yt-users January 2019

yt-users@python.org

14 participants
18 discussions

Stars on volume rendering
by Elizabeth Harper-Clark 11 Dec '21

11 Dec '21

Hi all, Thanks for all your help over the last couple of days. One more question: - Can I plot particles on a volume rendered image? I have stars and I want to show where they are! Thanks, Libby -- Elizabeth Harper-Clark MA MSci PhD Candidate, Canadian Institute for Theoretical Astrophysics, UofT Sciences and Engineering Coordinator, Teaching Assistants' Training Program, UofT www.astro.utoronto.ca/~h-clark <http://www.astro.utoronto.ca/%7Eh-clark> h-clark(a)cita.utoronto.ca Astronomy office phone: +1-416-978-5759

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Variance in phase/profiles
by david collins 11 Apr '20

11 Apr '20

Hi, Everybody! Does anyone out there have a technique for getting the variance out of a profile object? A profile object is good at getting <X> vs. B, I'd then like to get < (X - <X>)^2 > vs B. Matt and I had spittballed the possibility some time ago, but I was wondering if anyone out there had successfully done it. Thanks, d. -- Sent from my computer.

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3-D Mass power spectra
by 梁家豪 03 Jun '19

03 Jun '19

Dear yt Can current yt calculate 3-D Mass power spectra? I checked the website but I didn't find any information. I think calculating 3-D Mass power spectra is a very useful for cosmological simulations. So I guess maybe yt supports this function now....? Thanks in advance

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Re: Rockstar on Blue Waters
by Nick Gnedin 30 Jan '19

30 Jan '19

Britton, Thank you very much, this seems to work, although not without a quirk - there may be a bug in the yt_astro_analysis installer. I am using the version of yt that you so kindly created for me a while ago - the one that fixes the HOP parallel scaling bug; it also includes some of my modifications to the artio frontend. When I installed yt_astro_analysis per online instructions, the installer kicked out my version of yt and activated another one (not sure if it was the system wide one or it installed its own). I had to juggle with installing and uninstalling yt and yt_astro_analysis until I figured out the order that worked: I installed yt_astro_analysis first and then reinstalled my custom yt on top of it. Then the rockstar error disappeared. n On 1/25/19 1:14 PM, Britton Smith wrote: > Hi Nick, > > I think you're running into a bug related to running rockstar with > Python3. This has been fixed as of the last major yt release and the > release of the yt_astro_analysis package. I just tried a small rockstar > test on Blue Waters using yt_astro_analysis and it worked for me. If you > want to go that route, I recommend following the install instructions here: > https://yt-astro-analysis.readthedocs.io/en/latest/ > <https://urldefense.proofpoint.com/v2/url?u=https-3A__yt-2Dastro-2Danalysis.…> > and using the --user flag when you install with pip. > > Britton > > On Wed, Jan 23, 2019 at 8:50 AM Nick Gnedin <ngnedin(a)gmail.com > <mailto:ngnedin@gmail.com>> wrote: > > > Folks, > > I am trying to run Rickstar on Blue Waters, and I am getting an error > even for a very simple setup: 1 writer and 1 reader running on a single > node on a small test run. The same job runs just fine on a workstation. > > The script is simple: > --------------- > import yt, yt.funcs > import glob, sys, os.path > > yt.enable_parallelism() > from yt.analysis_modules.halo_finding.rockstar.api import > RockstarHaloFinder > > > root = "../B20" > n = 1 > > dirs = ( "D" ) > > for dir in dirs: > sets = glob.glob(root+"/"+dir+"/rei20c1_a0.*/*.art") > sets.sort() > ts = yt.DatasetSeries(sets) > rh = RockstarHaloFinder(ts, num_readers=n, num_writers=n, > outbase=root+"/"+dir+"/rs", dm_only=True, particle_type='N-BODY') > rh.run() > --------------- > > and the batch script is trivial: > -------- > #!/bin/csh > #PBS -l nodes=1:ppn=32:xe > #PBS -l walltime=30:00,vmem=64gb > #PBS -q debug > #PBS -N rshfc.1 > #PBS -e $PBS_JOBID.err > #PBS -o $PBS_JOBID.out > #PBS -m be > > cd $PBS_O_WORKDIR > > module load bwpy > module load bwpy-mpi > > setenv APRUN_XFER_LIMITS 1 > limit stacksize unlimited > > aprun -n 3 -N 3 python3 rs-hfc.py >& std.rshfc1 > -------- > > The error I get is not very informative: > > [Error] Couldn't open ^A:0! (Err: Name or service not known) > > and the ^A string varies in separate runs, c.f. > > [Error] Couldn't open 344ei20:0! (Err: Name or service not known) > > which may happen if a null or corrupted pointer is printed with a %s > specification, but that's all I can guess. Is there a way to obtain > more > information and localize the offending code segment? > > > > > > > > > _______________________________________________ > yt-users mailing list -- yt-users(a)python.org > <mailto:yt-users@python.org> > To unsubscribe send an email to yt-users-leave(a)python.org > <mailto:yt-users-leave@python.org> >

