[yt-users] Rockstar and RAMSES (DM only run). Rockstar appears to run, but no halo information is written.

Fri Oct 3 09:22:59 PDT 2014

Hello.

My simulation runs to z=0. Only with 10 timesteps though (purely a test
run). It identifies no halos in halos_0 (expected with it being the first
snapshot) and halos_9 (the final snapshot).. All files are the same size
too with no data.

My code is (with the filters taken out... it's a dark matter only one
anyway)

from mpi4py import MPI
import yt, sys, os
yt.enable_parallelism()
from yt.config import ytcfg
from yt.analysis_modules.halo_finding.rockstar.api import \
        RockstarHaloFinder
from yt.data_objects.particle_filters import \
        particle_filter
from yt.data_objects.time_series import DatasetSeries
import numpy as np

ncpu = MPI.COMM_WORLD.Get_size()
ytcfg.set('yt', '__global_parallel_size', str(ncpu))

outputs = np.arange(1, 11)
dirs = []
#Add the datasets
for ioutput in outputs:
    ds = yt.load('../output_%05d/info_%05d.txt'%(ioutput, ioutput))
    dirs.append(ds)

es = DatasetSeries(dirs)
readers = int(ncpu/4.)
writers = ncpu - readers - 1
rh = RockstarHaloFinder(es, num_readers=readers, num_writers=writers)
rh.run()

Ben

On Fri, Oct 3, 2014 at 5:09 PM, Cameron Hummels <chummels at gmail.com> wrote:

