Nathan,

Done (I tared 4 files together):

/data/gnedin/REI/TMP >tar cvf gnedin_hop.tar hop.*
hop.0.h5
hop.1.h5
hop.2.h5
hop.3.h5
/data/gnedin/REI/TMP >yt upload gnedin_hop.tar
Stream body handler: received 9687040 bytes
http://use.yt/upload/318d837f

The files are available on BlueWaters at:
/mnt/c/scratch/sciteam/ngnedin/PERM/B40/A.DMO/a=1.0008/hop/hop.*.h5

Thanks a lot.

Nick



On 05/16/2018 09:38 AM, Nathan Goldbaum wrote:

Hi,

Is there any chance you can share the hdf5 file? I'm not able to reproduce this warning using a test dataset I have so it might have something to do with the data.

You can share a dataset with "yt upload path/to/data.h5". That will upload to a server at NCSA and then print a link out to share here once its done.

If the data cannot be shared publicly you can send me an e-mail off-list with e.g. a dropbox link.

-Nathan

On Wed, May 16, 2018 at 10:32 AM, Nick Gnedin <ngnedin@gmail.com <mailto:ngnedin@gmail.com>> wrote:


    I am trying to make a plot of all halos found by HOP. I copied your
    example from http://yt-project.org/doc/cookbook/simple_plots.html
    <http://yt-project.org/doc/cookbook/simple_plots.html>

    If I just plot partile positions:

    --------------------- script -------------------
    import yt
    import numpy as np

    # load the dataset
    ds = yt.load('../B40/A.DMO/a=1.0008/hop/hop.0.h5')

    # create our plot
    p = yt.ParticlePlot(ds, 'particle_position_x', 'particle_position_y')

    m = ds.all_data()[('all', 'particle_mass')]
    print(np.amin(m),np.amax(m))

    # pick some appropriate units
    p.set_axes_unit('Mpc')
    p.set_unit('particle_mass', 'Msun')

    #save result
    p.save()
    -----------------------------------------------

    then everything works fine. However, if I use mass weighting:

      p = yt.ParticlePlot(ds, 'particle_position_x',
    'particle_position_y', 'particle_mass')

    I get the following error:

    ...
    yt : [INFO     ] 2018-05-16 09:27:39,004 Allocating for 1.997e+05
    particles (index particle type 'all')
    yt : [INFO     ] 2018-05-16 09:27:39,381 Identified 5.972e+04 octs
    yt : [INFO     ] 2018-05-16 09:27:40,021 xlim = 0.000000
    199229564535610884216586240.000000
    yt : [INFO     ] 2018-05-16 09:27:40,021 ylim = 0.000000
    199229564535610884216586240.000000
    yt : [INFO     ] 2018-05-16 09:27:40,023 xlim = 0.000000
    199229564535610884216586240.000000
    yt : [INFO     ] 2018-05-16 09:27:40,023 ylim = 0.000000
    199229564535610884216586240.000000
    yt : [INFO     ] 2018-05-16 09:27:40,042 Splatting (('all',
    'particle_mass')) onto a 800 by 800 mesh
    4.1036023233207635e+41 g 1.921697915571756e+47 g
    yt : [INFO     ] 2018-05-16 09:27:44,084 Saving plot
    hop.0.h5_Particle_z_particle_mass.png
    /u/sciteam/ngnedin/.local/lib/python3.5/site-packages/matplotlib/colors.py:1020:
    RuntimeWarning: invalid value encountered in less_equal
       mask |= resdat <= 0

    Notice, that there are no nonpositive masses in the catalog
    print(np.amin(m),np.amax(m)):
             4.1036023233207635e+41 g 1.921697915571756e+47 g




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