[santacruzgalaxy-list] Grackle proposal
Romain Teyssier
romain.teyssier at gmail.com
Fri Mar 21 11:22:49 PDT 2014
It would be awesome to have instead something like that:
int solve_chemistry(float dt_value,
float *density, float *internal_energy,
float *metal_density);
Does it mean that the input internal energy is modified on exit ?
Romain
> Cheers,
>
> Nathan
>
>
> On Fri, Mar 21, 2014 at 10:47 AM, Daniel Ceverino <daniel.ceverino at uam.es> wrote:
> Hi Britton,
>
> I need to implement Grackle into ART-NMSU, so I would need:
>
> +fortran support
> +simpler data structure
>
> I mostly agree with Romain that the current data structure is too heavy:
>
>
>>> int solve_chemistry(chemistry_data &my_chemistry, ???
>>> code_units &my_units, OK set to 1
>>> gr_float a_value, gr_float dt_value, why a ?
>>> gr_int grid_rank, gr_int *grid_dimension, ????
>>> gr_int *grid_start, gr_int *grid_end, ????
>>> gr_float *density, gr_float *internal_energy, OK
>>> gr_float *x_velocity, gr_float *y_velocity, gr_float *z_velocity, ???
>>> gr_float *HI_density, gr_float *HII_density, gr_float *HM_density, too much
>>> gr_float *HeI_density, gr_float *HeII_density, gr_float *HeIII_density, too much
>>> gr_float *H2I_density, gr_float *H2II_density, too much
>>> gr_float *DI_density, gr_float *DII_density, gr_float *HDI_density, too much
>>> gr_float *e_density, gr_float *metal_density); OK
>
> For equilibrium cooling, many of these grids are not necessary. If we agree that solve_chemistry is called once per each resolution element, I think we need to simply it and get rid of the 3D grids.
> This function is going to be called many times, so I would suggest a minimalistic approach that does the job.
> We can add more layers of complexity later, like the sobolev aprox, which needs the velocity gradients, right?, but first we need to agree on a minimum API.
>
> best
>
> Daniel
>
> On Mar 21, 2014, at 6:00 PM, Britton Smith wrote:
>
>> Sam, that is great news that no alterations need to be made for Grackle to work with ART. Thanks for your hard work on this!
>>
>> Other groups, what are your experiences/needs?
>>
>> Britton
>>
>>
>> On Fri, Mar 21, 2014 at 4:30 PM, Sam Leitner <sam.leitner at gmail.com> wrote:
>> Nick, that is not correct, my ART implementation uses the grackle solver. We can discuss it in the PR that I issued.
>>
>>
>> On Fri, Mar 21, 2014 at 12:23 PM, Nick Gnedin <gnedin at fnal.gov> wrote:
>>
>> At least with ART, the implementation is not what it is supposed to be.
>> It actually uses ART sub-cycling solver, and only extracts the cooling
>> rate from Grackle. I thought the plan was for everyone to use
>> solve_chemistry.
>>
>> That's why it is important to converge on the API first.
>>
>>
>> On 03/21/2014 11:14 AM, Britton Smith wrote:
>> > Hi all,
>> >
>> > This discussion seems to have ground to a halt, so I'll see if I can get
>> > it going again.
>> >
>> > It looks like the proposed API is pretty similar to what already exists,
>> > with mostly cosmetic changes related to what data the user is required
>> > to carry around. Since we have heard from so few regarding a new API,
>> > it doesn't seem that many people really want it. Perhaps we should
>> > establish what groups have completed the Grackle implementation, and
>> > then we can focus on what the remaining groups need in order to catch
>> > up. I heard a wise man once say, "You can't always get what you want,
>> > but if you try sometimes, well you might find you get what you need."
>> >
>> > We've heard from Ken Nagamine and Junhwan Choi on behalf of the Gadget
>> > group. I have done Enzo, and to be clear, the Grackle is slightly
>> > different from what is built in to Enzo, so Enzo now explicitly supports
>> > Grackle. Sam Leitner has told me that ART is now finished. Are there
>> > any other groups out there that can report in?
>> >
>> > So, it sounds to me that one thing that is /needed/ is a clear path to
>> > implementing the Grackle into a purely fortran code, like Ramses. Is
>> > that correct? If so, let's talk about how best that can be achieved.
>> >
>> > To the other groups out there that have not yet finished the
>> > implementation process, what are the things that you need to get this done?
