yt-users January 2015

yt-users@python.org

24 participants
21 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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Profile plot of a 2d projection FRB object
by Ben Thompson 03 Jun '15

03 Jun '15

Hello everyone. I was wondering if anyone has had experience with producing a profile plot from a 2d projection object (FRB object). Essentially, what I am trying to do is plot the stellar surface density of a galaxy as a function of radius. This is achieved by doing the following from a disk YT object called cylinder (in which the origional simulation object is called shot) center = cylinder.get_field_parameter("center") normal = cylinder.get_field_parameter("normal") image_width = (100,"kpc") three_image_width = YTArray((image_width[0], image_width[0], image_width[0]),image_width[1]) left = center - image_width right = center + image_width region = shot.region(center, left, right) proj = yt.ProjectionPlot(cylinder.ds,"z",[("deposit","stars_density")],center=center,width=image_width,data_source=region,axes_unit="kpc") the error arrises here prof = yt.create_profile(proj,bin_fields="cylindrical_r",fields=[("deposit","stars_density")],n_bins=128,weight_field=None ) where I get the error /gpfs/home/........./profiles.pyc in create_profile(data_source, bin_fields, fields, n_bins, extrema, logs, units, weight_field, accumulation, fractional) 1304 else: 1305 raise NotImplementedError -> 1306 bin_fields = data_source._determine_fields(bin_fields) 1307 fields = data_source._determine_fields(fields) 1308 if units is not None: AttributeError: 'FixedResolutionBuffer' object has no attribute '_determine_fields' Any ideas how to get around this error? Also some other things to add as a postscript. Since how the projection works, if I provide weights=None as a keyword argument within the ProjectionPlot object, I get a surface density (g/cm^2). But also a "cylindrical_r" in cm^2 as well. I *think* the way to get around this is to do another projection where weights="ones", get the radius values out of that profile.. and then in matplotlib, useing the surface density array from the former profile, and the radius bin array from the latter... Produce a plot of the surface density as a function of radius from those two arrays (I might check by hand afterwards to see if this does the trick). This seems kinda convoluted so I am wondering if there is an easier way than this. _______________________________________________ yt-users mailing list yt-users(a)lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

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can yt load file non-recursively?
by Yuxiang Qin 22 Jan '15

22 Jan '15

Dear yt-users, I have a tiny question about loading files. I understand when yt load files, it will load all the files in the directory. For example: if I do ds=yt.load('snap_103.0.hdf5’), then ds.field_list , yt would open all the files: snap_103.0.hdf5* snap_103.16.hdf5* snap_103.22.hdf5* snap_103.29.hdf5* snap_103.6.hdf5* snap_103.10.hdf5* snap_103.17.hdf5* snap_103.23.hdf5* snap_103.2.hdf5* snap_103.7.hdf5* snap_103.11.hdf5* snap_103.18.hdf5* snap_103.24.hdf5* snap_103.30.hdf5* snap_103.8.hdf5* snap_103.12.hdf5* snap_103.19.hdf5* snap_103.25.hdf5* snap_103.31.hdf5* snap_103.9.hdf5* snap_103.13.hdf5* snap_103.1.hdf5* snap_103.26.hdf5* snap_103.3.hdf5* snap_103.14.hdf5* snap_103.20.hdf5* snap_103.27.hdf5* snap_103.4.hdf5* snap_103.15.hdf5* snap_103.21.hdf5* snap_103.28.hdf5* snap_103.5.hdf5* However, if our data only has one file :snap_103.hdf5*, then if I do ds=yt.load('snap_103.hdf5’), then ds.field_list, yt would still try to open all the files from snap_103.0.hdf5, however there is no snap_103.0.hdf5. It would report error: IOError: Unable to open file (Unable to open file: name = '/lustre/projects/p071_swin/yqin/smaug/ref_eff_l010n0128/data/snapshot_102/snap_102.0.hdf5', errno = 2, error message = 'no such file or directory', flags = 0, o_flags = 0) Is there an argument saying I don’t want to do loading recursively? I can make a link named snap_103.0.hdf5 to snap_103.hdf5. But it’s kind of inconvenient. Cheers, -- Yuxiang Qin PhD Student School of Physics The University of Melbourne VIC, Australia, 3010 _______________________________________________ yt-users mailing list yt-users(a)lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