> Hi Ben,
>
> No, you don't need to have halos in the first timestep.  Rockstar will
> find the halos when they exist, so if you run it on all of the outputs and
> you get to a later redshift then 5 or so, rockstar will start to identify
> halos.  Does your simulation run to z=0?  If so, just look at the output
> file associated with that redshift and see if it identifies any halos.  It
> doesn't matter your starting redshift.
>
> Cameron
>
> On Fri, Oct 3, 2014 at 9:02 AM, Ben Thompson <bthompson2090 at gmail.com>
> wrote:
>
>> Hi Cameron.
>>
>> So it is dependent as of what timestep I start my run at? I start my run
>> (i.e there needs to be halos in the snapshot that you start with)? This is
>> the first time I have used Rockstar before (figured that since the package
>> is there, for free, I should use it) I have DM only runs that start at z=50
>> (of which I am not expecting to find halos there, as part of the loading
>> script I loop over all the snapshots)
>>
>> This is what I have
>>
>> cat halos_0.0.ascii
>> #id num_p mvir mbound_vir rvir vmax rvmax vrms x y z vx vy vz Jx Jy Jz E
>> Spin PosUncertainty VelUncertainty bulk_vx bulk_vy bulk_vz BulkVelUnc
>> n_core m200b m200c m500c m2500c Xoff Voff spin_bullock b_to_a c_to_a A[x]
>> A[y] A[z] b_to_a(500c) c_to_a(500c) A[x](500c) A[y](500c) A[z](500c) Rs
>> Rs_Klypin T/|U| M_pe_Behroozi M_pe_Diemer idx i_so i_ph num_cp mmetric
>> #a = 0.019608
>> #Bounds: (0.000000, 0.000000, 0.000000) - (99.816002, 99.816002,
>> 19.807144)
>> #Om = 0.300000; Ol = 0.700000; h = 0.700000
>> #FOF linking length: 0.280000
>> #Unbound Threshold: 0.500000; FOF Refinement Threshold: 0.700000
>> #Particle mass: 2.87164e+10 Msun/h
>> #Box size: 99.816005 Mpc/h
>> #Total particles processed: 419422
>> #Force resolution assumed: 0.780498 Mpc/h
>> #Units: Masses in Msun / h
>> #Units: Positions in Mpc / h (comoving)
>> #Units: Velocities in km / s (physical, peculiar)
>> #Units: Halo Distances, Lengths, and Radii in kpc / h (comoving)
>> #Units: Angular Momenta in (Msun/h) * (Mpc/h) * km/s (physical)
>> #Units: Spins are dimensionless
>> #Units: Total energy in (Msun/h)*(km/s)^2 (physical)
>> #Note: idx, i_so, and i_ph are internal debugging quantities
>> #Np is an internal debugging quantity.
>> #Rockstar Version: 0.99.9-RC3
>>
>> (yt-x86_64)[bthompson1 at leopard rockstar_halos]$ cat halos_9.0.ascii
>> #id num_p mvir mbound_vir rvir vmax rvmax vrms x y z vx vy vz Jx Jy Jz E
>> Spin PosUncertainty VelUncertainty bulk_vx bulk_vy bulk_vz BulkVelUnc
>> n_core m200b m200c m500c m2500c Xoff Voff spin_bullock b_to_a c_to_a A[x]
>> A[y] A[z] b_to_a(500c) c_to_a(500c) A[x](500c) A[y](500c) A[z](500c) Rs
>> Rs_Klypin T/|U| M_pe_Behroozi M_pe_Diemer idx i_so i_ph num_cp mmetric
>> #a = 1.000879
>> #Bounds: (0.000000, 0.000000, 0.000000) - (99.816002, 99.816002,
>> 19.667080)
>> #Om = 0.300000; Ol = 0.700000; h = 0.700000
>> #FOF linking length: 0.280000
>> #Unbound Threshold: 0.500000; FOF Refinement Threshold: 0.700000
>> #Particle mass: 2.87164e+10 Msun/h
>> #Box size: 99.816005 Mpc/h
>> #Total particles processed: 419437
>> #Force resolution assumed: 0.779813 Mpc/h
>> #Units: Masses in Msun / h
>> #Units: Positions in Mpc / h (comoving)
>> #Units: Velocities in km / s (physical, peculiar)
>> #Units: Halo Distances, Lengths, and Radii in kpc / h (comoving)
>> #Units: Angular Momenta in (Msun/h) * (Mpc/h) * km/s (physical)
>> #Units: Spins are dimensionless
>> #Units: Total energy in (Msun/h)*(km/s)^2 (physical)
>> #Note: idx, i_so, and i_ph are internal debugging quantities
>> #Np is an internal debugging quantity.
>> #Rockstar Version: 0.99.9-RC3
>>
>> Both exactly the same pretty much.
>>
>> If it is because I am starting at an early timestep, then I will cut out
>> the earlier ones from the initial setup.
>>
>> Thanks.
>>
>> Ben,
>>
>> On Fri, Oct 3, 2014 at 4:55 PM, Cameron Hummels <chummels at gmail.com>
>> wrote:
>>
>>> Hi Ben,
>>>
>>> Oftentimes, rockstar cannot find any halos for the first few snapshots
>>> of a cosmology DM-only sim because things have not collapsed enough.  In
>>> that case, you'll get files like this:
>>>
>>> $ % cat halos_0.0.ascii
>>> #id num_p mvir mbound_vir rvir vmax rvmax vrms x y z vx vy vz Jx Jy Jz E
>>> Spin PosUncertainty VelUncertainty bulk_vx bulk_vy bulk_vz BulkVelUnc
>>> n_core m200b m200c m500c m2500c Xoff Voff spin_bullock b_to_a c_to_a A[x]
>>> A[y] A[z] b_to_a(500c) c_to_a(500c) A[x](500c) A[y](500c) A[z](500c) Rs
>>> Rs_Klypin T/|U| M_pe_Behroozi M_pe_Diemer idx i_so i_ph num_cp mmetric