>> >
>> > Britton
>> >
>> > On Thu, Mar 20, 2014 at 3:07 PM, Junhwan Choi (최준환)
>> > <choi.junhwan at gmail.com <mailto:choi.junhwan at gmail.com>> wrote:
>> >
>> > Hi Romain,
>> >
>> > For me, it took about two weeks to make it works.
>> > But, I spend considerable time to find a way to pass the system unit
>> > to grackle properly.
>> > There are a few outstanding issues on this adjustment.
>> >
>> > 1. Grackle use C++ and wrap the FORTRAN cooling routine. It is not
>> > trivial to call this C++ wrapped the FORTRAN but there is example in
>> > the grackle example directory.
>> >
>> > 2. In the gadget case, I pass one particle by one particle to the
>> > grackle in order to calculate the cooling. The reason is that the
>> > gadget cooling and star formation routine is based on particle by
>> > particle. Indeed, it is least efficient way but so far I have not
>> > experienced significant slow down.
>> > [If I use tabulated H and He cooling rates from grackle, it takes
>> > almost the same time with the original gadget cooling.]
>> >
>> >
>> > 3. For unit adjustment, we can set as follow:
>> > my_units.comoving_coordinates = 0;
>> > my_units.density_units = udensity;
>> > my_units.length_units = ulength;
>> > my_units.time_units = utime;
>> > my_units.a_units = 1.0;
>> > [udensity, ulength, and utime is the conversion factor from system
>> > physical units to cgs.]
>> > In this case, you can pass the density, internal energy, and chemistry
>> > value in system physical unit.
>> >
>> > Besides these issues, the incorporating Grackle should not be very
>> > difficult.
>> >
>> > Best,
>> > Junhwan
>> >
>> >
>> >
>> >
>> >
>> > On Thu, Mar 20, 2014 at 2:35 AM, Romain Teyssier
>> > <romain.teyssier at gmail.com <mailto:romain.teyssier at gmail.com>> wrote:
>> > > That's great.
>> > > A very important question: how long did it take him to succeed ?
>> > > Since in my opinion, many "adjustments" need to be done, I would
>> > be curious to
>> > > have an estimate on the time required that have this working.
>> > >
>> > > Cheers,
>> > > Romain
>> > >
>> > > On 20 Mar 2014, at 00:33, Ken Nagamine <kn at physics.unlv.edu
>> > <mailto:kn at physics.unlv.edu>> wrote:
>> > >
>> > >> Dear all,
>> > >>
>> > >> Let me just mention that, on the SPH side, Junhwan Choi has
>> > already succeeded in
>> > >> implementing the Grackle package into Gadget3-UNLV version.
>> > >> We still need to do more checks, but at least the phase diagram
>> > >> looks reasonable compared to the previous TREECOOL table
>> > implementation of original Gadget.
>> > >> Junhwan can explain the details of his implementation method if
>> > it can be of help for this discussion.
>> > >>
>> > >> cheers,
>> > >> Ken
>> > >>
>> > >>
>> > >> On Mar 20, 2014, at 6:44 AM, Romain Teyssier wrote:
>> > >>
>> > >>>
>> > >>> On 19 Mar 2014, at 22:35, Matthew Turk <matthewturk at gmail.com
>> > <mailto:matthewturk at gmail.com>> wrote:
>> > >>>
>> > >>>> On Wed, Mar 19, 2014 at 5:26 PM, Romain Teyssier
>> > >>>> <romain.teyssier at gmail.com <mailto:romain.teyssier at gmail.com>>
>> > wrote:
>> > >>>>> Hi Matt,
>> > >>>>>
>> > >>>>>
>> > >>>>> For example:
>> > >>>>>
>> > >>>>> int solve_chemistry(chemistry_data &my_chemistry, ???
>> > >>>>> code_units &my_units, OK set to 1
>> > >>>>> gr_float a_value, gr_float dt_value, why a ?
>> > >>>>> gr_int grid_rank, gr_int *grid_dimension, ????
>> > >>>>> gr_int *grid_start, gr_int *grid_end, ????
>> > >>>>> gr_float *density, gr_float
>> > *internal_energy, OK
>> > >>>>> gr_float *x_velocity, gr_float *y_velocity,
>> > gr_float *z_velocity, ???
