[yt-users] memory usage of HOP halo finder

[Michael Kuhlen]

Oops, should have added that this is in
yt/analysis_modules/halo_finding/halo_objects.py under class
HOPHaloFinder.

On Wed, Feb 22, 2012 at 3:20 PM, Michael Kuhlen <mqk at astro.berkeley.edu> wrote:
> I have a question about memory usage of yt's HOP HaloFinder.
>
> I have a N=256^3 DM only Enzo simulation that I ran with a 512^3 root
> grid and fairly aggressive DM refinement with
> MaximumRefinementLevel=7. Although the run only has 256^3 particles,
> the AMR has resulted in 163,951 grids and more than 1.5e9 grid cells.
>
> Running HOP like so
>
> halo_list = HaloFinder(pf)
>
> I'm finding that yt is using around 14GB of memory during the particle
> reading (prior to actually starting the HOP process), which is way out
> of proportion to the relatively small number of particles. It seems
> that the memory usage is being driven by the huge number of grids
> rather than the number of particles.
>
> I've traced the memory increase to the calculation of the total mass,
> specifically to this line:
>
>                total_mass =
> self.comm.mpi_allreduce(self._data_source["ParticleMassMsun"].sum(dtype='float64'),
> op='sum')
>
> and again further down:
>
>            sub_mass =
> self._data_source["ParticleMassMsun"].sum(dtype='float64')
>
> When I specify the total mass as a keyword and comment out the
> sub_mass calculation (forcing sub_mass = total_mass), then the memory
> usage remains small. So there's something about the summing up that is
> leaking memory.
>
> Can anyone here shed any light on this puzzling memory hunger?
>
> Mike
>
>
>
> --
> *********************************************************************
> *                                                                   *
> *  Dr. Michael Kuhlen              Theoretical Astrophysics Center  *
> *  email: mqk at astro.berkeley.edu   UC Berkeley                      *
> *  cell phone: (831) 588-1468      B-116 Hearst Field Annex # 3411  *
> *  skype username: mikekuhlen      Berkeley, CA 94720               *
> *                                                                   *
> *********************************************************************



-- 
*********************************************************************
*                                                                   *
*  Dr. Michael Kuhlen              Theoretical Astrophysics Center  *
*  email: mqk at astro.berkeley.edu   UC Berkeley                      *
*  cell phone: (831) 588-1468      B-116 Hearst Field Annex # 3411  *
*  skype username: mikekuhlen      Berkeley, CA 94720               *
*                                                                   *
*********************************************************************