Mailman 3 April 2011 - yt-users

installing yt behind a firewall
by Wolfram Schmidt 28 Apr '11

28 Apr '11

Hi everyone, perhaps, others also have encountered the situation of having to install yt on a machine with tight security measures that do not allow access to the internet through its firewall. An awkward, yet doable workaround is to mount the installation directory via sshfs on a machine outside the firewall (let's call it machine B) to download the required packages and to execute everything else on machine A behind the firewall. With the most recent yt version, I encountered a problem once the installation of Python was completed. Going back to machine B to download the yt distribution, I found that the previously installed hg wouldn't work. The last lines of the installation log (see attachment) show that hg, running on machine B, attempts to use Python under the path that applies to machine A (/home/hlrb2/pr47bi/lu78tar3/yt/... instead of /home/raid2/schmidt/hlrb2/yt/...), athough I set DEST_DIR to the (sshfs-mounted) path that applies to machine B. What should I do about that? Cheers, Wolfram

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white background instead of black, for rendered images.
by Agarwal, Shankar 27 Apr '11

27 Apr '11

Hi, While volume rendering, is it possible to choose a white background instead of black? It may not look good on white but I just thought of trying that. I looked briefly at the source code but could not figure out where to make a change. Thanks Shankar ________________________________ From: yt-users-bounces(a)lists.spacepope.org [yt-users-bounces(a)lists.spacepope.org] on behalf of Britton Smith [brittonsmith(a)gmail.com] Sent: Monday, April 18, 2011 12:36 PM To: Discussion of the yt analysis package Subject: Re: [yt-users] VR: colorbar and camera Hi Shankar, Omega_baryon is not stored in the Enzo parameter file. You'll have to set it manually. Britton On Mon, Apr 18, 2011 at 12:44 PM, Agarwal, Shankar <sagarwal(a)ku.edu<mailto:sagarwal@ku.edu>> wrote: Hi, Thanks for the scripts, Britton. Also, in the following piece, I am getting an error : KeyError: 'CosmologyOmegaBaryonNow' def _Baryon_Overdensity(field, data): return data['Density'] / \ (data.pf<http://data.pf>['CosmologyOmegaBaryonNow'] * rho_crit_now * (data.pf<http://data.pf>['CosmologyHubbleConstantNow']**2) * ((1+data.pf<http://data.pf>['CosmologyCurrentRedshift'])**3)) add_field("Baryon_Overdensity",function=_Baryon_Overdensity,units=r"") I tried data.pf<http://data.pf>['CosmologySimulationOmegaBaryonNow'] but got the same error. Would I need to hard code these parameters in the python scripts? Shankar ________________________________________ From: yt-users-bounces(a)lists.spacepope.org<mailto:yt-users-bounces@lists.spacepope.org> [yt-users-bounces(a)lists.spacepope.org<mailto:yt-users-bounces@lists.spacepope.org>] on behalf of Britton Smith [brittonsmith(a)gmail.com<mailto:brittonsmith@gmail.com>] Sent: Sunday, April 17, 2011 1:28 PM To: Discussion of the yt analysis package Subject: Re: [yt-users] VR: colorbar and camera Hi Shankar, The image_writer was an integral part of making the movie you refer to in your email. In brief, I