[santacruzgalaxy-list] Grackle proposal

Nathan Goldbaum nathan12343 at gmail.com
Fri Mar 21 11:15:38 PDT 2014


Hi all,

I just want to clarify that there is also an equilibrium API with the
following signature (see grackle.h):

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,

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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