[yt-dev] Consolidating Boxlib frontends

Michael Zingale michael.zingale at stonybrook.edu
Thu May 16 11:55:50 PDT 2013


just to be clear, that is the number of MPI tasks, not the number of
processors (# pros = # MPI * OMP_NUM_THREADS)

I just looked at a big run I did for a paper on > 10,000 cores, and there
is just a single line:

Level_00/Cell



On Thu, May 16, 2013 at 2:52 PM, Matthew Turk <matthewturk at gmail.com> wrote:

> On Thu, May 16, 2013 at 2:47 PM, Chris Malone <chris.m.malone at gmail.com>
> wrote:
> > Yes, the comoving bit is not in the Castro anymore - or at least no one
> uses
> > it that I'm aware of.
> >
> > The number of Level_*/Cell_D_* files for each level is actually based on
> the
> > number of processors set to do IO.  This can be changed with a runtime
> > parameter; Maestro also does this.  The simple problems for which you
> have
> > Castro data (like the one I just uploaded to dickenson) were run on a
> single
> > core, so there is only one Cell_D file per level.
>
> The number of processors is also in the Cell_H file on the third line,
> to my understanding of the format.  But I think I'm still not making
> myself clear: will there ever be a data file that isn't
> Cell_Something.  Let me give an example.  In RadTube's global Header
> file we have:
>
> 0 8 7.26154130223839759212753081768e-07
> 500
> 0 16
> 0 16
> 0 16
> 112 128
> 0 16
> 0 16
> 96 112
> 0 16
> 0 16
> 80 96
> 0 16
> 0 16
> 64 80
> 0 16
> 0 16
> 48 64
> 0 16
> 0 16
> 32 48
> 0 16
> 0 16
> 16 32
> 0 16
> 0 16
> Level_0/Cell
> 1 36 7.26154130223839970970989895344e-07
>
> I am currently parsing this by getting each lo/hi/dimension pair, then
> assuming there is a *single* line following the set that describes the
> prefix for the level header, in this case Level_0/Cell , which is then
> followed by the *next level*.  The original frontend code was much
> more lenient, and in fact allowed for *multiple* filenames to be
> displayed there -- for instance, it would allow something like:
>
> Level_0/Cell
> Level_0/Dinosaurs
> Level_0/BlahBlah
>
> where it expects Level_0/Dinosaurs_H and Level_0/BlahBlah_H as well as
> their corresponding processor files.  *Is this real* or can I just
> assume there will only be one type of data file, in this case
> Level_0/Cell and its corresponding data?
>
> >
> > Chris
> >
> >
> >
> > On Thu, May 16, 2013 at 11:38 AM, Casey W. Stark <caseywstark at gmail.com>
> > wrote:
> >>
> >> 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
> >>> _______________________________________________
> >>> yt-dev mailing list
> >>> yt-dev at lists.spacepope.org
> >>> http://lists.spacepope.org/listinfo.cgi/yt-dev-spacepope.org
> >>
> >>
> >>
> >> _______________________________________________
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> >>
> >
> >
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>



-- 
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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