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SciPy installation problem
by Caroline Van Borm 22 Jan '15

22 Jan '15

Dear yt users, I'm having some trouble installing SciPy. I can install yt just fine using the install script, but if I turn the option for installing SciPy on, I get the following error: creating build/temp.linux-x86_64-2.7/scipy/fftpack/src/dfftpack compile options: '-I/data/users/borm/YT/yt-x86_64/lib/python2.7/site-packages/numpy/core/include -c' f77.sh:f77: scipy/fftpack/src/dfftpack/dsint.f Cannot open file dsint.f gcc: dsint.c: No such file or directory gcc: no input files Cannot open file dsint.f gcc: dsint.c: No such file or directory gcc: no input files error: Command "/iraf/iraf/unix/hlib//f77.sh -Wall -ffixed-form -fno-second-underscore -fPIC -O3 -funroll-loops -I/data/users/borm/YT/yt-x86_64/lib/python2.7/site-packages/numpy/core/include -c -c scipy/fftpack/src/dfftpack/dsint.f -o build/temp.linux-x86_64-2.7/scipy/fftpack/src/dfftpack/dsint.o" failed with exit status 1 I've tried uncommenting the NUMPY_ARGS lines one by one as suggested in the script, but none of that seems to work. I'm using yt version 2.6.1, changeset e0906fc5b6d5, if that helps. Any ideas on how to fix this? Thanks! Cheers, Caroline _______________________________________________ yt-users mailing list yt-users(a)lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

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Creating a sphere based on enclosed mass
by Daniel Fenn 22 Jan '15

22 Jan '15

Hi everyone, Is there a straightforward way of creating a spherical data object by specifying the total enclosed mass, rather than the radius? If not, I supposed I could write an iterative algorithm that would do it, but I'd rather avoid that if there's an easier way provided by yt. Thanks for your help. Dan _______________________________________________ yt-users mailing list yt-users(a)lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

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Still having issues with parallel yt on STAMPEDE
by Rick Sarmento 21 Jan '15

