[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 09:39:02 PDT 2014
I am using Ramses v3.11
The current version and changeset of YT I am using is:
---
Version = 3.0.1
Changeset = f66765a58a61 (stable) @
---
And yes, I have produced a projection plot of the simulation, and halo
structures exist (in z=0). The halos have also been identified by running
another halo finder independently (AHF)
I will run the updates to see that helps.
Will be back later.
Ben.
On Fri, Oct 3, 2014 at 5:30 PM, Cameron Hummels <chummels at gmail.com> wrote:
> That's odd. Could you produce a projection of the dark matter particles
> to identify if halos actually exist? Try something like this:
>
> http://paste.yt-project.org/show/5145/
>
> Also, what simulation code are you using?
>
> And what version of yt are you using? To determine your yt version, type:
>
> $ yt version
>
> I know that recently there were some changes in the output format of
> rockstar that broke yt's interaction with it. Perhaps that is related to
> the problem you're experiencing. You could try upgrading to the newest
> version of yt and rockstar with this:
>
> $ yt update --all
>
> This may resolve your problems.
>
> Cameron
>
>
> On Fri, Oct 3, 2014 at 9:22 AM, Ben Thompson <bthompson2090 at gmail.com>
> wrote:
>
>> 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
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> _______________________________________________
>>>>>> 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
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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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>>
>
>
> --
> 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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