[yt-users] yt-users Digest, Vol 80, Issue 7
John ZuHone
jzuhone at gmail.com
Fri Oct 3 09:56:05 PDT 2014
Corey,
Manuel's solution is probably the quickest for you, actually.
Thanks, Manuel!
If you need the particles to be actual fields in yt, we could still do that workaround.
Best,
John
John ZuHone
Kavli Center for Astrophysics and Space Research
Massachusetts Institute of Technology
77 Massachusetts Ave., 37-582G
Cambridge, MA 02139
(w) 617-253-2354
(m) 781-708-5004
jzuhone at space.mit.edu
jzuhone at gmail.com
http://www.jzuhone.com
> On Oct 3, 2014, at 12:37 PM, Manuel Zamora <mzamora06 at gmail.com> wrote:
>
> Hi Corey,
>
> This works for me:
>
> %%%%%%%%%%%%%%%%%%%%%%%%
> import h5py
>
> ...
>
> f = h5py.File("../r10f0/flows_hdf5_plt_cnt_0160","r")
> ParticleData = f['particle tracers']
> ppz = ParticleData["particle_z"]
> ppy = ParticleData["particle_y"]
> ppx = ParticleData["particle_x"]
> ppm = ParticleData["particle_mass"]
> data = {'particle_position_x': ppx,
> 'particle_position_y': ppy,
> 'particle_position_z': ppz,
> 'particle_mass': ppm}
> f.close()
> del ParticleData
> del f
>
> ...
>
> slc.annotate_marker([ppx,ppy,ppz], marker='o', plot_args={'color': 'black','s':10})
>
> %%%%%%%%%%%%%%%%%%%%%%%%
>
> I hope this helps :)
> _
> Manuel Zamora
>
>
>> On Oct 3, 2014, at 11:23 AM, yt-users-request at lists.spacepope.org wrote:
>>
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>> Today's Topics:
>>
>> 1. Annotating particles in FLASH2.5 (C.S. Howard)
>> 2. Re: Annotating particles in FLASH2.5 (John ZuHone)
>> 3. Re: Annotating particles in FLASH2.5 (C.S. Howard)
>> 4. Re: Rockstar and RAMSES (DM only run). Rockstar appears to
>> run, but no halo information is written. (Ben Thompson)
>>
>>
>> ----------------------------------------------------------------------
>>
>> Message: 1
>> Date: Fri, 3 Oct 2014 12:14:08 -0400
>> From: "C.S. Howard" <howardcs at mcmaster.ca>
>> To: yt-users at lists.spacepope.org
>> Subject: [yt-users] Annotating particles in FLASH2.5
>> Message-ID:
>> <CADaEBaZ=LwWfN3TLaE2KTnC35vksfvmLwYiZeMnOoJ7BOyb_Og at mail.gmail.com>
>> Content-Type: text/plain; charset="utf-8"
>>
>> Hi everyone,
>>
>> I'm trying to draw sink particles on a slice plot using FLASH 2.5 data. I'm
>> using yt 3.0 with the commands:
>>
>> pf = yt.load(pltfiles[k])
>> fig = plt.figure()
>> ax1 = fig.add_subplot(111)
>> axes = {'x':0, 'y':1, 'z':2}
>> slices = {'x':[0.0,0.5,0.5],\
>> 'y':[0.5,0.0,0.5],\
>> 'z':[0.5,0.5,0.5]}
>>
>> slc = SlicePlot(pf, 'z', 'density', center = slices['z'],origin='domain')
>> slc.annotate_particles(1.0, p_size=15.0, col="Black")
>>
>> but it doesn't work, giving me the following errors;
>>
>> Traceback (most recent call last):
>> File "./sliceplots.py", line 42, in <module>
>> slc.annotate_particles(1.0, p_size=15.0, col="Black")
>> File
>> "/1/home/howardcs/yt-3.0/yt-x86_64/src/yt-hg/yt/visualization/plot_container.py",
>> line 70, in newfunc
>> args[0]._setup_plots()
>> File
>> "/1/home/howardcs/yt-3.0/yt-x86_64/src/yt-hg/yt/visualization/plot_window.py",
>> line 862, in _setup_plots
>> self.run_callbacks(f)
>> File
>> "/1/home/howardcs/yt-3.0/yt-x86_64/src/yt-hg/yt/visualization/plot_container.py",
>> line 315, in run_callbacks
>> callback(cbw)
>> File
>> "/1/home/howardcs/yt-3.0/yt-x86_64/src/yt-hg/yt/visualization/plot_modifications.py",
>> line 1055, in __call__
>> & ( reg[pt, field_y] >= y0 ) & ( reg[pt, field_y] <= y1 ) )
>> File
>> "/1/home/howardcs/yt-3.0/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py",
>> line 233, in __getitem__
>> f = self._determine_fields([key])[0]
>> File
>> "/1/home/howardcs/yt-3.0/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py",
>> line 486, in _determine_fields
>> finfo = self.ds._get_field_info(ftype, fname)
>> File
>> "/1/home/howardcs/yt-3.0/yt-x86_64/src/yt-hg/yt/data_objects/static_output.py",
>> line 482, in _get_field_info
>> raise YTFieldNotFound((ftype, fname), self)
>> yt.utilities.exceptions.YTFieldNotFound: Could not find field '('all',
>> 'particle_position_x')' in DensProfTurb_flattop_hdf5_plt_cnt_0200
>>
>> Seems like its having trouble finding the particle information for
>> FLASH2.5. Any suggestions on where to go from here?
