[yt-dev] Consolidating Boxlib frontends

Casey W. Stark caseywstark at gmail.com
Thu May 16 11:38:38 PDT 2013 

Hi Matt.

I think castro.use_comoving was removed once Nyx was ripped out.

It sounds like there are more inconsistencies... Nyx datasets always have
the structure plt%05i/Level_%i, then in each level directory, the Cell_H
file and 64 data files Cell_D_%04d from 0000 to 0063.


On Thu, May 16, 2013 at 11:29 AM, Matthew Turk <matthewturk at gmail.com>wrote:

> On Thu, May 16, 2013 at 10:06 AM, Michael Zingale
> <michael.zingale at stonybrook.edu> wrote:
> > Yes, that is correct.
> >
> > Also, orion is C++ Box lib, not Fortran.
>
> Oops, thanks.
>
> >
> > Finally, because of how C++ boxlib works, it isn't easy to store runtime
> > parameters if the default was unchanged.  In Fortran box lib, a python
> > script parses parameter files and writes f90 code at compile time,
> making it
> > easy.
>
> Ah, okay, great.  That is helpful, and something we can do.
>
> >
> > So for Castro and Nyx, if you tell me exactly what info you might need
> from
> > the runtime paramters, I can add a section to job_info that provides the
> > info
>
> I will look into this, but I think right now it comes down to:
>
> amr.n_cell (We might be able to get this in the Header?)
> amr.ref_ratio (which I think we can get elsewhere?)
> Prob.lo_bc
> castro.use_comoving
> comoving_OmL
> comoving_OmM
> comoving_h
> comoving_a (Which is currently in a different  file)
>
> One thing I'm also wondering about is looking at the Header file, it
> seems that all of the examples I have only have a single data file for
> each level, of the form:
>
> Level_*/Cell
>
> with a corresponding Cell_H that contains the necessary header info.
> Is this how it always is -- as in, only one data file per Header?  Is
> there a way to read, from the header, how many types of data files
> there will be?  It would make things considerably easier if I knew how
> many types of data files.
>
> >
> > On May 16, 2013 9:53 AM, "Matthew Turk" <matthewturk at gmail.com> wrote:
> >>
> >> As a quick followup, I have noticed that in many cases we default to
> >> using the "inputs" values over the values in the Header file.  For
> >> instance, the domain edges and the index space.  I'd rather use the
> >> Header file since it's a fundamental component, whereas the inputs
> >> should not strictly be necessary to orient the data, if I understand
> >> Boxlib correctly.
> >>
> >> On Thu, May 16, 2013 at 9:18 AM, Matthew Turk <matthewturk at gmail.com>
> >> wrote:
> >> > Hi all,
> >> >
> >> > Okay, from reading this I think I see a few things to address:
> >> >
> >> >  * We should certainly ensure that the Fortran/C++ frontends both
> >> > work.  I believe -- but may be wrong -- that Maestro and Orion are the
> >> > "Boxlib Fortran" frontends, and Nyx and Castro are the "Boxlib C++"
> >> > frontends.  The differences seem to be in how level files are stored
> >> > and a bit about the parameters.
> >> >  * A clear message: make as many of the inputs files optional as
> >> > possible, and once the job_info changes have been deployed, that will
> >> > only leave Orion without job_info.
> >> >  * Particles should be delegated to subclasses.
> >> >  * Almost none of the Enzo-isms are necessary anymore, and we can work
> >> > around the gamma/refine_by stuff.
> >> >  * Get rid of paranoia mode
> >> >  * Put off changes to the Pluto/Chombo frontends
> >> >
> >> > For what it's worth, I've gotten a "boxlib" frontend that can load up