>>> #a = 0.009901
>>> #Bounds: (0.000000, 0.000000, 0.000000) - (40.000000, 40.000000,
>>> 3.099222)
>>> #Om = 0.282000; Ol = 0.718000; h = 0.697000
>>> #FOF linking length: 0.280000
>>> #Unbound Threshold: 0.500000; FOF Refinement Threshold: 0.700000
>>> #Particle mass: 2.98630e+08 Msun/h
>>> #Box size: 40.000000 Mpc/h
>>> #Total particles processed: 1290100
>>> #Force resolution assumed: 0.15625 Mpc/h
>>> #Units: Masses in Msun / h
>>> #Units: Positions in Mpc / h (comoving)
>>> #Units: Velocities in km / s (physical, peculiar)
>>> #Units: Halo Distances, Lengths, and Radii in kpc / h (comoving)
>>> #Units: Angular Momenta in (Msun/h) * (Mpc/h) * km/s (physical)
>>> #Units: Spins are dimensionless
>>> #Units: Total energy in (Msun/h)*(km/s)^2 (physical)
>>> #Note: idx, i_so, and i_ph are internal debugging quantities
>>> #Np is an internal debugging quantity.
>>> #Rockstar Version: 0.99.9-RC3
>>>
>>>
>>> Is this what you're seeing or are your files truly empty?  If you're
>>> seeing this, you may just need to run Rockstar on data files that are more
>>> evolved in time, so as to allow for more non-linear collapse of the halos.
>>> For my DM-only runs, depending on the mass resolution that I use, I may not
>>> start to see halos until after z=10 to z=5, with the first outputs all
>>> looking like the stuff above: empty.
>>>
>>> Cameron
>>>
>>> On Fri, Oct 3, 2014 at 8:46 AM, Ben Thompson <bthompson2090 at gmail.com>
>>> wrote:
>>>
>>>> P.S sorry if I sent the same email twice.. this is the actual email...
>>>> accidental press send before I sent the email out.
>>>>
>>>> Hello everyone.
>>>>
>>>> I am currently using YT to run rockstar on my simulation.
>>>>
>>>> I have been following the instructions which are around and about and
>>>> have managed to write a script to run rockstar via MPI
>>>>
>>>> readers = int(ncpu/4.)
>>>> #Reserve one cpu for the server
>>>> writers = ncpu - readers - 1
>>>> print 'Running rockstar with %i writers and %i readers'%(writers,
>>>> readers)
>>>> rh = RockstarHaloFinder(es, num_readers=readers, num_writers=writers,
>>>>                         particle_type="dark_matter", dm_only=True)
>>>> rh.run()
>>>>
>>>> using a particle filter on the datasets
>>>>
>>>> @yt.particle_filter("dark_matter", requires=[('particle_mass')])
>>>> def dark_matter(pfilter, data):
>>>>         if ('all', 'particle_age') in data.ds.field_list:
>>>>                 return data[("all", "particle_age")] == 0.0
>>>>         else:
>>>>                 arr = np.zeros(len(data['particle_mass']))
>>>>                 return arr == 0.0
>>>>
>>>> def setup_ds(ds):
>>>>         #Return only dark matter particles, and assert that the filter
>>>> holds
>>>>         print 'Here'
>>>>         assert(ds.add_particle_filter("dark_matter"))
>>>>
>>>>
>>>> It seems to run fine.... e.g
>>>>
>>>>
>>>> [   111s] Sending projection requests...
>>>> [   112s] Transferring particles to writers...
>>>> [   116s] Analyzing for FoF groups...
>>>> [   116s] Transferring boundary particles between writers...
>>>> [   117s] Linking boundary particles...
>>>> [   117s] Analyzing for halos / subhalos...
>>>> [   119s] Loading merger tree information...
>>>> [   120s] Constructing merger tree...
>>>> [   121s] [Success] Done with snapshot 7.
>>>> [   121s] Reading 6 blocks for snapshot 8...
>>>> P001 yt : [INFO     ] 2014-10-03 16:19:28,101 Loading field plugins.
>>>> P002 yt : [INFO     ] 2014-10-03 16:19:28,101 Loading field plugins.
>>>> P001 yt : [INFO     ] 2014-10-03 16:19:28,101 Loaded angular_momentum
>>>> (8 new fields)
>>>> P001 yt : [INFO     ] 2014-10-03 16:19:28,101 Loaded astro (14 new
>>>> fields)
>>>> P001 yt : [INFO     ] 2014-10-03 16:19:28,102 Loaded cosmology (20 new
>>>> fields)
>>>> P001 yt : [INFO     ] 2014-10-03 16:19:28,102 Loaded fluid (56 new
>>>> fields)
>>>> P001 yt : [INFO     ] 2014-10-03 16:19:28,103 Loaded fluid_vector (88
>>>> new fields)
>>>> P001 yt : [INFO     ] 2014-10-03 16:19:28,103 Loaded geometric (102 new
>>>> fields)
>>>> P001 yt : [INFO     ] 2014-10-03 16:19:28,103 Loaded local (102 new
>>>> fields)
>>>> P001 yt : [INFO     ] 2014-10-03 16:19:28,104 Loaded magnetic_field
>>>> (108 new fields)
>>>> P001 yt : [INFO     ] 2014-10-03 16:19:28,104 Loaded species (108 new
>>>> fields)
>>>> P006 yt : [INFO     ] 2014-10-03 16:19:28,127 Loading field plugins.
>>>> P005 yt : [INFO     ] 2014-10-03 16:19:28,128 Loading field plugins.
>>>> P003 yt : [INFO     ] 2014-10-03 16:19:28,128 Loading field plugins.