>>
>> Thanks,
>> Corey
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>> ------------------------------
>>
>> Message: 2
>> Date: Fri, 3 Oct 2014 12:18:49 -0400
>> From: John ZuHone <jzuhone at gmail.com>
>> To: Discussion of the yt analysis package
>> <yt-users at lists.spacepope.org>
>> Subject: Re: [yt-users] Annotating particles in FLASH2.5
>> Message-ID: <5851849E-3256-47D4-9FCA-45C02C3AA248 at gmail.com>
>> Content-Type: text/plain; charset="us-ascii"
>>
>> Hi Corey,
>>
>> Unfortunately, we don't support FLASH 2.5 particle data, because it is in a different format from v. 3.0 and above.
>>
>> If you like, I'd be happy to help figure out some kind of workaround.
>>
>> Best,
>>
>> John
>>
>> John ZuHone
>> Kavli Center for Astrophysics and Space Research
>> Massachusetts Institute of Technology
>> 77 Massachusetts Ave., 37-582G
>> Cambridge, MA 02139
>> (w) 617-253-2354
>> (m) 781-708-5004
>> jzuhone at space.mit.edu
>> jzuhone at gmail.com
>> http://www.jzuhone.com
>>
>>> On Oct 3, 2014, at 12:14 PM, C.S. Howard <howardcs at mcmaster.ca> wrote:
>>>
>>> Hi everyone,
>>>
>>> I'm trying to draw sink particles on a slice plot using FLASH 2.5 data. I'm using yt 3.0 with the commands:
>>>
>>> pf = yt.load(pltfiles[k])
>>> fig = plt.figure()
>>> ax1 = fig.add_subplot(111)
>>> axes = {'x':0, 'y':1, 'z':2}
>>> slices = {'x':[0.0,0.5,0.5],\
>>> 'y':[0.5,0.0,0.5],\
>>> 'z':[0.5,0.5,0.5]}
>>>
>>> slc = SlicePlot(pf, 'z', 'density', center = slices['z'],origin='domain')
>>> slc.annotate_particles(1.0, p_size=15.0, col="Black")
>>>
>>> but it doesn't work, giving me the following errors;
>>>
>>> Traceback (most recent call last):
>>> File "./sliceplots.py", line 42, in <module>
>>> slc.annotate_particles(1.0, p_size=15.0, col="Black")
>>> File "/1/home/howardcs/yt-3.0/yt-x86_64/src/yt-hg/yt/visualization/plot_container.py", line 70, in newfunc
>>> args[0]._setup_plots()
>>> File "/1/home/howardcs/yt-3.0/yt-x86_64/src/yt-hg/yt/visualization/plot_window.py", line 862, in _setup_plots
>>> self.run_callbacks(f)
>>> File "/1/home/howardcs/yt-3.0/yt-x86_64/src/yt-hg/yt/visualization/plot_container.py", line 315, in run_callbacks
>>> callback(cbw)
>>> File "/1/home/howardcs/yt-3.0/yt-x86_64/src/yt-hg/yt/visualization/plot_modifications.py", line 1055, in __call__
>>> & ( reg[pt, field_y] >= y0 ) & ( reg[pt, field_y] <= y1 ) )
>>> File "/1/home/howardcs/yt-3.0/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py", line 233, in __getitem__
>>> f = self._determine_fields([key])[0]
>>> File "/1/home/howardcs/yt-3.0/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py", line 486, in _determine_fields
>>> finfo = self.ds._get_field_info(ftype, fname)
>>> File "/1/home/howardcs/yt-3.0/yt-x86_64/src/yt-hg/yt/data_objects/static_output.py", line 482, in _get_field_info
>>> raise YTFieldNotFound((ftype, fname), self)
>>> yt.utilities.exceptions.YTFieldNotFound: Could not find field '('all', 'particle_position_x')' in DensProfTurb_flattop_hdf5_plt_cnt_0200
>>>
>>> Seems like its having trouble finding the particle information for FLASH2.5. Any suggestions on where to go from here?
>>>
>>> Thanks,
>>> Corey
>>> _______________________________________________
>>> yt-users mailing list
>>> yt-users at lists.spacepope.org
>>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
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>> ------------------------------
>>
>> Message: 3
>> Date: Fri, 3 Oct 2014 12:22:02 -0400
>> From: "C.S. Howard" <howardcs at mcmaster.ca>
>> To: Discussion of the yt analysis package
>> <yt-users at lists.spacepope.org>
>> Subject: Re: [yt-users] Annotating particles in FLASH2.5
>> Message-ID:
>> <CADaEBaapFJaCWnyWfS5s8NMp8KR7SQTf35-3BJEqWKutiCJY1A at mail.gmail.com>
>> Content-Type: text/plain; charset="utf-8"
>>
>> That would be awesome, as long as it isn't a huge headache. I'll be moving
>> to the newer versions of FLASH soon, but for now I'm stuck with version 2.5.
