yt-users November 2011

yt-users@python.org

22 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

8 14

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.

6 8

pickle
by Elizabeth Tasker 02 Dec '11

02 Dec '11

Hi, A bigger problem.... The lastest version of yt The current version of the code is: --- a519b8754ba8 (yt) tip --- has problems with pickle. If I pickle a data set and then try and unpickle it, I see: unpickle core data --------------------------------------------------------------------------- KeyError Traceback (most recent call last) /home/tasker/yt/src/yt-hg/scripts/iyt in <module>() 338 339 #file = open('cores.pickle','rb') --> 340 allcloudcores = cPickle.load(file('cores.pickle', 'rb')) 341 file.close() 342 /home/tasker/yt/src/yt-hg/yt/data_objects/data_containers.pyc in _reconstruct_object(*args, **kwargs) 3676 else: new_args.append(arg) 3677 pfs = ParameterFileStore() -> 3678 pf = pfs.get_pf_hash(pfid) 3679 cls = getattr(pf.h, dtype) 3680 obj = cls(*new_args) /home/tasker/yt/src/yt-hg/yt/utilities/parameter_file_storage.pyc in get_pf_hash(self, hash) 106 def get_pf_hash(self, hash): 107 """ This returns a parameter file based on a hash. """ --> 108 return self._convert_pf(self._records[hash]) 109 110 def get_pf_ctid(self, ctid): KeyError: (('283b7c4d88671dbff7acf083098da6ae',), <function _reconstruct_object at 0x272c938>, ('283b7c4d88671dbff7acf083098da6ae', 'region', array([ 16., 16., 16.]), array([ 0., 0., 0.]), array([ 32., 32., 32.]), {'disk_center': array([16, 16, 16]), 'center': array([ 16., 16., 16.]), 'bulk_velocity': array([ 0., 0., 0.]), 'disk_vector': array([0, 0, 1]), 'disk_radius': array([ 0.1 , 0.1358, 0.1716, 0.2074, 0.2432, 0.279 , The fact it mentions the field parameters in the last line, might mean it's an error introduced because of the corrections to them (that I have been demanding!)? The script I have works fine (pickles and all) on yt version: --- 16e8d749a806 (yt) tip --- Elizabeth

2 13

field parameters (you know I want to use them everywhere...)
by Elizabeth Tasker 01 Dec '11

01 Dec '11

Hi, Two small problems: 1. Another issue with field parameters. I can't pass them to a slice if the derived field also needs ValidateSpatial. i.e. def _EffectivePotential(field, data): center = na.array(data.get_field_parameter("disk_center")) h_vec = na.array(data.get_field_parameter("disk_vector")) omega = na.array(data.get_field_parameter("thiscore_omega")) . . blah . . add_field("EffectivePotential", function=_EffectivePotential, validators=[ValidateSpatial(1, ["x-velocity", "y-velocity", "z-velocity", "x", "y", "z"])]) p = pc.add_slice("EffectivePotential", 2, field_parameters={"disk_vector":disk_vector, "disk_center":disk_center, "thiscore_omega":core_omega[c]}) can't find its field parameters but if I change the end line of the function to: add_field("EffectivePotential", function=_EffectivePotential) everything is fine. It actually seems to work OK even without the ValidateSpatial (I have cross products in the function so pain has the potential to happen without the full data) so perhaps this isn't a problem, but I think it is a small bug? 2. For some reason, yt has decided to save all my image files in: /home/tasker/.yt/my_plugins.py_Slice_z_EffectivePotential.png This is less than intuitive. Does anyone know why and how I can stop it? Thanks! Elizabeth

2 4

Registration for yt workshop in January 2012 is open
by matthewturk＠gmail.com 29 Nov '11

29 Nov '11

If you have trouble viewing or submitting this form, you can fill it out online: https://docs.google.com/spreadsheet/viewform?formkey=dElGU0sxcXRHNmlCZW5GOW… yt workshop 2012 registration Registration is now open for the yt workshop, to be held at the FLASH center in Chicago, from Jan 24-26, 2012. This workshop will start with basic yt usage, move on to advanced and parallel usage, and then finally address how to modify, extend and contribute to yt. For more information, see the blog post: http://blog.yt-project.org/announcing-the-2012-yt-workshop and keep an eye on http://yt-project.org/workshop2012/ for more info. We have secured housing in downtown Chicago (near the river, just off Michigan Avenue) that we are able to book double-occupancy rooms for $99/night, pre-tax. We are eagerly pursuing funding opportunities and are very optimistic about their prospects, but we are still waiting on funding for participant costs. If we are able to secure funding, it will likely cover hotel costs for most attendees as well as a number of small travel grants. We have reserved the block of rooms for four nights, starting the 23rd and including the final day of the conference, to encourage attendance at all three days. We also hope to offer a social gathering and a trip to the Adler planetarium during the workshop. This is the registration form: PLEASE FILL IT OUT EVEN IF YOU FILLED OUT THE PREVIOUS SURVEY. We have used the pre-registration form to gauge interest, secure accommodations, and request funding, and we are now looking for binding commitments. There are also several questions here that will help us in constructing a set of talks and tutorials for the first portion of the workshop. If you indicate you would like to stay in the hotel block of rooms, we will contact you with more information about securing your reservation. Organizing Committee: Matthew Turk, Britton Smith, John ZuHone (For inquiries: workshop2012(a)yt-project.org ) Name * Email address * I would like to stay in the block of rooms allocated for the workshop. These rooms are at below-market prices and will cost $99/night plus tax per room. Preference will be given to those willing to share a room; assignments and roommate information can be decided later. Yes (and I am willing to share a room) Yes (and I am unwilling to share a room) No I require funding for: Hotel funding may be contingent on sharing a room. While we are still awaiting information about funding, we are optimistic that both hotel and limited travel grants will be available. Hotel Travel What is your skill level with yt? What is your skill level with Python / NumPy / matplotlib? If appropriate, what would you consider your primary simulation code to be? Enzo FLASH RAMSES Boxlib-based code Chombo-based code ART Gadget Other: Position What position do you currently occupy? Undergraduate student Graduate student Postdoctoral Researcher Faculty Staff Scientist Other: Do you have any dietary concerns that may be relevant? Any other comments or suggestions? Powered by Google Docs Report Abuse - Terms of Service - Additional Terms