21 Jan '15

Hello all, I still can’t get parallel yt running… please pass along any ideas… I’ve got the ipcluster running ok … yt 3.1 going — but I’m still getting "AttributeError: 'module' object has no attribute ‘utilities’” when trying to load a RAMSES output file… Here’s the cluster running.. 11:14:02 earnric /home1/02744/earnric $ ipcluster start --engines=MPI … 2015-01-20 23:14:10.653 [IPClusterStart] Starting 16 Engines with MPI 2015-01-20 23:14:40.657 [IPClusterStart] Engines appear to have started successfully Here are the modules loaded: 11:21:47 earnric /home1/02744/earnric $ module list Currently Loaded Modules: 1) TACC-paths 3) cluster-paths 5) cluster 7) intel/14.0.1.106 9) python/2.7.6 2) Linux 4) xalt/0.4.6 6) TACC 8) mvapich2/2.0b 10) hdf5/1.8.13 and my ENVs: 11:22:13 earnric /home1/02744/earnric $ echo $PYTHONPATH /home1/02744/earnric/.local/lib/python2.7/site-packages/:/opt/apps/intel14/mvapich2_2_0/python/2.7.6/lib/python2.7/site-packages: 11:22:23 earnric /home1/02744/earnric $ echo $PATH /home1/02744/earnric/.local/bin:/home1/02744/earnric/bin:/opt/apps/intel14/hdf5/1.8.13/x86_64/bin:/opt/apps/intel14/mvapich2_2_0/python/2.7.6/bin:/opt/apps/intel14/mvapich2/2.0b/bin:/opt/apps/intel/13/vtune_amplifier_xe_2013/bin64:/opt/apps/intel/13/composer_xe_2013_sp1.1.106/mpirt/bin/intel64:/opt/intel/sep/bin:/opt/apps/xalt/0.4.6/bin:/usr/lib64/qt-3.3/bin:/usr/local/bin:/bin:/usr/bin:/usr/X11R6/bin:/opt/ofed/bin:/opt/ofed/sbin:.:/opt/apps/intel/13/composer_xe_2013_sp1.1.106/bin/intel64:/opt/apps/intel/13/composer_xe_2013_sp1.1.106/bin/intel64_mic:/opt/apps/intel/13/composer_xe_2013_sp1.1.106/debugger/gui/intel64 11:22:31 earnric /home1/02744/earnric $ echo $LD_LIBRARY_PATH /opt/apps/intel14/mvapich2_2_0/python/2.7.6/lib:/opt/apps/intel14/mvapich2/2.0b/lib:/opt/apps/intel14/mvapich2/2.0b/lib/shared:/opt/apps/intel/13/composer_xe_2013_sp1.1.106/tbb/lib/intel64:/opt/apps/intel/13/composer_xe_2013_sp1.1.106/compiler/lib/intel64:/opt/intel/mic/coi/host-linux-release/lib:/opt/intel/mic/myo/lib:/opt/apps/intel/13/composer_xe_2013_sp1.1.106/mpirt/lib/intel64:/opt/apps/intel/13/composer_xe_2013_sp1.1.106/ipp/../compiler/lib/intel64:/opt/apps/intel/13/composer_xe_2013_sp1.1.106/ipp/lib/intel64:/opt/apps/intel/13/composer_xe_2013_sp1.1.106/compiler/lib/intel64:/opt/apps/intel/13/composer_xe_2013_sp1.1.106/mkl/lib/intel64:/opt/apps/intel/13/composer_xe_2013_sp1.1.106/tbb/lib/intel64 Here’s what I’m seeing — if you have any ideas I’d appreciate it: In [1]: from IPython.parallel import Client rc = Client() In [2]: rc.ids Out[2]: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15] In [3]: %autopx %autopx enabled In [4]: from mpi4py import MPI MPI.COMM_WORLD.Get_rank() Out[0:1]: 8 Out[1:1]: 12 Out[2:1]: 9 Out[3:1]: 6 Out[4:1]: 10 Out[5:1]: 1 Out[6:1]: 2 Out[7:1]: 11 Out[8:1]: 13 Out[9:1]: 5 Out[10:1]: 3 Out[11:1]: 14 Out[12:1]: 7 Out[13:1]: 0 Out[14:1]: 15 Out[15:1]: 4 In [7]: import yt yt.enable_parallelism() import numpy as np import os import shutil import h5py import gc import glob [0:execute]: --------------------------------------------------------------------------- AttributeError Traceback (most recent call last)<ipython-input-4-34dfdffceb1e> in <module>() ----> 1 import yt 2 yt.enable_parallelism() 3 import numpy as np 4 import os 5 import shutil /home1/02744/earnric/.local/lib/python2.7/site-packages/yt-3.1dev-py2.7-linux-x86_64.egg/yt/__init__.py in <module>() 97 from yt.utilities.logger import ytLogger as mylog 98 ---> 99 import yt.utilities.physical_constants as physical_constants 100 import yt.units as units 101 from yt.units.yt_array import \ AttributeError: 'module' object has no attribute 'utilities' [1:execute]: --------------------------------------------------------------------------- AttributeError Traceback (most recent call last)<ipython-input-4-34dfdffceb1e> in <module>() ----> 1 import yt 2 yt.enable_parallelism() 3 import numpy as np 4 import os 5 import shutil /home1/02744/earnric/.local/lib/python2.7/site-packages/yt-3.1dev-py2.7-linux-x86_64.egg/yt/__init__.py in <module>() 97 from yt.utilities.logger import ytLogger as mylog 98 ---> 99 import yt.utilities.physical_constants as physical_constants 100 import yt.units as units 101 from yt.units.yt_array import \ AttributeError: 'module' object has no attribute 'utilities' [2:execute]: --------------------------------------------------------------------------- AttributeError Traceback (most recent call last)<ipython-input-4-34dfdffceb1e> in <module>() ----> 1 import yt 2 yt.enable_parallelism() 3 import numpy as np 4 import os 5 import shutil /home1/02744/earnric/.local/lib/python2.7/site-packages/yt-3.1dev-py2.7-linux-x86_64.egg/yt/__init__.py in <module>() 97 from yt.utilities.logger import ytLogger as mylog 98 ---> 99 import yt.utilities.physical_constants as physical_constants 100 import yt.units as units 101 from yt.units.yt_array import \ AttributeError: 'module' object has no attribute 'utilities' [3:execute]: --------------------------------------------------------------------------- AttributeError Traceback (most recent call last)<ipython-input-4-34dfdffceb1e> in <module>() ----> 1 import yt 2 yt.enable_parallelism() 3 import numpy as np 4 import os 5 import shutil /home1/02744/earnric/.local/lib/python2.7/site-packages/yt-3.1dev-py2.7-linux-x86_64.egg/yt/__init__.py in <module>() 97 from yt.utilities.logger import ytLogger as mylog 98 ---> 99 import yt.utilities.physical_constants as physical_constants 100 import yt.units as units 101 from yt.units.yt_array import \ AttributeError: 'module' object has no attribute 'utilities' ... 12 more exceptions ... Cheers! Rick Sarmento SESE Astronomy/Astrophysics Grad Student rsarment(a)asu.edu _______________________________________________ yt-users mailing list yt-users(a)lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