made the frames for the images and colorbars separately, then grafted them together using another script. I have pasted an example of a script I used to make the colorbar portion of the frames here: http://paste.enzotools.org/show/1580/ I then used the script below to attach the colorbar image to the volume render frame. http://paste.enzotools.org/show/1581/ Note the line in this script: cmap = cmap[1:,:,:] I am chopping off one pixel from the colorbar image so that it has the same dimension as the rendering image on the side that they are being attached. If you look at the script, the images are just arrays that are being concatenated so you have to make sure that your image dimension work. I hope this helps. Britton p.s. - Thanks again to Matt and Sam who made all of that possible! On Sun, Apr 17, 2011 at 1:01 PM, Agarwal, Shankar <sagarwal(a)ku.edu<mailto:sagarwal@ku.edu><mailto:sagarwal@ku.edu<mailto:sagarwal@ku.edu>>> wrote: Hi, I recently made some volume rendered images using the following script (along the lines of Britton's http://paste.enzotools.org/show/1472/). Basically, it loops over all the redshifts, creating a snapshot - each snapshot rotated a bit using the YT-camera object. I wanted to know how can I add a colorbar (something as in http://vimeo.com/17100442)? Also, I would like to display a few cosmology variables like: pf['CosmologyCurrentRedshift'] pf['CosmologyOmegaBaryonNow'] My attempts with the image_writer are a disaster. I found that Libby had the same question a few months back, where she had a separate colorbar image and she joined 2 images. Please let me know how to modify the following script. Regards Shankar my_script.py ----------------- from yt.mods import * import yt.visualization.volume_rendering.api as vr output_dir = 'movie' c = [0.5]*3 # Center L = [1.0,1.0,1.0] # Viewpoint W = na.sqrt(4.0) # Width N = 1024 # Pixels up = [0.,0.,1.] # Set the north vector n_colors = 3 angle = 4 * na.pi / 360.0 for n in range(0,112): # each n is a unique redshift dump fin = 'lp7/seed1/RD%04i/RedshiftOutput%04i' % (n,n) # parameter file to load pf = load(fin) # load data dd = pf.h.all_data() min, max = na.log10(dd.quantities["Extrema"]("Density")[0]) print min, max fout = "%s/%04i.png" % (output_dir,n) width = 0.3 * (max - min) / float(n_colors) alpha = na.logspace(-3.5, -1, n_colors) tf = vr.ColorTransferFunction((min-3, max+1)) tf.add_layers(n_colors,w=width, alpha=alpha, min=min, max=max, col_bounds=(min,max), colormap='gist_ncar') cam = vr.Camera(c, L, W, (N,N), fields=['Density'], transfer_function=tf, pf=pf, use_kd=True, l_max=None, north_vector=up, tree_type='domain',no_ghost=True, steady_north=True) cam.rotate((n * angle)) cam.snapshot(fout) del cam del tf del alpha _______________________________________________ yt-users mailing list yt-users(a)lists.spacepope.org<mailto:yt-users@lists.spacepope.org><mailto:yt-users@lists.spacepope.org<mailto:yt-users@lists.spacepope.org>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org _______________________________________________ yt-users mailing list yt-users(a)lists.spacepope.org<mailto:yt-users@lists.spacepope.org> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