>>
>>> On Fri, Oct 3, 2014 at 12:18 PM, John ZuHone <jzuhone at gmail.com> wrote:
>>>
>>> Hi Corey,
>>>
>>> Unfortunately, we don't support FLASH 2.5 particle data, because it is in
>>> a different format from v. 3.0 and above.
>>>
>>> If you like, I'd be happy to help figure out some kind of workaround.
>>>
>>> Best,
>>>
>>> John
>>>
>>> John ZuHone
>>> Kavli Center for Astrophysics and Space Research
>>> Massachusetts Institute of Technology
>>> 77 Massachusetts Ave., 37-582G
>>> Cambridge, MA 02139
>>> (w) 617-253-2354
>>> (m) 781-708-5004
>>> jzuhone at space.mit.edu
>>> jzuhone at gmail.com
>>> http://www.jzuhone.com
>>>
>>> On Oct 3, 2014, at 12:14 PM, C.S. Howard <howardcs at mcmaster.ca> wrote:
>>>
>>> Hi everyone,
>>>
>>> I'm trying to draw sink particles on a slice plot using FLASH 2.5 data.
>>> I'm using yt 3.0 with the commands:
>>>
>>> pf = yt.load(pltfiles[k])
>>> fig = plt.figure()
>>> ax1 = fig.add_subplot(111)
>>> axes = {'x':0, 'y':1, 'z':2}
>>> slices = {'x':[0.0,0.5,0.5],\
>>> 'y':[0.5,0.0,0.5],\
>>> 'z':[0.5,0.5,0.5]}
>>>
>>> slc = SlicePlot(pf, 'z', 'density', center = slices['z'],origin='domain')
>>> slc.annotate_particles(1.0, p_size=15.0, col="Black")
>>>
>>> but it doesn't work, giving me the following errors;
>>>
>>> Traceback (most recent call last):
>>> File "./sliceplots.py", line 42, in <module>
>>> slc.annotate_particles(1.0, p_size=15.0, col="Black")
>>> File
>>> "/1/home/howardcs/yt-3.0/yt-x86_64/src/yt-hg/yt/visualization/plot_container.py",
>>> line 70, in newfunc
>>> args[0]._setup_plots()
>>> File
>>> "/1/home/howardcs/yt-3.0/yt-x86_64/src/yt-hg/yt/visualization/plot_window.py",
>>> line 862, in _setup_plots
>>> self.run_callbacks(f)
>>> File
>>> "/1/home/howardcs/yt-3.0/yt-x86_64/src/yt-hg/yt/visualization/plot_container.py",
>>> line 315, in run_callbacks
>>> callback(cbw)
>>> File
>>> "/1/home/howardcs/yt-3.0/yt-x86_64/src/yt-hg/yt/visualization/plot_modifications.py",
>>> line 1055, in __call__
>>> & ( reg[pt, field_y] >= y0 ) & ( reg[pt, field_y] <= y1 ) )
>>> File
>>> "/1/home/howardcs/yt-3.0/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py",
>>> line 233, in __getitem__
>>> f = self._determine_fields([key])[0]
>>> File
>>> "/1/home/howardcs/yt-3.0/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py",
>>> line 486, in _determine_fields
>>> finfo = self.ds._get_field_info(ftype, fname)
>>> File
>>> "/1/home/howardcs/yt-3.0/yt-x86_64/src/yt-hg/yt/data_objects/static_output.py",
>>> line 482, in _get_field_info
>>> raise YTFieldNotFound((ftype, fname), self)
>>> yt.utilities.exceptions.YTFieldNotFound: Could not find field '('all',
>>> 'particle_position_x')' in DensProfTurb_flattop_hdf5_plt_cnt_0200
>>>
>>> Seems like its having trouble finding the particle information for
>>> FLASH2.5. Any suggestions on where to go from here?
>>>
>>> Thanks,
>>> Corey
>>>
>>> _______________________________________________
>>> 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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>> ------------------------------
>>
>> Message: 4
>> Date: Fri, 3 Oct 2014 17:22:59 +0100
>> From: Ben Thompson <bthompson2090 at gmail.com>
>> To: Discussion of the yt analysis package
>> <yt-users at lists.spacepope.org>
>> Subject: Re: [yt-users] Rockstar and RAMSES (DM only run). Rockstar
>> appears to run, but no halo information is written.
>> Message-ID:
>> <CAFO9rXeHkwzeLCLg8vuKQ66JgVu3j0LziYXPH7uOzPgQhNO_OA at mail.gmail.com>
>> Content-Type: text/plain; charset="utf-8"
>>
>> 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
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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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