[yt-users] Rockstar and RAMSES (DM only run). Rockstar appears to run, but no halo information is written.
Ben Thompson
bthompson2090 at gmail.com
Sat Oct 11 13:17:07 PDT 2014
Hi Britton and everyone.
I have finally had some time to look into the rockstar halos a little more
(Sorry for the delayed response to this, I had to work on a few other
things this week)
Anyway. I am starting to think that this might be a units issue...
Within a 20 Mpc/h box (dark matter only). I have run both the AHF halo
finder and the rockstar halofinder. Of which I have identified the halo
with the most number of particles via each halofinder code
First thing to note, number of halos
len(ahfhalos) = 771
len(rk_halos) = 61 !
These positions are in a similar region.. give or take < 100 kpc
abs(rkhalos[0]["pos"] - ahfhalos[0]["pos"]).in_units("kpc")
YTArray([ 16.67015648, 54.59806824, 83.17473602], dtype=float32) kpc
Now lets wrap a data sphere container around each of these halos and
explore some of the properties in more detail.. out to the virial radius
rocksphere = ds.sphere(rk_halos[0]["pos"], rk_halos[0]["Rvir"])
ahfsphere = ds.sphere(ahf_halos[0]["pos"], ahf_halos[0]["Rvir"])
Comparing the virial radius
>>> rk_halos[0]["Rvir"].in_units("kpc/h")
711.183418249 kpc/h
>>> ahf_halos[0]["Rvir"].in_units("kpc/h")
877.551515684 kpc/h
Not too much to cause concern here compared to what follows on
more specifically, the properties of this halo as quoted in rockstar are
3 -1 4.2275e+13 540.21 542.04 711.012 110.933 92746 2.16471 5.12865 0.58479
-58.35 92.88 26.16 5.501e+14 8.955e+13 3.073e+14 0.02475 136.33844
4.2275e+13 4.6532e+13 3.5057e+13 2.2415e+13 0.0000e+00 42.64141 98.28
0.02960 0.67428 0.49493 -71.84635 25.39820 137.49133 0.64392 0.51116
-18.93683 37.49042 101.71218 0.6312 4.403e+13 3.002e+13
Lets take a look at the difference in masses of the spheres
abs(rocksphere.quantities.total_quantity(["particle_mass"]).in_units("Msun")
- rk_halos[0]["Mvir"].in_units("Msun")) = 1.0623502593e+11 Msun
where rk_halos[0]["Mvir"].in_units("Msun") = 6.03928545573e+13 Msun and
rocksphere.quantities.total_quantity(["particle_mass"]).in_units("Msun") =
6.02866195313e+13 Msun
nothing immediately strikes me as problematic.. until you investigate the
number of particles
abs(rk_halos[0]["num_p"] - len(ahfsphere["particle_position_x"])) = 79229.0
dimensionless in which the data container has 171975 particles and the halo
has 92746 particles.
That is a lot of missing particles.
Looking at my config, there is also a particle mass 2.73991e+08 and
rocksphere["particle_mass"][0].in_units("Msun/h") = 273990947.215 Msun/h ..
so the particle mass is fine.. but what I do not understand is that with a
difference in number of particles being that large, then how can the mass
of the halo and the data container be approximatly the same?
rocksphere.quantities.bulk_velocity(use_gas=False,use_particles=True).in_units("km/s")
= YTArray([ 4.80047835, 41.30041047, -29.83890759]) km/s
rk_halos[0]["vel"] = YTArray([-58.34999847, 92.87999725, 26.15999985],
dtype=float32) km/s
So we have some contradictory values with regards to the particle count and
the velocity/bulk velocity of the componants
interestingly with the AHF sphere
>>> ahf_halos[0]["vel"].in_units("km/s")
YTArray([ 0.47 , 35.36999893, -24.67000008], dtype=float32) km/s
>>>
ahfsphere.quantities.bulk_velocity(use_gas=False,use_particles=True).in_units("km/s")
YTArray([ 0.46971136, 35.36391688, -24.66292379]) km/s
I.e the AHF halo finder is getting results as to what you would expect with
this simulation.
------------------------------------------
In conclusion... I am getting contradictory particle counts within the
rockstar halo and the data container. As well as the bulk velocity being
wrong too (maybe as a result of the particle count?)
I have also attatched a copy of rockstar.cfg too.
Ben.
On Tue, Oct 7, 2014 at 3:42 PM, Britton Smith <brittonsmith at gmail.com>
wrote:
> Hi Ben,
>
> This still sounds like it could be a units issue? Can you confirm that
> the masses, positions, and velocities of the particles are correct? You
> should be able to just create a data container and query a few particles.
>
> Britton
>
> On Mon, Oct 6, 2014 at 10:38 AM, Ben Thompson <bthompson2090 at gmail.com>
> wrote:
>
>> Hello all.
>>
>> So I have decided to test my code on a smaller box ( 20 Mpc/h @ level 7,
>> one of my previous runs with 430 snapshots ) and I am getting halos (i.e
>> Rockstar is working) within the earlier snapshots with Rockstar. I am
>> currently running rockstar all the way through on that run now.
>>
>> A part of me now is suspecting that I am doing something wrong with the
>> resolution side of things maybe? I have kept the particle number the same,
>> but increased the box size (thus decreased the spatial resolution).
>>
>> Basically, rockstar is working. But I need to relax some initial
>> conditions somewhere with a larger box by the sounds of it.
>>
>> Currently running some more tests on the 20 Mpc box series (i.e seeing
>> what happens when you allow for the spatial (but not particle mass)
>> resolution to increase., rather than having a uniform grid run spatially
>>
>> Any thoughts, suggestions on why it might be complaining about the larger
>> box size runs?
>>
>> Ben
>>
>> On Sat, Oct 4, 2014 at 8:53 PM, Nathan Goldbaum <nathan12343 at gmail.com>
>> wrote:
>>
>>> If you are comfortable sharing the data, one of us could probably help
>>> out with debugging. It's hard to debug these things remotely but if we have
>>> the dataset you're using and the script you're running it becomes much
>>> easier to quickly figure out what's going wrong.
>>>
>>> In the past we've found sharing data via Dropbox or Google drive to work
>>> pretty well.
>>>
>>>
>>> On Saturday, October 4, 2014, Ben Thompson <bthompson2090 at gmail.com>
>>> wrote:
>>>
>>>> Reinstalling YT did not resolve the problem (although now I am on the
>>>> latest version of YT which is cool :) )
>>>>
>>>> I will have a serious debug with it on Monday.
>>>>
>>>> Ben.
>>>>
>>>> On Fri, Oct 3, 2014 at 11:29 PM, Britton Smith <brittonsmith at gmail.com>
>>>> wrote:
>>>>
>>>>> My guess is that this is a units issue. It might be worth it to stick
>>>>> some debugging statements into
>>>>> yt/analysis_modules/halo_finding/rockstar/rockstar.py where the particles
>>>>> are loaded up to be sent to rockstar. I believe the units that rockstar is
>>>>> expecting are positions in Mpc/h, masses in Msun/h, and velocities in km/s.
>>>>>
>>>>> Britton
>>>>>
>>>>> On Fri, Oct 3, 2014 at 11:39 AM, Ben Thompson <bthompson2090 at gmail.com
>>>>> > wrote:
>>>>>
>>>>>> 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
>>>>>>>>>> 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
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> 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
>>>>>>
>>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> 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
>>>
>>>
>>
>> _______________________________________________
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>> yt-users at lists.spacepope.org
>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
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