>> > >>>>> gr_float *HI_density, gr_float
>> > *HII_density, gr_float *HM_density, too much
>> > >>>>> gr_float *HeI_density, gr_float
>> > *HeII_density, gr_float *HeIII_density, too much
>> > >>>>> gr_float *H2I_density, gr_float
>> > *H2II_density, too much
>> > >>>>> gr_float *DI_density, gr_float
>> > *DII_density, gr_float *HDI_density, too much
>> > >>>>> gr_float *e_density, gr_float
>> > *metal_density); OK
>> > >>>>>
>> > >>>>> What are the *grid related variables ?
>> > >>>>
>> > >>>> Good question! These, like the code units variables, are
>> > designed to
>> > >>>> minimize the overhead of any simulation that wants to put its code
>> > >>>> into it. For instance, if one had a patch/block-based code (like
>> > >>>> Enzo, FLASH, Nyx, etc) or an Octree code where the 2x2x2 zones
>> > were
>> > >>>> included in (2+2*NGZ, 2+2*NGZ, 2+2*NGZ) blocks and one didn't
>> > want to
>> > >>>> spend time solving the ghost zones, they can be masked out.
>> > These are
>> > >>>> the variables:
>> > >>>>
>> > >>>> grid_start => array of size (grid_rank) indicating the indices to
>> > >>>> start at in each rank of dimensionality
>> > >>>> grid_end => array of size (grid_rank) indicating the indices
>> > to *end*
>> > >>>> at in each rank of dimensionality
>> > >>>> grid_dimension => size of the block of data in each dimension
>> > >>>> grid_rank => dimensionality; if you're supplying a pencil
>> > beam, this would be 1.
>> > >>>>
>> > >>>> While these typically are better for block or patch based
>> > solvers, I
>> > >>>> think that the primary goal -- *minimizing* the overhead to
>> > using a
>> > >>>> new code -- is met with them.
>> > >>>
>> > >>> Well I clearly disagree.
>> > >>> It is brain damaging to say the least.
>> > >>>
>> > >>>>
>> > >>>> As I mentioned in our previous email, the velocities are
>> > supplied for
>> > >>>> the Sobolev approximation. You can see the full discussion on the
>> > >>>> public Grackle mailing list here:
>> > >>>>
>> > >>>>
>> > https://groups.google.com/forum/#!searchin/grackle-cooling-users/velocity/grackle-cooling-users/Dr77TM2te9g/225RNzoZADEJ
>> > >>>>
>> > >>>>>
>> > >>>>> If chemistry_data is an external variable, this is a pain
>> > because this variable need to be declared in the main code.
>> > >>>>> Same thing for code_units.
>> > >>>>
>> > >>>> The alternative is that it be a global defined in a different
>> > >>>> namespace, loading in by the dlloader at runtime. Not sure that's
>> > >>>> substantially different.
>> > >>>>
>> > >>>
>> > >>> Well I think this should be completely hidden to the user.
>> > >>> This is a very substantial difference.
>> > >>>
>> > >>>> Code units, if you want to convert to CGS, will just be 1.0
>> > for all of
>> > >>>> them, which can be constant.
>> > >>>>
>> > >>>
>> > >>> Yes but you still have to create a code_unit type, and set the
>> > variable to 1.
>> > >>> Unless you change the calling sequence.
>> > >>>
>> > >>>>> This is all too ENZO specifics.
>> > >>>>
>> > >>>> I'm not sure I believe that argument. Perhaps the names of the
>> > >>>> variables share too much with Enzo naming schemes, but I think
>> > it's
>> > >>>> rather intuitive to think of the 3D dataset as a base starting
>> > point
>> > >>>> and then reducing overhead by supplying 1-dimensional arrays.
>> > >>>>
>> > >>>
>> > >>> For a purely local process like cooling and chemistry, the
>> > natural data type is 1D.
>> > >>> Cells, particles and what not, could then be sent as a 1D array
>> > to the chemistry solver.
>> > >>> 3D structures are relevant only for patch based codes.
>> > >>>
>> > >>>
>> > >>>> -Matt
>> > >>>>
>> > >>>>>
>> > >>>>> Romain
>> > >>>>>
>> > >>>>>
>> > >>>>>
>> > >>>>> On 19 Mar 2014, at 22:08, Matthew Turk <matthewturk at gmail.com
>> > <mailto:matthewturk at gmail.com>> wrote:
>> > >>>>>
>> > >>>>>> Hi all,
>> > >>>>>>
>> > >>>>>> On Wed, Mar 19, 2014 at 4:58 PM, Romain Teyssier
>> > >>>>>> <romain.teyssier at gmail.com
>> > <mailto:romain.teyssier at gmail.com>> wrote:
>> > >>>>>>>
>> > >>>>>>> I totally agree with the 3 routines that need to be used.