> >> > the example Orion data as well as a Maestro dataset that Mike provided
> >> > me.  The biggest issue was with the fortran-formatted numbers we
> >> > corrected for previously, but I think I've got a workaround.
> >> >
> >> > In digging through the code I also found a number of routines that
> >> > have been largely unchanged since their first implementation some
> >> > years ago, which I'm going to try to clean up.
> >> >
> >> > Thanks everyone.  I've been using the bookmark "boxlib" in my repo at
> >> > https://bitbucket.org/MatthewTurk/yt .
> >> >
> >> > -Matt
> >> >
> >> >
> >> >
> >> > On Wed, May 15, 2013 at 8:36 PM, Michael Zingale
> >> > <michael.zingale at stonybrook.edu> wrote:
> >> >> Maestro particles are also their own thing, and we shouldn't worry
> >> >> about
> >> >> them.  We use them for postprocessing, and not really visualization.
> >> >>
> >> >> Looking in BoxLib, it is the case that the F90 BoxLib
> >> >> (Src/F_BaseLib/fabio.f90) specifies Level_XX instead of Level_X names
> >> >> for
> >> >> the directory.
> >> >>
> >> >>
> >> >> On Wed, May 15, 2013 at 7:30 PM, Andrew Myers <atmyers2 at gmail.com>
> >> >> wrote:
> >> >>>
> >> >>> Hi Folks,
> >> >>>
> >> >>> The Orion particles are completely independent of BoxLib. I don't
> know
> >> >>> if
> >> >>> new BoxLib specifies a way for particle data to be stored, or if all
> >> >>> the
> >> >>> Boxlib codes just do their own thing, so I'm not sure whether:
> >> >>>
> >> >>> 1. The base class should be agnostic about particles and particle
> >> >>> readers
> >> >>> get implemented in each subclass, or
> >> >>> 2. The base class should implement the Nyx-style particles and the
> >> >>> Orion
> >> >>> subclass should overwrite this.
> >> >>>
> >> >>> Matt, on your specific questions:
> >> >>>
> >> >>>
> >> >>>  * Is it okay to get rid of the old enzo parameter mappings?
> >> >>>
> >> >>> If I'm reading the code correctly, this is currently needed for
> >> >>> "Gamma"
> >> >>> and "Refineby" to get set correctly, but nothing else.
> >> >>>
> >> >>>  * Do we need to have all of the paranoid IO still?
> >> >>>
> >> >>> I'm not 100% sure what this does, but currently paranoid_read is
> False
> >> >>> by
> >> >>> default and I've never noticed a problem with that.
> >> >>>
> >> >>>  * Do you mind if I reword some of the names?
> >> >>>
> >> >>> Not at all.
> >> >>>
> >> >>> -Andrew
> >> >>>
> >> >>> On Wed, May 15, 2013 at 3:32 PM, Casey W. Stark
> >> >>> <caseywstark at gmail.com>
> >> >>> wrote:
> >> >>>>
> >> >>>> Hi Matt.
> >> >>>>
> >> >>>> That all sounds right.
> >> >>>>
> >> >>>> Really unifying the BoxLib codes sounds like tricky business to
> me. I
> >> >>>> think the current boxlib codes castro, maestro, and nyx will be
> using
> >> >>>> basically the same versions of boxlib, but orion could be different
> >> >>>> altogether. I haven't seen the code, so I can't say, but I bet this
> >> >>>> is the
> >> >>>> reason for the particle difference.
> >> >>>>
> >> >>>> > * Castro was originally going to be a frontend
> >> >>>>
> >> >>>> Nyx was originally part of Castro, but we ripped it out around the
> >> >>>> same
> >> >>>> time. Is anyone using yt with Castro data now?
> >> >>>>
> >> >>>> >  * Some weird differences like Level_%i and Level_%02i for level
> >> >>>> > filenames.
> >> >>>>
> >> >>>> Hm, I don't know about this one since we never use more than a few
> >> >>>> levels, and that's rare.
> >> >>>>
> >> >>>> >  * Is it okay to get rid of the old enzo parameter mappings?