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ANN: yt dev workshop, March 4-6
by Matthew Turk 30 Jan '19

30 Jan '19

Hi everyone! We are delighted to invite you to a yt development workshop at the University of Illinois Urbana-Champaign, March 4-6 of 2019. Please feel encouraged to pass this information on to others that may find it interesting! Information on logistics and registration may be found at the workshop website: http://yt-project.org/workshops/spring2019/ This workshop will be focused on extending existing functionality, building collaborations with other software projects, and ingestion of new types and classes of data into yt. The workshop will take place at the National Center for Supercomputing Applications building on the north end of the UIUC campus. The NCSA building is about a block away from the conference hotel and is next door to a parking structure that offers metered all-day parking. There are a number of food trucks nearby, a university-run cafeteria about 2 blocks away, and a university business district with many good lunch restaurants about a half a mile away. We are planning to offer funding for hotel and travel for those requesting support. If you request funding, you will be notified of available funds by February 16. Travel awards will be made in the form of arranged lodging and airfare, with reservations being made by the conference organizers. Best regards, The Organizing Committee MT Campbell Nathan Goldbaum Madicken Munk Matt Turk Samantha Walkow

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Trying to install yt on XSEDE Comet
by Danielle Skinner 25 Jan '19

25 Jan '19

Hi all, I have been having many issues running yt on Comet recently. I initially installed yt using conda, and quickly ran into problems with yt.enable_plugins(). I found that only some of my fields were being added, and I ended up having to manually load in the fields that were not added (although this also proved to be a struggle). I was able to run the same script, using the same plugins file, on a different computer, but with yt version 3.4.0. So today I decided to revert to yt version 3.4.0 and try to run my script. Now, when I "import yt", I get the following error: Traceback (most recent call last): File "trace_halos_full.py", line 3, in <module> import yt File "/home/drenniks/software/anaconda3/lib/python3.6/site-packages/yt/__init__.py", line 102, in <module> from yt.visualization.api import \ File "/home/drenniks/software/anaconda3/lib/python3.6/site-packages/yt/visualization/api.py", line 22, in <module> from .particle_plots import \ File "/home/drenniks/software/anaconda3/lib/python3.6/site-packages/yt/visualization/particle_plots.py", line 18, in <module> from yt.visualization.fixed_resolution import \ File "/home/drenniks/software/anaconda3/lib/python3.6/site-packages/yt/visualization/fixed_resolution.py", line 23, in <module> from .volume_rendering.api import off_axis_projection File "/home/drenniks/software/anaconda3/lib/python3.6/site-packages/yt/visualization/volume_rendering/api.py", line 23, in <module> from .camera import Camera File "/home/drenniks/software/anaconda3/lib/python3.6/site-packages/yt/visualization/volume_rendering/camera.py", line 21, in <module> from .utils import data_source_or_all File "/home/drenniks/software/anaconda3/lib/python3.6/site-packages/yt/visualization/volume_rendering/utils.py", line 11, in <module> from yt.utilities.lib import mesh_traversal File "rtcore_scene.pxd", line 61, in init yt.utilities.lib.mesh_traversal ValueError: pyembree.rtcore_scene.EmbreeScene has the wrong size, try recompiling. Expected 32, got 24 It would be great to hear from other yt users on comet to hear how they installed yt, or if someone can help me out with this error, that would be much appreciated! Please let me know what other info you may need from me. I'll do my best to quickly respond.

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Rockstar on Blue Waters
by Nick Gnedin 25 Jan '19

25 Jan '19

Folks, I am trying to run Rickstar on Blue Waters, and I am getting an error even for a very simple setup: 1 writer and 1 reader running on a single node on a small test run. The same job runs just fine on a workstation. The script is simple: --------------- import yt, yt.funcs import glob, sys, os.path yt.enable_parallelism() from yt.analysis_modules.halo_finding.rockstar.api import RockstarHaloFinder root = "../B20" n = 1 dirs = ( "D" ) for dir in dirs: sets = glob.glob(root+"/"+dir+"/rei20c1_a0.*/*.art") sets.sort() ts = yt.DatasetSeries(sets) rh = RockstarHaloFinder(ts, num_readers=n, num_writers=n, outbase=root+"/"+dir+"/rs", dm_only=True, particle_type='N-BODY') rh.run() --------------- and the batch script is trivial: -------- #!/bin/csh #PBS -l nodes=1:ppn=32:xe #PBS -l walltime=30:00,vmem=64gb #PBS -q debug #PBS -N rshfc.1 #PBS -e $PBS_JOBID.err #PBS -o $PBS_JOBID.out #PBS -m be cd $PBS_O_WORKDIR module load bwpy module load bwpy-mpi setenv APRUN_XFER_LIMITS 1 limit stacksize unlimited aprun -n 3 -N 3 python3 rs-hfc.py >& std.rshfc1 -------- The error I get is not very informative: [Error] Couldn't open ^A:0! (Err: Name or service not known) and the ^A string varies in separate runs, c.f. [Error] Couldn't open 344ei20:0! (Err: Name or service not known) which may happen if a null or corrupted pointer is printed with a %s specification, but that's all I can guess. Is there a way to obtain more information and localize the offending code segment?

