[yt-users] Not able to read 2D BoxLib files
Chris Malone
chris.m.malone at gmail.com
Wed Jul 24 08:58:04 PDT 2013
Hi Mani,
The pull request mentioned by the others is your best bet. That being
said, I don't think any of the BoxLib frontend has been written for
two-dimensional datasets, yet. It would be a useful addition. Our groups'
current MO of getting Matplotlib-like plots of 2d BoxLib data is cumbersome
and uses some fortran code that interfaces with the BoxLib underlying data
formats, wrapped in f2py calls to get the data into numpy arrays.
I too have been bandwidth-limited lately, but hopefully I can get back to
working out the issue to which Matt alluded.
For completeness, is there anything in particular outside of the standard
Header file (or job_info, if that exists) that is needed to visualize or
make sense of your dataset?
Chris
On Wed, Jul 24, 2013 at 8:03 AM, Matthew Turk <matthewturk at gmail.com> wrote:
> Hi Mani,
>
> Nathan and Andrew's suggestions are about right -- the boxlib frontend
> rewrite is definitely going to be the best way to do this, as I think
> it's much more generic than the current fragmented state. I've been
> bandwidth limited on that front, but if you look in the main PR you'll
> see the outstanding issues. I think the last one that was presenting
> a problem was the issue of varying refinement factors between levels,
> but I think Chris Malone and I have figured that out. I hope to be
> able to implement it soon, but I'm going to be on vacation for a few
> weeks starting Friday and so I won't be able to look at it during that
> time.
>
> Best,
>
> Matt
>
> On Tue, Jul 23, 2013 at 10:41 PM, Mani Chandra <mc0710 at gmail.com> wrote:
> > Thanks Nathan! That looks like a good place to start.
> >
> >
> > On Wed, Jul 24, 2013 at 12:29 AM, Nathan Goldbaum <nathan12343 at gmail.com
> >
> > wrote:
> >>
> >> Hi Mani,
> >>
> >> Take a look at this pull request from Matt:
> >>
> https://bitbucket.org/yt_analysis/yt/pull-request/501/consolidation-of-boxlib-frontends
> >>
> >> I suspect it will be a lot easier to write a frontend using this new
> >> framework. I think there are still a few minor issues to work out
> (that's
> >> why it's not in the codebase yet) but it should be a good place to
> start.
> >>
> >> Andrew and Matt should have more information about this.
> >>
> >> -Nathan
> >>
> >>
> >> On Tue, Jul 23, 2013 at 10:27 PM, Mani Chandra <mc0710 at gmail.com>
> wrote:
> >>>
> >>> Hi Andrew,
> >>>
> >>> This is a code which I'm writing now using the BoxLib framework, so it
> is
> >>> not exactly any of Nyx, Castro, Maestro or Orion. But I thought that
> since
> >>> they all use BoxLib, I could simply use any of those frontends
> (although
> >>> those frontends require a lot of parameters specific to those codes,
> which I
> >>> just commented out).
> >>>
> >>> So I guess I'll have to write a frontend then.
> >>>
> >>> Thanks,
> >>> Mani
> >>>
> >>>
> >>> On Wed, Jul 24, 2013 at 12:21 AM, Andrew Myers <atmyers2 at gmail.com>
> >>> wrote:
> >>>>
> >>>> Hi Mani,
> >>>>
> >>>> To my knowledge, no one has ever used yt with 2D Orion data. I'm not
> >>>> sure if any of the other BoxLib codes support 2D. I think the reason
> the
> >>>> Orion code is getting called is because yt can tell your dataset uses
> >>>> BoxLib, but not that it belongs to any of the other BoxLib-based
> codes (Nyx,
> >>>> Castro, or Maestro), so it falls back to Orion.
> >>>>
> >>>> What simulation code generated this dataset? If it's not one of Nyx,
> >>>> Castro, Maestro, or Orion, then you'll probably need to write a new
> frontend
> >>>> for your data.
> >>>>
> >>>> -Andrew Myers
> >>>>
> >>>> On Tue, Jul 23, 2013 at 7:50 PM, Mani Chandra <mc0710 at gmail.com>
> wrote:
> >>>>>
> >>>>> Hi Everyone,
> >>>>>
> >>>>> I'm trying to load a 2D BoxLib file into yt. It looks like it is
> using
> >>>>> the same code as the Orion frontend and it fails with the following
> error:
> >>>>>
> >>>>>
> >>>>>
> /home/mc/Downloads/yt/yt-x86_64/src/yt-hg/yt/data_objects/static_output.pyc
> >>>>> in hierarchy(self)
> >>>>> 191 raise RuntimeError("You should not
> instantiate
> >>>>> StaticOutput.")
> >>>>> 192 self._instantiated_hierarchy =
> >>>>> self._hierarchy_class(
> >>>>> --> 193 self, data_style=self.data_style)
> >>>>> 194 return self._instantiated_hierarchy
> >>>>> 195 h = hierarchy # alias
> >>>>>
> >>>>>
> >>>>>
> /home/mc/Downloads/yt/yt-x86_64/src/yt-hg/yt/frontends/orion/data_structures.py
> >>>>> in __init__(self, pf, data_style)
> >>>>> 119 self.data_style = data_style
> >>>>> 120
> >>>>> --> 121
> >>>>>
> self.readGlobalHeader(header_filename,self.parameter_file.paranoid_read) #
> >>>>> also sets up the grid objects
> >>>>> 122 self.__cache_endianness(self.levels[-1].grids[-1])
> >>>>> 123 AMRHierarchy.__init__(self,pf, self.data_style)
> >>>>>
> >>>>>
> >>>>>
> /home/mc/Downloads/yt/yt-x86_64/src/yt-hg/yt/frontends/orion/data_structures.py
> >>>>> in readGlobalHeader(self, filename, paranoid_read)
> >>>>> 194 self.dimension =
> >>>>> int(self.__global_header_lines[counter])
> >>>>> 195 if self.dimension != 3:
> >>>>> --> 196 raise RunTimeError("Orion must be in 3D to use
> >>>>> yt.")
> >>>>> 197 counter += 1
> >>>>> 198 self.Time =
> float(self.__global_header_lines[counter])
> >>>>>
> >>>>> Has anyone managed to load 2D Orion files into yt?
> >>>>>
> >>>>> Thanks,
> >>>>> Mani
> >>>>>
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