Mailman 3 February 2011 - yt-users

modify - radiation pressure
by Elizabeth Harper-Clark Feb. 21, 2011

Feb. 21, 2011

Hi all, I would like to plot radiation pressure vectors in the style of p.modify["velocity"](). Now, my radiation pressure acceleration is in my data as three baryon fields (they appear in pf.h.field_list) : RadAccel1, RadAccel2, RadAccel3 for the three spacial dimensions. Now I am embarrassed to admit I have not done much yt development in the past so I was hoping someone more familiar with the code could point me in the direction of where I can add code for this? I am hoping it will be as simple as finding all the places code exists for p.modify["velocity"]() and copy and paste it changing the fields used to the radiation pressure ones. Will it be? Where is the code for p.modify["velocity"]()? Are there any tricky bits I should be aware of? Many 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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Re: [yt-users] error when running on cluster nodes
by Stephen Skory Feb. 18, 2011

Feb. 18, 2011

Tsz Ka, > I used the same python (~/yt-ppc64/bin/python) as I did in the command > line. I think I tried python2.6 but I got the same error. (Actually how > are they different?) The machine I am using is the Turing cluster in UI > (http://www.cse.illinois.edu/turing/), which is an Apple Xserve cluster > using G5 processors. You can find on the website some information about > it. Sorry I am not that familiar with cluster issues. I suppose the > nodes have full installation, though I don't know where to check. I am > using the default compilers on Turing, which are gcc for C/C++ and xlf > for Fortran. I'm going to chime in here. I noticed that on their FAQ page: http://www.cse.illinois.edu/turing/faq.html There's something about path problems on compute nodes. Your error could be due to a library problem (i.e. DYLD_LIBRARY_PATH). Have you tried submitting your job with a "#PBS -V" that keeps your environment for the job? Matt may have some other bright ideas... Stephen Skory stephenskory(a)yahoo.com http://stephenskory.com/ 510.621.3687 (google voice)

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error when running on cluster nodes
by Tsz Ka Li Feb. 17, 2011

Feb. 17, 2011

Hi all, I run into an error which occurs when I submit a yt script to run on cluster nodes. The script runs successfully from the command line though, and I am NOT running MPI here. The error is as follows: /Traceback (most recent call last): File "MergerTree.py", line 1, in <module> from yt.mods import * File "/turing/home/tszkali2/yt-ppc64/src/yt-hg/yt/mods.py", line 92, in <module> from yt.visualization.api import \ File "/turing/home/tszkali2/yt-ppc64/src/yt-hg/yt/visualization/api.py", line 34, in <module> from plot_collection import \ File "/turing/home/tszkali2/yt-ppc64/src/yt-hg/yt/visualization/plot_collection.py", line 26, in <module> from matplotlib import figure File "/turing/home/tszkali2/yt-ppc64/lib/python2.6/site-packages/matplotlib/figure.py", line 16, in <module> import artist File "/turing/home/tszkali2/yt-ppc64/lib/python2.6/site-packages/matplotlib/artist.py", line 6, in <module> from transforms import Bbox, IdentityTransform, TransformedBbox, TransformedPath File "/turing/home/tszkali2/yt-ppc64/lib/python2.6/site-packages/matplotlib/transforms.py", line 34, in <module> from matplotlib._path import affine_transform ImportError: /turing/home/tszkali2/yt-ppc64/lib/python2.6/site-packages/matplotlib/_path.so: undefined symbol: _ZZN2Py15PythonExtensionINS_22ExtensionModuleBasePtrEE9behaviorsEvE1p/ Apparently it is related to matplotlib. I tried to do something similar to the instructions on the wiki for CrayXT5 Installation (http://yt.enzotools.org/wiki/CrayXT5Installation) in the section 'Running on a compute node', but I still got the same error. Does anyone have ideas on what this means? I appreciate any help from you. Thanks, Tsz Ka

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Re: [yt-users] Couldn't figure out output type?
by Stephen Skory Feb. 15, 2011

Feb. 15, 2011

Hi Tsz Ka, >> yt ERROR 2011-02-15 19:40:44,354 Couldn't figure out > output type for DD0025/DD0025 I was able to reproduce your problem, and it appears that now a "from yt.mods import *" is required at the top of the merger tree script. The examples as they are currently in the docs will not work - that will be fixed soon. Please add that line and let us know if you still have problems. Stephen Skory stephenskory(a)yahoo.com http://stephenskory.com/ 510.621.3687 (google voice)

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Re: [yt-users] Couldn't figure out output type?
by Stephen Skory Feb. 15, 2011

Feb. 15, 2011

Hi Tsz Ka, > line 219, in _run_halo_finder_add_to_db >> self.period = self.pf.domain_right_edge - > self.pf.domain_left_edge >> AttributeError: 'MergerTree' object has no attribute 'pf' > Sorry for the error! I just made a simple fix, and if you update your yt install, it should work now (or fail for an entirely different reason!). Let us know if you have more problems. Stephen Skory stephenskory(a)yahoo.com http://stephenskory.com/ 510.621.3687 (google voice)