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Problems with RAMSES output
by Matteo Tomassetti 25 Apr '11

25 Apr '11

Hi there, after installing yt I tried to import the result of my Ramses simulation with this code: from yt.mods import * pf = load("output_00007/info_00007.txt") print pf.h.field_list print pf.h.derived_field_list but ... it doesn't work! My simulation consists only of DM for now and yt is searching for hydro files that of course does not exists. I just wanted to find DM halos but it seems that yt does not support this function for RAMSES data yet, does it? cheers, Matteo

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from yt.analysis_modules.api import EnzoSimulation
by Agarwal, Shankar 25 Apr '11

25 Apr '11

Hi, I just downloaded the latest http://hg.enzotools.org/yt/raw/stable/doc/install_script.sh and installed YT. Now, my python script (at the end of the email) quits with a "Segmentation fault" error at line-8 (yt.analysis_modules.api): [sagarwal@ember ~/junk]$ python colorbars.py parameterfile Segmentation fault If I comment out line8, then (obviously) I get the following error: Adding gaussian at -2.0 with width 0.5 and colors (0.0, 0.0, 0.502, 0.00031622776601683794) Adding gaussian at 0.5 with width 0.5 and colors (0.85737517232758309, 1.0, 0.12482388288648784, 0.005623413251903491) Adding gaussian at 3.0 with width 0.5 and colors (0.99609999999999999, 0.97250000000000003, 0.99609999999999999, 0.10000000000000001) Traceback (most recent call last): File "colorbars.py", line 36, in <module> es = EnzoSimulation(par_file, get_redshift_outputs=True, initial_redshift=50, final_redshift=0) NameError: name 'EnzoSimulation' is not defined Any ideas? Shankar python_script... ------------------------------------------------------------- import numpy as na from yt.mods import * import yt.visualization.volume_rendering.api as vr import matplotlib.pylab as pl import sys from yt.mods import * from yt.visualization.image_writer import write_bitmap from yt.analysis_modules.api import EnzoSimulation blah..blah... par_file = sys.argv[1] es = EnzoSimulation(par_file, get_redshift_outputs=True, initial_redshift=50, final_redshift=0) -------------------------------------------------------------

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installing yt on mac osx 10.6
by Matteo Tomassetti 25 Apr '11

25 Apr '11

Hi there, I'm trying to install yt on the new Mac OSX 10.6, Snow Leopard and I have some problems. I run the install script modifying "wget" with "curl -o" and the installation went ok. But then, when I type "yt" in my terminal I receive the "command not found error". Moreover, if I go the the bin directory of yt and type ./yt I enter the program but, trying to run the first example I get this error message: this is what I type in the bin directory: ./yt halos src/yt-hg/tests/DD0010/moving7_0010/ this is the error: Traceback (most recent call last): File "./yt", line 9, in <module> load_entry_point('yt==2.1stable', 'console_scripts', 'yt')() File "/Users/matteotomassetti/yt-i386/src/yt-hg/yt/utilities/command_line.py", line 961, in run_main sys.exit(YT.main()) File "/Users/matteotomassetti/yt-i386/src/yt-hg/yt/utilities/cmdln.py", line 257, in main return self.cmd(args) File "/Users/matteotomassetti/yt-i386/src/yt-hg/yt/utilities/cmdln.py", line 280, in cmd retval = self.onecmd(argv) File "/Users/matteotomassetti/yt-i386/src/yt-hg/yt/utilities/cmdln.py", line 412, in onecmd return self._dispatch_cmd(handler, argv) File "/Users/matteotomassetti/yt-i386/src/yt-hg/yt/utilities/cmdln.py", line 1100, in _dispatch_cmd return handler(argv[0], opts, *args) File "/Users/matteotomassetti/yt-i386/src/yt-hg/yt/utilities/command_line.py", line 387, in do_halos hp = HP.HaloProfiler(arg,opts.halo_parameter_file,**kwargs) TypeError: __init__() got an unexpected keyword argument 'radius' so my questions are: 1) how can I call yt in any shell without going to the bin directory of the program every time? 2) how can I fix the above bug? Please help me, yt looks really nice for what I have to do and I really don't want to miss the chance to use it! Cheers, M.

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User defined fields
by Mike Butler 21 Apr '11

21 Apr '11

Hi everyone, This is probably a dumb question, but is there an easier way to say, change the axis label of a Density projection from "Density (g/cm^2)" to the more accurate "Surface Density (g/cm^2)" or "\Sigma (g/cm^2)" besides adding a new field named that? When you create a field you can specify projection units, but for Density the name stays as "Density", which causes confusion. Creating a new field is easy enough, but it would be convenient if there was a simpler way. If anyone has any suggestions they would be appreciated. Thanks, Mike

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Raw data
by Elizabeth Tasker 21 Apr '11

21 Apr '11

Hi, Is it possible in yt to see the raw energy data? That is the field prior to any unit conversation? I'm seeing odd white areas of oblivion in my simulation (see attached picture) that seem to be where the total energy goes negative. I strongly suspect this happens sometime during the yt analysis, rather than the raw Enzo data (since the simulation doesn't crash the MSCL scheme), but I want to be totally sure. Elizabeth

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VR: colorbar and camera
by Agarwal, Shankar 18 Apr '11

