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

Cameron Hummels chummels at gmail.com
Fri Oct 3 09:09:27 PDT 2014


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
>>>
>>>
>>>
>>>
>>>
>>> _______________________________________________
>>> yt-users mailing list
>>> 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
>>
>>
>
> _______________________________________________
> yt-users mailing list
> 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
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/20141003/ae6c2650/attachment.html>


More information about the yt-users mailing list