>> > >>>>>>> Nothing else should be required on the code's side, except
>> > passing the required variables.
>> > >>>>>>>
>> > >>>>>>>
>> > >>>>>>>> grackle_init_run()
>> > >>>>>>>> called once per simulation
>> > >>>>>>>>
>> > >>>>>>>
>> > >>>>>>> The parameters that should be passed here are
>> > >>>>>>> - some cosmological model parameters
>> > >>>>>>> - UV background model (spectrum, reionization redshift...)
>> > >>>>>>> - starting redshift to compute the initial temperature and
>> > ionisation state
>> > >>>>>>>
>> > >>>>>>>> grackle_init_step(aexp,...)
>> > >>>>>>>> called once per each time-step, uses the value of the scale
>> > >>>>>>>> factor and other parameters as needed
>> > >>>>>>>
>> > >>>>>>> In principle at this stage, only aexp is required for cosmo
>> > runs.
>> > >>>>>>> For non cosmo runs, the cooling tables do not need to be
>> > modified.
>> > >>>>>>>
>> > >>>>>>>>
>> > >>>>>>>> grackle_solve_chemistry(dt,den,tem,...)
>> > >>>>>>>> called for each resolution element one or more times per one
>> > >>>>>>>> global time-step, uses gas properties to update internal
>> > energy.
>> > >>>>>>>> Input gas properties may be required to have specific
>> > units and
>> > >>>>>>>> be of specific data type. It should internally sense if it
>> > >>>>>>>> runs within an OpenMP construct and support OpenMP
>> > >>>>>>>> parallelization.
>> > >>>>>>>>
>> > >>>>>>>
>> > >>>>>>> I would rather give the possibility of passing an array of
>> > cell.
>> > >>>>>>> Users could also set the array size to 1 to deal with cells
>> > one by one.
>> > >>>>>>> The required information could be
>> > >>>>>>> nH, T or Tovermu or specific energy, metallicity in some
>> > units, dt_hydro, ncell
>> > >>>>>>> On output, Delta T or Delta Tovermu or Delta specific energy
>> > >>>>>>> I suggest we use fixed units (cgs or mks) for all input and
>> > output variables.
>> > >>>>>>>
>> > >>>>>>> These 3 routines are the only one that the user should care
>> > about.
>> > >>>>>>>
>> > >>>>>>
>> > >>>>>> This is awfully similar to the existing API:
>> > >>>>>>
>> > >>>>>>
>> > https://bitbucket.org/brittonsmith/grackle/src/642cd133535a2dd3c57626b768c7c8c107096ac7/src/clib/grackle.h?at=default
>> > >>>>>>
>> > >>>>>> The only necessary functions, according to
>> > >>>>>> http://grackle.readthedocs.org/en/latest/Integration.html , are:
>> > >>>>>>
>> > >>>>>> initialize_chemistry_data
>> > >>>>>> solve_chemistry or solve_chemistry for tabular data
>> > >>>>>>
>> > >>>>>> Looking at the example (non-equilibrium) executable:
>> > >>>>>>
>> > >>>>>>
>> > https://bitbucket.org/brittonsmith/grackle/src/642cd133535a2dd3c57626b768c7c8c107096ac7/src/example/example.C?at=default
>> > >>>>>>
>> > >>>>>> those are the only *functional* routines. Everything else is to
>> > >>>>>> provide additional information, *not* to actually do any
>> > computation.
>> > >>>>>> I think that we have actually met these standards. All of
>> > the units
>> > >>>>>> are provided so as the *avoid* any boilerplate -- but if you
>> > want to
>> > >>>>>> supply in CGS, you can set the input unit conversions to 1.0.
>> > >>>>>>
>> > >>>>>> To compute the equilibrium tables:
>> > >>>>>>
>> > >>>>>>
>> > https://bitbucket.org/brittonsmith/grackle/src/642cd133535a2dd3c57626b768c7c8c107096ac7/src/example/table_example.C?at=default
>> > >>>>>>
>> > >>>>>> it's even simpler. The only *active* routine is called on
>> > line 120,
>> > >>>>>> "solve_chemistry". I am genuinely being earnest when I ask,
>> > from the
>> > >>>>>> .h file linked above, which arguments to the functions would
>> > you like
>> > >>>>>> to see removed? I've included the full function signatures
>> > below. If
>> > >>>>>> you want to get *out* various things, you can utilize the other
>> > >>>>>> functions -- like the cooling time function and so on.
