[yt-users] yt-users Digest, Vol 80, Issue 7
C.S. Howard
howardcs at mcmaster.ca
Fri Oct 3 10:39:46 PDT 2014
Thanks a lot Manuel, that worked perfectly! This is all I really need John,
but thank you for offering the workaround.
Cheers guys,
Corey
On Fri, Oct 3, 2014 at 12:56 PM, John ZuHone <jzuhone at gmail.com> wrote:
> 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
>
>
>
>
>
> _______________________________________________
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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
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>
>
>
>
> --
> Cameron Hummels
> Postdoctoral Researcher
> Steward Observatory
> University of Arizona
> http://chummels.org
>
> _______________________________________________
> yt-users mailing list
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