18 Apr '11

Hi, I recently made some volume rendered images using the following script (along the lines of Britton's http://paste.enzotools.org/show/1472/). Basically, it loops over all the redshifts, creating a snapshot - each snapshot rotated a bit using the YT-camera object. I wanted to know how can I add a colorbar (something as in http://vimeo.com/17100442)? Also, I would like to display a few cosmology variables like: pf['CosmologyCurrentRedshift'] pf['CosmologyOmegaBaryonNow'] My attempts with the image_writer are a disaster. I found that Libby had the same question a few months back, where she had a separate colorbar image and she joined 2 images. Please let me know how to modify the following script. Regards Shankar my_script.py ----------------- from yt.mods import * import yt.visualization.volume_rendering.api as vr output_dir = 'movie' c = [0.5]*3 # Center L = [1.0,1.0,1.0] # Viewpoint W = na.sqrt(4.0) # Width N = 1024 # Pixels up = [0.,0.,1.] # Set the north vector n_colors = 3 angle = 4 * na.pi / 360.0 for n in range(0,112): # each n is a unique redshift dump fin = 'lp7/seed1/RD%04i/RedshiftOutput%04i' % (n,n) # parameter file to load pf = load(fin) # load data dd = pf.h.all_data() min, max = na.log10(dd.quantities["Extrema"]("Density")[0]) print min, max fout = "%s/%04i.png" % (output_dir,n) width = 0.3 * (max - min) / float(n_colors) alpha = na.logspace(-3.5, -1, n_colors) tf = vr.ColorTransferFunction((min-3, max+1)) tf.add_layers(n_colors,w=width, alpha=alpha, min=min, max=max, col_bounds=(min,max), colormap='gist_ncar') cam = vr.Camera(c, L, W, (N,N), fields=['Density'], transfer_function=tf, pf=pf, use_kd=True, l_max=None, north_vector=up, tree_type='domain',no_ghost=True, steady_north=True) cam.rotate((n * angle)) cam.snapshot(fout) del cam del tf del alpha

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Slices display incorrectly when many grids are used
by Nathan Roth 17 Apr '11

17 Apr '11

Hi yt crew, I am analyzing some orion data, and I am finding that slices will not display correctly for a simulation with 64 coarse AMR grids, although they will display just fine if use 8 coarse grids. Outer grids on my slices are appearing as blank white, and I've attached an example. I think the data itself is fine, and if I plot along a ray in the same slice I see what I expect (I've attached that, too). Note that the program units are cgs, which is why the density field values on the ray are on the order of 1e-22. I'd be happy to provide more details if they are needed. Thanks, Nathan

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running volume_render.py in a batch script
by Agarwal, Shankar 14 Apr '11

14 Apr '11

Hi, I have a volume_render.py script that runs fine on the login node on NCSA-EMBER. But the same script crashes with the following error when run through qsub. MPI: MPI_COMM_WORLD rank 0 has terminated without calling MPI_Finalize() MPI: aborting job MPI: Received signal 11 My batch script is... #!/bin/sh -x #PBS -l walltime=00:10:00 #PBS -l mem=32000mb #PBS -l ncpus=1 #PBS -q debug #PBS -V #PBS -A TG-AST080030N #PBS -N movie #PBS -m be #export MPI_MEMMAP_OFF=1 cd /gpfs1/u/ac/sagarwal/junk mpirun -np 1 /u/ac/sagarwal/software/enzo/src/yt/doc/yt-x86_64/bin/python2.6 volume_render.py Here are the first few lines of the volume_render.py... import matplotlib;matplotlib.use("Agg");import pylab import numpy as na import time from yt.config import ytcfg; ytcfg["yt","loglevel"] = '50' ; ytcfg["lagos","serialize"] = "False" from yt.mods import * from yt.extensions.volume_rendering import * from yt.funcs import * mh = na.log10(1.67e-24) from mpi4py import MPI Please let me know if it may have something to do with mpi4py. Shankar

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