2 1

Installing yt without hg
by david collins 29 Nov '11

29 Nov '11

Hi there-- I'm on a system that has a pretty fierce firewall so that things like pip, wget, and mercurial can't see the outside world through any http based protocol. I got the zips from a different machine and things worked basically fine until I got to the bit where it tries to install easy_install. (error below) Has anyone had experience with such a problem, and have suggestions for getting around the need for a network connection? Thanks, d. Installing easy_install script to /usr/projects/magnetic/david_c/local/bin Installing easy_install-2.7 script to /usr/projects/magnetic/david_c/local/bin Installed /usr/projects/magnetic/david_c/local/lib/python2.7/site-packages/distribute-0.6.21-py2.7.egg Processing dependencies for distribute==0.6.21 Finished processing dependencies for distribute==0.6.21 After install bootstrap. Creating /usr/projects/magnetic/david_c/local/lib/python2.7/site-packages/setuptools-0.6c11-py2.7.egg-info Creating /usr/projects/magnetic/david_c/local/lib/python2.7/site-packages/setuptools.pth Searching for pip Reading http://pypi.python.org/simple/pip/ Download error on http://pypi.python.org/simple/pip/: timed out -- Some packages may not be found! Reading http://pypi.python.org/simple/pip/ Download error on http://pypi.python.org/simple/pip/: timed out -- Some packages may not be found! Couldn't find index page for 'pip' (maybe misspelled?) Scanning index of all packages (this may take a while) Reading http://pypi.python.org/simple/ Download error on http://pypi.python.org/simple/: timed out -- Some packages may not be found! No local packages or download links found for pip error: Could not find suitable distribution for Requirement.parse('pip') -- Sent from my computer.