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Trying to change axis on phaseplot
by Stephanie Tonnesen 20 Jan '19

20 Jan '19

Hi all, I am making a phaseplot where the x-axis is the distance along the z-axis and the y-axis is the velocity in the z direction. I am really, however, plotting distance above the disk, which is at [0.5,0.5,0.5] or [80,80,80] in kpc. Instead of my x-axis going from 70 to 120 where 80 is the disk position, I would like it to go from -10 to 40 where 0 is the disk position. So, I thought I would define a new variable, zdisk, and use that, but have run into some problems. Since this plot works beautifully when I am not messing with the z-values, I am guessing that I have done something wrong defining my variable. Any help is much appreciated!! Thanks, Stephanie yt version: --- Version = 3.5.dev0 Changeset = f7ac18f5bf99 --- Okay, so the code: import sys import numpy as np import yt from yt.units import kpc def _zdisk(field,data): return data['index','z'].in_units('kpc')-(80.,'kpc') ds = yt.load("/mnt/ceph/users/stonnesen/data1/BPr16vs30arcfo/DD"+loop[i]+"/BPr16vs30arcfo"+loop[i]) yt.add_field(("gas","zdisk"), function=_zdisk,units="kpc") ad = ds.all_data() diska = ad.cut_region(["obj['Metal_Density']/obj['density'] > 0.25"]) profile = yt.create_profile(diska, ['zdisk','velocity_z'], 'cell_mass',n_bins=80,weight_field=None) histogram = profile.field_data['gas','cell_mass'] histogram[histogram < 1e37] = 0 plot2 = yt.PhasePlot.from_profile(profile) plot2.set_unit('zdisk','kpc') plot2.set_log('zdisk',False) plot2.set_unit('velocity_z','km/s') plot2.set_log('velocity_z',False) plot2.set_xlim(-10,40) plot2.set_ylim(-6e2,1.5e3) plot2.set_zlim('cell_mass',1e37,1e42) plot2.save('BPr16vs30arcfo'+loop[i]+'_tp25_alls_mcut_nbin80_zdisk') ______________________________ ______________________________ and now the error: yt : [INFO ] 2019-01-19 15:55:25,744 Parameters: current_time = 3119.9999022826 yt : [INFO ] 2019-01-19 15:55:25,744 Parameters: domain_dimensions = [256 256 256] yt : [INFO ] 2019-01-19 15:55:25,744 Parameters: domain_left_edge = [ 0. 0. 0.] yt : [INFO ] 2019-01-19 15:55:25,745 Parameters: domain_right_edge = [ 1. 1. 1.] yt : [INFO ] 2019-01-19 15:55:25,746 Parameters: cosmological_simulation = 0.0 /mnt/home/stonnesen/yt-conda/yt/yt/fields/local_fields.py:46: UserWarning: Because 'sampling_type' not specified, yt will assume a cell 'sampling_type' warnings.warn("Because 'sampling_type' not specified, yt will " Parsing Hierarchy : 0%| | 0/4284 [00:00<?, ?it/s] Parsing Hierarchy : 23%|██▎ | 968/4284 [00:00<00:00, 9672.70it/s] Parsing Hierarchy : 40%|███▉ | 1702/4284 [00:00<00:00, 8971.55it/s] Parsing Hierarchy : 62%|██████▏ | 2643/4284 [00:00<00:00, 9101.75it/s] Parsing Hierarchy : 77%|███████▋ | 3298/4284 [00:00<00:00, 8334.29it/s] Parsing Hierarchy : 99%|█████████▉| 4241/4284 [00:00<00:00, 8660.50it/s] Parsing Hierarchy : 100%|██████████| 4284/4284 [00:00<00:00, 8466.80it/s] yt : [INFO ] 2019-01-19 15:55:26,407 Gathering a field list (this may take a moment.) Traceback (most recent call last): File "yt_allphaseplot_newz.py", line 40, in <module> profile = yt.create_profile(diska, ['zdisk','velocity_z'], 'cell_mass',n_bins=80,weight_field=None) File "/mnt/home/stonnesen/yt-conda/yt/yt/data_objects/profiles.py", line 1042, in create_profile bin_fields = data_source._determine_fields(bin_fields) File "/mnt/home/stonnesen/yt-conda/yt/yt/data_objects/data_containers.py", line 1165, in _determine_fields finfo = self.ds._get_field_info("unknown", fname) File "/mnt/home/stonnesen/yt-conda/yt/yt/data_objects/static_output.py", line 756, in _get_field_info self.index File "/mnt/home/stonnesen/yt-conda/yt/yt/data_objects/static_output.py", line 514, in index self.create_field_info() File "/mnt/home/stonnesen/yt-conda/yt/yt/data_objects/static_output.py", line 571, in create_field_info self.field_info.load_all_plugins(self.default_fluid_type) File "/mnt/home/stonnesen/yt-conda/yt/yt/fields/field_info_container.py", line 276, in load_all_plugins self.find_dependencies(loaded) File "/mnt/home/stonnesen/yt-conda/yt/yt/fields/field_info_container.py", line 289, in find_dependencies deps, unavailable = self.check_derived_fields(loaded) File "/mnt/home/stonnesen/yt-conda/yt/yt/fields/field_info_container.py", line 362, in check_derived_fields fd = fi.get_dependencies(ds = self.ds) File "/mnt/home/stonnesen/yt-conda/yt/yt/fields/derived_field.py", line 216, in get_dependencies e[self.name] File "/mnt/home/stonnesen/yt-conda/yt/yt/fields/field_detector.py", line 108, in __missing__ vv = finfo(self) File "/mnt/home/stonnesen/yt-conda/yt/yt/fields/derived_field.py", line 256, in __call__ dd = self._function(self, data) File "yt_allphaseplot_newz.py", line 21, in _zdisk return data['index','z'].in_units('kpc')-(80.,'kpc') File "/mnt/home/stonnesen/yt-conda/yt/yt/units/yt_array.py", line 1391, in __array_ufunc__ inps, units, ufunc, ret_class) File "/mnt/home/stonnesen/yt-conda/yt/yt/units/yt_array.py", line 161, in handle_preserve_units any_nonzero = [np.any(inps[0]), np.any(inps[1])] File "/mnt/xfs1/home/stonnesen/yt-conda/lib/python3.6/site-packages/numpy/core/fromnumeric.py", line 1970, in any return arr.any(axis=axis, out=out, **kwargs) File "/mnt/xfs1/home/stonnesen/yt-conda/lib/python3.6/site-packages/numpy/core/_methods.py", line 38, in _any return umr_any(a, axis, dtype, out, keepdims) TypeError: cannot perform reduce with flexible type -- Dr. Stephanie Tonnesen Associate Research Scientist CCA, Flatiron Institute New York, NY stonnes(a)gmail.com

