.gr</a>> wrote:<br>
><br>
>> Hello all!<br>
>><br>
>> I am quite new to yt, so please bear with my ignorance!<br>
>><br>
>> I need to perform analysis on the open data of the Dark Sky<br>
>> Simulation<br>
>> (<a href="http://darksky.slac.stanford.edu" rel="noreferrer" target="_blank">http://darksky.slac.stanford.edu</a>). In particular I need to create 1<br>
>> dimensional profiles of the radial velocity of dark matter particles<br>
>> around halos.<br>
>><br>
>> Attached, you'll find my attempt at producing such a profile.<br>
>><br>
>> When I do this on a GADGET2 simulation I've run, I can use the<br>
>> 'radial_velocity' field without a problem. However, this script,<br>
>> where<br>
>> the data is that of the Dark Sky simulation, produces the following<br>
>> output :<br>
>><br>
>> '<br>
>> (...)<br>
>> yt.utilities.exceptions.YTFieldNotFound: Could not find field<br>
>> '('all',<br>
>> 'radial_velocity')' in ds14_a_1.0000.'<br>
>><br>
>> However, as I understand it, the field 'radial_velocity' is native<br>
>> to<br>
>> yt. How can I surpass this problem?<br>
>><br>
>> Any help will be appreciated.<br>
>><br>
>> Thank you very much for your time,<br>
>> Tsouros Alexandros<br>
>> _______________________________________________<br>
>> yt-users mailing list<br>
>> <a href="mailto:yt-users@lists.spacepope.org" target="_blank">yt-users@lists.spacepope.org</a><br>
>> <a href="http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org" rel="noreferrer" target="_blank">http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org</a><br>
> _______________________________________________<br>
> yt-users mailing list<br>
> <a href="mailto:yt-users@lists.spacepope.org" target="_blank">yt-users@lists.spacepope.org</a><br>
> <a href="http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org" rel="noreferrer" target="_blank">http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org</a><br>
_______________________________________________<br>
yt-users mailing list<br>
<a href="mailto:yt-users@lists.spacepope.org" target="_blank">yt-users@lists.spacepope.org</a><br>
<a href="http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org" rel="noreferrer" target="_blank">http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org</a><br>
</blockquote></div></div>