>>>> P004 yt : [INFO     ] 2014-10-03 16:19:28,135 Loading field plugins.
>>>> [   129s] Sending projection requests...
>>>> [   130s] Transferring particles to writers...
>>>> [   132s] Analyzing for FoF groups...
>>>> [   133s] Transferring boundary particles between writers...
>>>> [   133s] Linking boundary particles...
>>>> [   134s] Analyzing for halos / subhalos...
>>>> [   137s] Loading merger tree information...
>>>> [   138s] Constructing merger tree...
>>>> [   139s] [Success] Done with snapshot 8.
>>>> [   139s] Reading 6 blocks for snapshot 9...
>>>> [   143s] Sending projection requests...
>>>> [   144s] Transferring particles to writers...
>>>> [   146s] Analyzing for FoF groups...
>>>> [   147s] Transferring boundary particles between writers...
>>>> [   147s] Linking boundary particles...
>>>> [   148s] Analyzing for halos / subhalos...
>>>> [   150s] Loading merger tree information...
>>>> [   151s] Constructing merger tree...
>>>> [   152s] Constructing merger tree...
>>>> [   153s] [Success] Done with snapshot 9.
>>>> [   153s] [Finished]
>>>>
>>>> generates the outputs
>>>>
>>>>
>>>> halos_0.0.ascii    halos_1.14.bin    halos_2.4.ascii
>>>> halos_3.9.bin     halos_5.14.ascii  halos_6.3.bin     halos_7.9.ascii
>>>> halos_9.13.bin
>>>> halos_0.0.bin      halos_1.15.ascii  halos_2.4.bin
>>>> halos_4.0.ascii   halos_5.14.bin    halos_6.4.ascii   halos_7.9.bin
>>>> halos_9.14.ascii
>>>> halos_0.10.ascii   halos_1.15.bin    halos_2.5.ascii
>>>> halos_4.0.bin     halos_5.15.ascii  halos_6.4.bin     halos_8.0.ascii
>>>> halos_9.14.bin
>>>> halos_0.10.bin     halos_1.16.ascii  halos_2.5.bin
>>>> halos_4.10.ascii  halos_5.15.bin    halos_6.5.ascii   halos_8.0.bin
>>>> halos_9.15.ascii
>>>> halos_0.11.ascii   halos_1.16.bin    halos_2.6.ascii
>>>> halos_4.10.bin    halos_5.16.ascii  halos_6.5.bin     halos_8.10.ascii
>>>> halos_9.15.bin
>>>>
>>>>
>>>> but they are all empty.... yet within profiling, it seems to imply that
>>>> there were some particles submitted to be analised
>>>>
>>>>
>>>> [Prof] S0,C0 0s: 10191 fofs, 123365 particles, 0s for conf.
>>>> [Prof] S0,C0: 0p,0h,0w; wt:0s; rcv:0s,0s; snd:0s; wk:0s; idl:1s
>>>> [Prof] S1,C0 0s: 10377 fofs, 123363 particles, 0s for conf.
>>>> [Prof] S1,C0: 1814p,73h,1w; wt:1s; rcv:0s,0s; snd:0s; wk:0s; idl:1s
>>>> [Prof] S2,C0 0s: 9843 fofs, 123353 particles, 0s for conf.
>>>> [Prof] S2,C0: 5115p,139h,1w; wt:1s; rcv:0s,0s; snd:0s; wk:0s; idl:1s
>>>> [Prof] S3,C0 0s: 9616 fofs, 123359 particles, 0s for conf.
>>>> [Prof] S3,C0: 9637p,221h,1w; wt:1s; rcv:0s,0s; snd:0s; wk:0s; idl:1s
>>>> [Prof] S4,C0 1s: 9256 fofs, 123367 particles, 0s for conf.
>>>> [Prof] S4,C0: 14849p,314h,1w; wt:0s; rcv:0s,1s; snd:0s; wk:0s; idl:0s
>>>> [Prof] S5,C0 0s: 9233 fofs, 123361 particles, 0s for conf.
>>>> [Prof] S5,C0: 17771p,369h,1w; wt:0s; rcv:0s,0s; snd:1s; wk:0s; idl:0s
>>>> [Prof] S6,C0 0s: 8964 fofs, 123365 particles, 0s for conf.
>>>> [Prof] S6,C0: 19888p,388h,1w; wt:0s; rcv:0s,1s; snd:0s; wk:0s; idl:0s
>>>> [Prof] S7,C0 0s: 8996 fofs, 123356 particles, 0s for conf.
>>>> [Prof] S7,C0: 22352p,426h,1w; wt:0s; rcv:0s,1s; snd:0s; wk:0s; idl:1s
>>>> [Prof] S8,C0 0s: 8801 fofs, 123361 particles, 0s for conf.
>>>> [Prof] S8,C0: 22553p,441h,1w; wt:0s; rcv:0s,1s; snd:0s; wk:0s; idl:1s
>>>> [Prof] S9,C0 1s: 8806 fofs, 123361 particles, 0s for conf.
>>>> [Prof] S9,C0: 22685p,440h,1w; wt:0s; rcv:0s,1s; snd:0s; wk:0s; idl:1s
>>>>
>>>>
>>>> Is there anything I should consider looking at to debug this problem?
>>>> Any suggestions of what to look at?
>>>>
>>>> Thanks
>>>>
>>>> Ben
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> _______________________________________________
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>>>> yt-users at lists.spacepope.org
>>>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>>>>
>>>>
>>>
>>>
>>> --
>>> Cameron Hummels
>>> Postdoctoral Researcher
>>> Steward Observatory
>>> University of Arizona
>>> http://chummels.org
>>>
>>> _______________________________________________
>>> yt-users mailing list
>>> yt-users at lists.spacepope.org
>>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>>>
>>>
>>
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>>
>
>
> --
> Cameron Hummels
> Postdoctoral Researcher
> Steward Observatory
> University of Arizona
> http://chummels.org
>
> _______________________________________________
> yt-users mailing list
> yt-users at lists.spacepope.org
> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>
>
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