6 8

only_on_root
by Christine Simpson 22 Nov '11

22 Nov '11

Hi, I'm trying to run a script with parallel yt that does some non-yt io. I'm a little confused about how to use only_on_root. Here is a test script I've tried: from yt.mods import * from yt.visualization.api import PlotCollection import matplotlib.colorbar as cb path = "/scratch/01112/tg803911/halo88_therm_feed_3.7e-6_LW_RadiationShield_lmax12/DD0010/" fn = "output_0010" pf = load(path+fn) pc = PlotCollection(pf) pc.add_projection("Density",0) pc.set_width(20,'kpc') pc.save(fn) filename = 'hello_world' file = only_on_root(open(filename,'w')) only_on_root(file.write("hello_world \n")) only_on_root(file.close()) Pasted below is the error. I'm uncertain about the syntax of only_on_root. Do I just wrap it around normal commands? Also, it seems that the write command is trying to execute on all the processors. That shouldn't be happening, right? P007 yt : [INFO ] 2011-11-22 09:50:20,558 Saved output_0010_Projection_x_Density.png P008 yt : [INFO ] 2011-11-22 09:50:20,558 Saved output_0010_Projection_x_Density.png P009 yt : [INFO ] 2011-11-22 09:50:20,560 Saved output_0010_Projection_x_Density.png Traceback (most recent call last): Traceback (most recent call last): File "test_parallel_yt.py", line 19, in <module> File "test_parallel_yt.py", line 19, in <module> Traceback (most recent call last): File "test_parallel_yt.py", line 19, in <module> only_on_root(file.write("hello_world \n")) AttributeError: 'NoneType' object has no attribute 'write' only_on_root(file.write("hello_world \n")) AttributeError : only_on_root(file.write("hello_world \n")) 'NoneType' object has no attribute 'write' P010 yt : [INFO ] 2011-11-22 09:50:20,561 Saved output_0010_Projection_x_Density.png AttributeErrorP011 yt : [INFO ] 2011-11-22 09:50:20,561 Saved output_0010_Projection_x_Density.png : 'NoneType' object has no attribute 'write' Traceback (most recent call last): File "test_parallel_yt.py", line 19, in <module> only_on_root(file.write("hello_world \n")) Traceback (most recent call last): AttributeError: File "test_parallel_yt.py", line 19, in <module> 'NoneType' object has no attribute 'write' P005 yt : [INFO ] 2011-11-22 09:50:20,562 Saved output_0010_Projection_x_Density.png P004 yt : [INFO ] 2011-11-22 09:50:20,562 Saved output_0010_Projection_x_Density.png only_on_root(file.write("hello_world \n")) AttributeError: 'NoneType' object has no attribute 'write' Traceback (most recent call last): File "test_parallel_yt.py", line 19, in <module> only_on_root(file.write("hello_world \n")) AttributeError: 'NoneType' object has no attribute 'write' Traceback (most recent call last): File "test_parallel_yt.py", line 19, in <module> only_on_root(file.write("hello_world \n")) AttributeError: 'NoneType' object has no attribute 'write' Traceback (most recent call last): File "test_parallel_yt.py", line 19, in <module> only_on_root(file.write("hello_world \n")) AttributeError: 'NoneType' object has no attribute 'write' P002 yt : [INFO ] 2011-11-22 09:50:20,583 Saved output_0010_Projection_x_Density.png Traceback (most recent call last): File "test_parallel_yt.py", line 19, in <module> only_on_root(file.write("hello_world \n")) AttributeError: 'NoneType' object has no attribute 'write' P001 yt : [INFO ] 2011-11-22 09:50:20,589 Saved output_0010_Projection_x_Density.png P003 yt : [INFO ] 2011-11-22 09:50:20,589 Saved output_0010_Projection_x_Density.png Traceback (most recent call last): File "test_parallel_yt.py", line 19, in <module> only_on_root(file.write("hello_world \n")) AttributeError: 'NoneType' object has no attribute 'write' Traceback (most recent call last): File "test_parallel_yt.py", line 19, in <module> only_on_root(file.write("hello_world \n")) AttributeError: 'NoneType' object has no attribute 'write' P013 yt : [INFO ] 2011-11-22 09:50:20,593 Saved output_0010_Projection_x_Density.png P014 yt : [INFO ] 2011-11-22 09:50:20,593 Saved output_0010_Projection_x_Density.png Traceback (most recent call last): File "test_parallel_yt.py", line 19, in <module> only_on_root(file.write("hello_world \n")) AttributeError: 'NoneType' object has no attribute 'write' Traceback (most recent call last): File "test_parallel_yt.py", line 19, in <module> only_on_root(file.write("hello_world \n")) AttributeError: 'NoneType' object has no attribute 'write' P012 yt : [INFO ] 2011-11-22 09:50:20,596 Saved output_0010_Projection_x_Density.png Traceback (most recent call last): File "test_parallel_yt.py", line 19, in <module> only_on_root(file.write("hello_world \n")) AttributeError: 'NoneType' object has no attribute 'write' P015 yt : [INFO ] 2011-11-22 09:50:20,599 Saved output_0010_Projection_x_Density.png Traceback (most recent call last): File "test_parallel_yt.py", line 19, in <module> only_on_root(file.write("hello_world \n")) AttributeError: 'NoneType' object has no attribute 'write' P000 yt : [INFO ] 2011-11-22 09:50:21,410 Saved output_0010_Projection_x_Density.png Traceback (most recent call last): File "test_parallel_yt.py", line 18, in <module> file = only_on_root(open(filename,'w')) File "/share/home/01112/tg803911/yt_17May2011/yt-x86_64/src/yt-hg/yt/funcs.py", line 357, in only_on_root return func(*args, **kwargs) TypeError: 'file' object is not callable mpispawn.c:303 Unexpected exit status Child exited abnormally! Killing remote processes...DONE

4 3

YT on NASA Pleiades
by James Guillochon 17 Nov '11

17 Nov '11

I am getting a failure in the "load" statement when trying to run YT on NASA Pleiades. It seems that it is having problems with the numpy package. Here is the traceback: http://paste.yt-project.org/show/1947/ My script is just: from yt.mods import * > load('filename') Any ideas? -- James Guillochon Department of Astronomy & Astrophysics University of California, Santa Cruz jfg(a)ucolick.org

3 6

rendering with streamlines
by Bo Zhao 14 Nov '11

14 Nov '11

Dear all, I'm new to yt. Got a very basic question here: If I want to render a volume image(say "density"), along with some magnetic or velocity streamlines. Is there a way to plot both together? Thanks a lot beforehand! Sincerely Bo Zhao ======================

2 1

re-calculate function
by Elizabeth Tasker 10 Nov '11

10 Nov '11

Hi, Simpler question (I think!) Can I force yt to re-calculate a derived field? I'd like to call dd["Radius"] muliple times, but changing the position of the center field parameter in the same script. Currently, yt knows it's already calculated dd["Radius"] once and doesn't repeat it, even though "center" has changed. Ideally, I'd like to clear just that field, so yt doesn't go and recalculate any other fields. Elizabeth

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yt-users November 2011