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[Enzo 2.5] issue with running rockstar for Dark Matter only simulation
by Andrew Cook 19 Jan '19

19 Jan '19

Hello, I'm trying to run rockstar on some Dark Matter data to get merger trees but I keep getting this error: Traceback (most recent call last): File "halos_rockstar.py", line 53, in <module> rh = RockstarHaloFinder(es, num_readers= 2, num_writers= 4, particle_type= "dark_matter_nested") File "/opt/apps/yt/3.3.5b/yt-conda/src/yt-git/yt/analysis_modules/halo_finding/rockstar/rockstar.py", line 203, in __init__ self.runner = StandardRunner(num_readers, num_writers) File "/opt/apps/yt/3.3.5b/yt-conda/src/yt-git/yt/analysis_modules/halo_finding/rockstar/rockstar.py", line 85, in __init__ raise RuntimeError RuntimeError Not entirely sure what this means I've been able to run rockstar before on the same halo with baryons on. But now rockstar isn't running on anything. Hope someone can shed some light on this situation. Thank you very much Andy

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overplot ~100,000 points onto a figure
by Huanqing 16 Jan '19

16 Jan '19

Hi, I want to overlie >100,000 points onto a plot. Using annotate_marker I have no issue with a small number of points, however if I want to plot more than 10,0000 points to overlie, it takes almost an hour to produce that plot. Here is the code I use: for ipar in range(len(xpMpc)): slc.annotate_marker(ds.arr([xpMpc[ipar],ypMpc[ipar],zpMpc[ipar]],'Mpc').in_units('code_length'),coord_system='data',marker='.',plot_args={'color':'cyan','s':1,'alpha':0.3}) I wonder is there any way I can speed this up? Thank you very much, Huanqing

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yt-users January 2019