yt-users May 2011

yt-users@python.org

26 participants
34 discussions

by Elizabeth Tasker

Hi, Is there any way in yt to get a script to delete (or ignore) all the .yt and .harray files and clear its memory? I run into errors when I'm re-doing a plot or I've re-run the simulation and over-written the last data set I looked at with yt. I have to exit yt, delete the above files by hand and restart, which is a bit of a pain. Elizabeth

10 years, 1 month

new fields in output

by Elizabeth Tasker

Hi, I've added PotentialField to the data that gets outputted. I'd like to read this into yt, but how does this work when yt won't be expecting PotentialField to be one of the data sets? Elizabeth

10 years, 3 months

Reason

by Christine Simpson

Hi all, I'm not sure if this is the right list to send this to, but I think a bunch of knowledgeable people read this one, and hopefully one of you can help me. I'm trying to use Reason and I'm kind of confused about the ssh tunneling part. I start up yt serve on a remote machine (ranger) and I'm told to create a ssh tunnel by executing these commands: ~C -L55185:localhost:55185 My local machine doesn't recognize "~C" and I'm not sure what it is either. I tried creating an ssh tunnel with this: ssh tg803911(a)ranger.tacc.utexas.edu -L 55185:localhost:55185 I was then able to successfully open the gui in a browser with the url provided, but I am unable to load data (I can view the help though). In order to do the ssh tunnel properly do I need to install something on my local machine? Christine

10 years, 4 months

Trestles module

by Matthew Turk

Hi all, Adam Jundt at SDSC just let me know that there's now a yt module on Trestles. If you're running there you should be able to load yt with "module load yt". We now have modules at Trestles, Nautilus, Kraken and I'm also told on Odyssey and SciNet. Having modules created for community usage is a strategy we're going to try to keep pursuing, so let me know if there are modules elsewhere; this will soon be on a central wiki or document of "maintained installations." Best, Matt

10 years, 4 months

Support for cylindrical coordinates?

by Pan, Kuo-Chuan

Hi, Does yt support FLASH data with 2D cylindrical coordinates? If yes, how to enable it? If not, is it easy to implement it? I couldn't find info about it in the website. Thank you very much. Sincerely yours, Kuo-Chuan

10 years, 4 months

question about the star analysis module

by Christine Simpson

Hi all, I have a question about the star analysis module. I understand how to run it and print out a file with the results, but is there a way to run it and access the results within the script? I am ignorant of how classes work in python, and I am uncertain whether there is a trivial way to access the contents of a star analysis object, or whether I need a method to access its contents. I looked at the code for the class and I didn't see a method that does this, so I'm guessing there is a simple way to do this? Christine

10 years, 4 months

YT's treecode

by Andrew Davis

Hello again, First, thanks for the code fix. I am, however having some problems with the speed up -- at the moment, I'm not seeing any, unfortunately. I'm testing this with ~ 140000 cells of a zoom in AMR simulation. The number of levels in the region is 11, so it's very similar to what is posted on the YT clump-finding help page (http://yt.enzotools.org/doc/analysis_modules/clump_finding.html#treecode-op…) -- namely the first figure for L=10 dataset with slightly fewer cells. When I run: > sp = pf.h.sphere(c,0.065/pf['pc']) > pot = sp.quantities["IsBound"](truncate=False, include_thermal_energy=False, treecode=False, opening_angle=0.0) the timing is just ~230 seconds. However, just changing to opening_angle=1.0 and treecode=True, the time is roughly 900 seconds. Higher opening angles only decrease the time by a little bit (opening_angle = 8.0 takes rougly 850 seconds). The error is still very small, so it is calculating the right number at least, just slower than I think it should, as the figures on the help page suggest around a factor of two speedup is expected. Is there anything that you see that I'm doing wrong? Thanks! Andrew ************************************************************* ** Andrew J. Davis andrew.davis(a)yale.edu ** ** Dept. of Astronomy 203-432-5119 ** ** Yale University www.astro.yale.edu/adavis ** *************************************************************

10 years, 4 months

Treecode question

by Andrew Davis

Hi folks, I just updated my yt yesterday to use the new treecode algorithm in calculating binding energies. Many many thanks to those who worked on it and tested it. However, I'm looking at the code, and I see this in the function (on line 388 of derived_quantities.py): octree = Octree(cover_ActiveDimensions, 1, True) #print 'here', cover_ActiveDimensions # Now discover what levels this data comes from, not assuming # symmetry. dxes = na.unique(data['dx']) # unique returns a sorted array, dyes = na.unique(data['dy']) # so these will all have the same --->>>> dzes = na.unique(data['dx']) # order. # We only need one dim to figure out levels, we'll use x. dx = 1./data.pf.domain_dimensions[0] I've marked the line where I would think it should be getting data['dz'] instead of 'dx'. Am I just not getting this or should this be changed? Thanks! Andrew ************************************************************* ** Andrew J. Davis andrew.davis(a)yale.edu ** ** Dept. of Astronomy 203-432-5119 ** ** Yale University www.astro.yale.edu/adavis ** *************************************************************

10 years, 4 months

halo profiling memory problem

by gso＠physics.ucsd.edu

Hi Stephen, I'm trying to do halo profiling with parallelHP on a 1024 cube dataset 14 Mpc/h at z=5. I used to be able to do this on data of the same size on Triton with 256GB of RAM, and I'm trying it on Nautilus with the same amount of RAM. Should I be using more processors for faster results or should I cut down the number of processors as there's memory overhead as I increase the core count? From G.S.

10 years, 4 months

Re: [yt-users] Problem with common unstable branch on Kraken

by Anthony Harness

Britton, Adding those lines works for the stable install, which I guess is maintained by Hari. My problem was running the unstable install maintained by Stephen, which he informed me does not work in parallel. As Stephen mentioned before, if Hari could update his development install, I could use that instead. Thanks, Anthony

10 years, 4 months

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yt-users May 2011