[yt-users] Rockstar and RAMSES (DM only run). Rockstar appears to run, but no halo information is written.
Ben Thompson
bthompson2090 at gmail.com
Fri Oct 3 09:02:35 PDT 2014
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
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/20141003/36f2e737/attachment.html>
More information about the yt-users
mailing list