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Re: [yt-users] ipython on a cluster
by Nathan Goldbaum 20 Jan '15

20 Jan '15

Hey Rick, Can we keep this discussion on the mailing list? Just in case others in the future have similar problems. How did you install yt? If you used the install script, did you remember to activate the yt environment before launching ipcluster? Is IPython installed into yt's environment? -Nathan On Tue, Jan 20, 2015 at 3:31 PM, Rick Sarmento <rsarment(a)asu.edu> wrote: > Hum… I used the ipcluster command on the vis node I’m using > > And I get through all your init steps: > > In [1]: > > from IPython.parallel import Client > rc = Client() > In [2]: > > rc.ids > Out[2]: > [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15] > In [3]: > > %autopx > %autopx enabled > > In [4]: > > from mpi4py import MPI > > MPI.COMM_WORLD.Get_rank() > > Out[0:1]: 8 > Out[1:1]: 1 > Out[2:1]: 14 > Out[3:1]: 7 > Out[4:1]: 9 > Out[5:1]: 15 > Out[6:1]: 6 > Out[7:1]: 12 > Out[8:1]: 4 > Out[9:1]: 0 > Out[10:1]: 5 > Out[11:1]: 10 > Out[12:1]: 2 > Out[13:1]: 11 > Out[14:1]: 3 > Out[15:1]: 13 > In [5]: > > > But then it can’t find yt!! > > import yt > yt.enable_parallelism() > import numpy as np > import os > import shutil > import h5py > import gc > import glob > > > AttributeError Traceback (most recent call last)<ipython-input-3-915313e529f2> in <module>()----> 1 import yt > > ... > > > Weird tho … cuz if I kill the cluster and try again, import YT loads… *Can > you think of anything obvious?* It’s like my path to yt goes away once I > start the cluster … and I’m getting some default version (old) on stampede. > > Thanks Nathan .. I’m watching the tutorial now … > > *Cheers!* > > *Rick Sarmento* > SESE Astronomy/Astrophysics Grad Student > rsarment(a)asu.edu > > > > > > > > On Jan 17, 2015, at 12:54 PM, Rick Sarmento <rsarment(a)asu.edu> wrote: > > Thanks for the info Nathan… > > I’m trying to use STAMPEDE out at Texas (http://vis.tacc.xsede.org/), and > they have a way to kick-off access to their 16 core visualization nodes via > the web… But that probably doesn’t help given the info below. I’ll try to > work with support to see how I can get it to work… > > If I start the cluster using your instructions (via a ssh session), below, > I’d have to login — but then I can’t get remote access to the notebook > interface because of the firewalls, etc. Although there’s like a way to > setup an ssh tunnel, I haven’t figured it out yet. > > Thx! > > *Cheers!* > > *Rick Sarmento* > SESE Astronomy/Astrophysics Grad Student > rsarment(a)asu.edu > > Hi Rick, > > You need to launch the notebook in parallel using an MPI parallel IPython > cluster. In addition, you will need to configure the notebook to hook into > IPython's built-in parallelism. > > I've uploaded a notebook that uses parallel IPython here: > > http://nbviewer.ipython.org/gist/ngoldbaum/32ca07cf4f5b3dd06add > > Note that all the yt operations aren't really important, but the first few > cells where I check to make sure IPython's parallelism works and that MPI > parllelism is working are quite important. > > Note also that you will need to launch the IPython cluster separately from > the notebook server using the "ipcluster" command. > > If you want to learn more about parallel IPython, I'd encourage you to > take a look at Min Ranger-Kelley's tutorial from scipy 2014: > http://pyvideo.org/video/2738/interactive-parallel-computing-with-ipython-p… > > All that said, it does add a significant amount of semantic overhead to > use the IPython notebook in parallel. It's generally much more > straightforward to work with yt in parallel using regular python scripts. > > Hope that helps, > > Nathan > > > _______________________________________________ yt-users mailing list yt-users(a)lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