>> > >>>>>>
>> > >>>>>> -Matt
>> > >>>>>>
>> > >>>>>> int initialize_chemistry_data(chemistry_data &my_chemistry,
>> > >>>>>> code_units &my_units, gr_float
>> > a_value);
>> > >>>>>>
>> > >>>>>> int solve_chemistry(chemistry_data &my_chemistry,
>> > >>>>>> code_units &my_units,
>> > >>>>>> gr_float a_value, gr_float dt_value,
>> > >>>>>> gr_int grid_rank, gr_int *grid_dimension,
>> > >>>>>> gr_int *grid_start, gr_int *grid_end,
>> > >>>>>> gr_float *density, gr_float *internal_energy,
>> > >>>>>> gr_float *x_velocity, gr_float *y_velocity, gr_float
>> > *z_velocity,
>> > >>>>>> gr_float *HI_density, gr_float *HII_density, gr_float
>> > *HM_density,
>> > >>>>>> gr_float *HeI_density, gr_float *HeII_density, gr_float
>> > *HeIII_density,
>> > >>>>>> gr_float *H2I_density, gr_float *H2II_density,
>> > >>>>>> gr_float *DI_density, gr_float *DII_density, gr_float
>> > *HDI_density,
>> > >>>>>> gr_float *e_density, gr_float *metal_density);
>> > >>>>>>
>> > >>>>>> int solve_chemistry(chemistry_data &my_chemistry,
>> > >>>>>> code_units &my_units,
>> > >>>>>> gr_float a_value, gr_float dt_value,
>> > >>>>>> gr_int grid_rank, gr_int *grid_dimension,
>> > >>>>>> gr_int *grid_start, gr_int *grid_end,
>> > >>>>>> gr_float *density, gr_float *internal_energy,
>> > >>>>>> gr_float *x_velocity, gr_float *y_velocity,
>> > >>>>>> gr_float *z_velocity,
>> > >>>>>> gr_float *metal_density);
>> > >>>>>>
>> > >>>>>>> Cheers,
>> > >>>>>>> Romain
>> > >>>>>>>
>> > >>>>>>>
>> > >>>>>>>
>> > >>>>>>>> The API can also define its own data types with natutal
>> > conversion from
>> > >>>>>>>> standard types, for example the following code should be
>> > valid:
>> > >>>>>>>>
>> > >>>>>>>> float f;
>> > >>>>>>>> double d;
>> > >>>>>>>> gr_float gr_f;
>> > >>>>>>>>
>> > >>>>>>>> gr_f = f;
>> > >>>>>>>> gr_f = d;
>> > >>>>>>>>
>> > >>>>>>>> An analogous API should be provided for F77.
>> > >>>>>>>>
>> > >>>>>>>> Then in a code the API will be implemented as follows:
>> > >>>>>>>>
>> > >>>>>>>> Begin_code
>> > >>>>>>>>
>> > >>>>>>>> grackle_init_run()
>> > >>>>>>>>
>> > >>>>>>>> Loop_over_timesteps(aexp)
>> > >>>>>>>>
>> > >>>>>>>> grackle_init_step(aexp,...)
>> > >>>>>>>>
>> > >>>>>>>> #pragma omp parallel loop
>> > >>>>>>>> Loop_over_resolution_elements(elem)
>> > >>>>>>>> {
>> > >>>>>>>> gr_float dt = code_time_step*time_unit;
>> > >>>>>>>> gr_float den = code_density(elem)*den_unit;
>> > >>>>>>>> gr_float tem = code_temperature(elem)*tem_unit;
>> > >>>>>>>> grackle_solve_chemistry(dt,den,tem,...)
>> > >>>>>>>> }
>> > >>>>>>>>
>> > >>>>>>>> End_loop
>> > >>>>>>>>
>> > >>>>>>>> End_code
>> > >>>>>>>>
>> > >>>>>>>> Let's converge on the API, and then the Grackle team will
>> > be able to
>> > >>>>>>>> write a couple of wrappers that will suit everyone.
>> > >>>>>>>>
>> > >>>>>>>> Given the wrappers, if Grackle is installed as an external
>> > library and
>> > >>>>>>>> provides a proper Linus-style installer (that will handle
>> > all HDF5 and
>> > >>>>>>>> other dependencies), then it should be trivial to
>> > integrate it in any code.
>> > >>>>>>>>
>> > >>>>>>>> Nick
>> > >>>>>>>>
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