> >> >>>> > * Do we need to have all of the paranoid IO still?
> >> >>>>
> >> >>>> I'm not sure what these were for... If things like parameter names
> >> >>>> are
> >> >>>> fine without the remapping, then great. The IO seems fine, so I
> doubt
> >> >>>> we
> >> >>>> need a paranoid option.
> >> >>>>
> >> >>>> >  * Do you mind if I reword some of the names?
> >> >>>>
> >> >>>> Go for it.
> >> >>>>
> >> >>>>
> >> >>>>
> >> >>>> On Wed, May 15, 2013 at 11:50 AM, Matthew Turk
> >> >>>> <matthewturk at gmail.com>
> >> >>>> wrote:
> >> >>>>>
> >> >>>>> Hi all,
> >> >>>>>
> >> >>>>> I'm spending a bit of time today looking over the Boxlib frontends
> >> >>>>> and
> >> >>>>> identifying commonalities and differences.  I wanted to write with
> >> >>>>> some of my initial findings as well as some specific questions.
> >> >>>>>
> >> >>>>> Casey, Andrew, and Jeff I would particularly like your feedback,
> but
> >> >>>>> I
> >> >>>>> also intend to submit this for detailed review and collaboration.
> >> >>>>> My
> >> >>>>> general plan is to consolidate the data_structures, IO and
> >> >>>>> definitions
> >> >>>>> into a single Boxlib frontend, with subclasses that cover each of
> >> >>>>> the
> >> >>>>> specific differences.
> >> >>>>>
> >> >>>>> The main differences I am seeing:
> >> >>>>>
> >> >>>>>  * Castro was originally going to be a frontend, but morphed into
> >> >>>>> the
> >> >>>>> Nyx frontend, and I don't believe anything Castro-specific is left
> >> >>>>> anymore.  I am inclined to remove it and in the future add on any
> >> >>>>> subclass-specific items when Castro comes back into the fold.
> >> >>>>>  * Nyx and Orion handle particles completely differently.
> >> >>>>>  * Nyx has optimized IO, particularly for fluids, which we should
> >> >>>>> use
> >> >>>>> everywhere.
> >> >>>>>  * Some weird differences like Level_%i and Level_%02i for level
> >> >>>>> filenames.
> >> >>>>>  * Units will need to be set individually.
> >> >>>>>  * Parsing the Fortran and non-Fortran parameter files (i.e.,
> >> >>>>> Maestro
> >> >>>>> and everyone else) will be tricky.
> >> >>>>>
> >> >>>>> There were a few other things I wanted to get feed back on.
> >> >>>>>
> >> >>>>>  * Is it okay to get rid of the old enzo parameter mappings?
> >> >>>>>  * Do we need to have all of the paranoid IO still?
> >> >>>>>  * Do you mind if I reword some of the names?
> >> >>>>>
> >> >>>>> What do you all think?  If anybody wants to help out, I'll be in
> IRC
> >> >>>>> working on this for a while today, but I'll also try to submit a
> PR
> >> >>>>> as
> >> >>>>> early as possible to iterate on and get feedback from.
> >> >>>>>
> >> >>>>> -Matt
> >> >>>>> _______________________________________________
> >> >>>>> yt-dev mailing list
> >> >>>>> yt-dev at lists.spacepope.org
> >> >>>>> http://lists.spacepope.org/listinfo.cgi/yt-dev-spacepope.org
> >> >>>>
> >> >>>>
> >> >>>>
> >> >>>> _______________________________________________
> >> >>>> yt-dev mailing list
> >> >>>> yt-dev at lists.spacepope.org
> >> >>>> http://lists.spacepope.org/listinfo.cgi/yt-dev-spacepope.org
> >> >>>>
> >> >>>
> >> >>
> >> >>
> >> >>
> >> >> --
> >> >> Michael Zingale
> >> >> Associate Professor
> >> >>
> >> >> Dept. of Physics & Astronomy • Stony Brook University • Stony Brook,
> NY
> >> >> 11794-3800
> >> >> phone:  631-632-8225
> >> >> e-mail: Michael.Zingale at stonybrook.edu
> >> >> web: http://www.astro.sunysb.edu/mzingale
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