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Index error while using covering_grid
by Yang Haifeng 18 Jan '15

18 Jan '15

Dear yt users, I am trying to make covering_grid from an enzo simulation. The code is very simple: (somewhat sloppy since it's running with ipython. ) ds=yt.load("data0201") ad_c=ds.covering_grid(level=3, left_edge=0.4375, dims=[64,64,64]) ad_c["x"] where the ad_c["x"] will give an Index Error on my desktop. However, the same piece of code runs great in a different machine. The version of yt are the same in both machines, which is 3.0.2. Both of them installed yt through anaconda. The error message I got was following. Thanks for your help! --------------------------------------------------------------------------- IndexError Traceback (most recent call last) <ipython-input-6-ff78a8bccc54> in <module>() ----> 1 ad_c["x"] /home/fxyang/software/anaconda/lib/python2.7/site-packages/yt/data_objects/data_containers.pyc in __getitem__(self, key) 243 if f in self._container_fields: 244 self.field_data[f] = \ --> 245 self.ds.arr(self._generate_container_field(f)) 246 return self.field_data[f] 247 else: /home/fxyang/software/anaconda/lib/python2.7/site-packages/yt/data_objects/construction_data_containers.pyc in _generate_container_field(self, field) 587 np.multiply(rv, self.dds[2], rv) 588 elif field == ("index", "x"): --> 589 x = np.mgrid[self.left_edge[0] + 0.5*self.dds[0]: 590 self.right_edge[0] - 0.5*self.dds[0]: 591 self.ActiveDimensions[0] * 1j] /home/fxyang/software/anaconda/lib/python2.7/site-packages/yt/units/yt_array.pyc in __getitem__(self, item) 981 982 def __getitem__(self, item): --> 983 ret = super(YTArray, self).__getitem__(item) 984 if ret.shape == (): 985 return YTQuantity(ret, self.units) IndexError: too many indices for array -- Best, Haifeng

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parallel computation
by Yuxiang Qin 17 Jan '15

17 Jan '15

Dear YT-Users, I am a fresh man to YT-project. I got a few questions for parallel computation on yt. May I ask for help? I tried to do mpirun -np 4 myscript.py , but it always failed even when I used very simple script like #!/usr/bin/env python import yt yt.enable_parallelism() fname=('../../Smaug/NOZCOOL_LateRe_L010N0512/data/snapshot_103/snap_103.0.hdf5') ds = yt.load(fname) pz = yt.ProjectionPlot(ds, 'z', ('gas', 'temperature'),weight_field='density') pz.save() I am using the data from Dr. Alan Duffy. His data is similar to OWLS. So when I tried to run a similar script with sample data downloaded from yt website, it works. Does anyone know what’s going on here? Is anything wrong with my data format or script? How to check it? Warmest sincerely, -- Yuxiang Qin PhD Student School of Physics The University of Melbourne VIC, Australia, 3010 _______________________________________________ yt-users mailing list yt-users(a)lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

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