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Couldn't figure out output type?
by Tsz Ka Li Feb. 15, 2011

Feb. 15, 2011

Hi, I am running into an error when trying to build the merger tree database for a dark matter only unigrid simulation. The error is as follows: //turing/home/tszkali2/yt-ppc64/src/yt-hg/yt/analysis_modules/halo_merger_tree/merger_tree.py:27: DeprecationWarning: the md5 module is deprecated; use hashlib instead import os, glob, time, gc, md5, sys yt ERROR 2011-02-15 17:22:56,701 Couldn't figure out output type for DD0025/DD0025 Traceback (most recent call last): File "MergerTree.py", line 25, in <module> MergerTree(restart_files=files, database=my_database) File "/turing/home/tszkali2/yt-ppc64/src/yt-hg/yt/analysis_modules/halo_merger_tree/merger_tree.py", line 186, in __init__ self._run_halo_finder_add_to_db() File "/turing/home/tszkali2/yt-ppc64/src/yt-hg/yt/analysis_modules/halo_merger_tree/merger_tree.py", line 219, in _run_halo_finder_add_to_db self.period = self.pf.domain_right_edge - self.pf.domain_left_edge AttributeError: 'MergerTree' object has no attribute 'pf'/ Does anyone know why it "couldn't figure out output type for DD0025/DD0025"? I load DD0025/DD0025 separately it is just fine. The script I used is just the basic one from the online documentation: /from yt.analysis_modules.halo_merger_tree.api import * # Pick our snapshots to use. files = [] start = 25 finish = 320 for i in range(start, finish + 1): files.append('DD%04d/DD%04d' % (i, i)) my_database = 'halos.db' # Build the tree. MergerTree(restart_files=files, database=my_database) / I am using yt v2.0 and enzo v2.0. Thank you very much for answering my question. Cheers, Tsz Ka

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arr_vec2pix_nest?
by Michael Kuhlen Feb. 14, 2011

Feb. 14, 2011

Hi I just updated my yt distribution to the most recent yt-branch changeset (8f67aaa2e0d), and I now get this error: >>> from yt.mods import * Traceback (most recent call last): File "<stdin>", line 1, in <module> File "/global/home/users/mqk/local/yt-x86_64/yt/yt/mods.py", line 97, in <module> from yt.visualization.volume_rendering.api import \ File "/global/home/users/mqk/local/yt-x86_64/yt/yt/visualization/volume_rendering/api.py", line 44, in <module> from camera import Camera, PerspectiveCamera, StereoPairCamera File "/global/home/users/mqk/local/yt-x86_64/yt/yt/visualization/volume_rendering/camera.py", line 33, in <module> from yt.utilities.amr_utils import TransferFunctionProxy, VectorPlane, \ ImportError: cannot import name arr_vec2pix_nest It works fine if I just comment out the 'arr_vec2pix_nest, arr_pix2vec_nest' from the import in yt/visualization/volume_rendering/camera.py. Mike -- ********************************************************************* * * * Dr. Michael Kuhlen Theoretical Astrophysics Center * * email: mqk(a)astro.berkeley.edu UC Berkeley * * cell phone: (831) 588-1468 601 Campbell Hall * * skype username: mikekuhlen Berkeley, CA 94720 * * * *********************************************************************

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basic plotting questions
by Molly Peeples Feb. 9, 2011

Feb. 9, 2011

Hi, I have a few quick questions: 1. How can I label the boxsize/axes for, e.g., box projections/slices? 2. How can I draw/outline the grid on a slice so it's immediately obvious what the resolution is? I know these are pretty basic questions, but after several hours of search I haven't been able to solve them... Thanks! --Molly

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p = pc.add_slice("Density", ax)
by Agarwal, Shankar Feb. 9, 2011

Feb. 9, 2011

Hi, I have made gas density projections (attached) for two identical simulations, except than one was run with GriDims=512 while the second was run with GridDims=1024. The BoxSize=200 Mpc/h and ParticleDims=256 for both. Can anyone tell me why does the 1024grid.png look a lot grainier than the 512grid.png ? Is it something to do with this command... p = pc.add_slice("Density", ax) I guess the slice is too thin for 1024, so I can't really compare the 2 plots. Let me know. Sorry to have attached 2 huge files. Are there other ways? Shankar

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yt installation
by Orsola De Marco Feb. 9, 2011

Feb. 9, 2011

Dear yt users, I have an installation issue on my Mac running Snow Leopard 10.6.5 with ifort Something to do with Python installation and zlib. Can anybody help? I am appending the log file of the error. Thanks, Orsola Orsola De Marco, Ph.D. Associate Professor Department of Physics & Astronomy Macquarie University Sydney, NSW 2109 Australia Tel: +61 2 9850 4241 Fax: +61 2 9850 8115 http://web.science.mq.edu.au/~orsola/ orsola.demarco(a)mq.edu.au

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