[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 08:55:19 PDT 2014
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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>
>
--
Cameron Hummels
Postdoctoral Researcher
Steward Observatory
University of Arizona
http://chummels.org
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