<div dir="ltr">Hi Hilary,<div><br></div><div>Fist, thank you very much for your help, I really appreciate it. </div><div><br></div><div>Sorry for the delay, the <span class="" id=":18o.19" tabindex="-1" style="background-color:yellow">dataset</span> took a while to upload.</div><div>Here is a <span class="" id=":18o.20" tabindex="-1" style="background-color:yellow">dropbok</span> link to the <span class="" id=":18o.21" tabindex="-1" style="background-color:yellow">dataset</span> I'm using, its a TIPSY binary file, you can also find the the most fundamental version of my code there:</div><div><br></div><div> <a href="https://www.dropbox.com/sh/tgtd3b57jkpvyjc/AACnx4QFO99TxUpF2qadXMDWa?dl=0">https://www.dropbox.com/sh/tgtd3b57jkpvyjc/AACnx4QFO99TxUpF2qadXMDWa?dl=0</a></div><div><br></div><div>I think that the problem is that I'm not setting the mass and <span class="" id=":18o.22" tabindex="-1" style="background-color:yellow">length</span> conversion factors for the <span class="" id=":18o.23" tabindex="-1" style="background-color:yellow">TipsyDataset</span> correctly (I haven't figured out how to do this).</div><div><br></div><div>Again, thanks a lot for your help, let me know if I can help with something else.</div><div><br></div><div>-Bruno</div><div><br></div><div><br></div><div><br></div><div><br></div><div><br></div><div><br></div></div><div class="gmail_extra"><br><div class="gmail_quote">2014-09-18 15:07 GMT-05:00 Hilary Egan <span dir="ltr"><<a href="mailto:hilaryye@gmail.com" target="_blank">hilaryye@gmail.com</a>></span>:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">Hi Bruno,<div><br></div><div>I'm not able to recreate you issue with any of my test datasets, so having access to some of your data might make debugging a little bit easier. If you could share a test dataset (via dropbox, google drive, etc), I'll take a look at this!</div><span class="HOEnZb"><font color="#888888"><div><br></div><div>-Hilary</div></font></span></div><div class="HOEnZb"><div class="h5"><div class="gmail_extra"><br><div class="gmail_quote">On Thu, Sep 18, 2014 at 1:22 PM, Bruno Villasenor <span dir="ltr"><<a href="mailto:br1villasen@gmail.com" target="_blank">br1villasen@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div>Hi,</div><div><br></div>I just tested the change and it works fine, this is the new output<div><br></div><div>########################################</div><div><div>P000 yt : [INFO ] 2014-09-18 13:55:50,652 <a href="http://adsabs.harvard.edu/abs/2013ApJ...762..109B" target="_blank">http://adsabs.harvard.edu/abs/2013ApJ...762..109B</a></div><div>P002 yt : [INFO ] 2014-09-18 13:55:50,652 Rockstar is using 1 readers and 1 writers</div><div>P001 yt : [INFO ] 2014-09-18 13:55:50,652 Rockstar is using 1 readers and 1 writers</div><div>P000 yt : [INFO ] 2014-09-18 13:55:50,652 Rockstar is using 1 readers and 1 writers</div><div>P001 yt : [WARNING ] 2014-09-18 13:55:50,719 Total Particle Count: 3.154e+05</div><div>[ 0s] Accepting connections...</div><span><div>[ 1s] Accepted all reader / writer connections.</div><div>[ 1s] Verified all reader / writer connections.</div><div>[ 1s] Transmitted all client connection info.</div></span><div>[ 1s] Reading 1 blocks for snapshot 0...</div><span><div>Exception yt.utilities.exceptions.YTFieldNotFound: YTFieldNotFound() in 'yt.analysis_modules.halo_finding.rockstar.rockstar_interface.rh_read_particles' ignored</div><div>[ 2s] Transferring particles to writers...</div><div>[ 2s] Analyzing for FoF groups...</div><div>[ 2s] Transferring boundary particles between writers...</div><div>[ 2s] Linking boundary particles...</div></span><div>[ 2s] Analyzing for halos / subhalos...</div><span><div>[ 3s] Loading merger tree information...</div><div>[ 3s] Constructing merger tree...</div><div>[ 3s] [Success] Done with snapshot 0.</div><div>[ 3s] [Finished]</div></span><div>P001 yt : [INFO ] 2014-09-18 13:55:53,597 Parameters: current_time = 2.44801700503e+17 s</div><div>P001 yt : [INFO ] 2014-09-18 13:55:53,597 Parameters: domain_dimensions = [2 2 2]</div><div>P001 yt : [INFO ] 2014-09-18 13:55:53,597 Parameters: domain_left_edge = [ 0. 0. 0.]</div><div>P001 yt : [INFO ] 2014-09-18 13:55:53,598 Parameters: domain_right_edge = [ 1.12666939e+23 1.12666939e+23 1.12666939e+23]</div><div>P001 yt : [INFO ] 2014-09-18 13:55:53,598 Parameters: cosmological_simulation = 1</div><div>P001 yt : [INFO ] 2014-09-18 13:55:53,598 Parameters: current_redshift = 0.6</div><div>P001 yt : [INFO ] 2014-09-18 13:55:53,598 Parameters: omega_lambda = 0.699999988079</div><div>P001 yt : [INFO ] 2014-09-18 13:55:53,598 Parameters: omega_matter = 0.300000011921</div><div>P001 yt : [INFO ] 2014-09-18 13:55:53,599 Parameters: hubble_constant = 0.699999988079</div><div>P000 yt : [INFO ] 2014-09-18 13:55:53,603 Parameters: current_time = 2.44801700503e+17 s</div><div>P000 yt : [INFO ] 2014-09-18 13:55:53,604 Parameters: domain_dimensions = [2 2 2]</div><div>P000 yt : [INFO ] 2014-09-18 13:55:53,604 Parameters: domain_left_edge = [ 0. 0. 0.]</div><div>P000 yt : [INFO ] 2014-09-18 13:55:53,605 Parameters: domain_right_edge = [ 1.12666939e+23 1.12666939e+23 1.12666939e+23]</div><div>P000 yt : [INFO ] 2014-09-18 13:55:53,605 Parameters: cosmological_simulation = 1</div><div>P000 yt : [INFO ] 2014-09-18 13:55:53,605 Parameters: current_redshift = 0.6</div><div>P000 yt : [INFO ] 2014-09-18 13:55:53,605 Parameters: omega_lambda = 0.699999988079</div><div>P000 yt : [INFO ] 2014-09-18 13:55:53,605 Parameters: omega_matter = 0.300000011921</div><div>P000 yt : [INFO ] 2014-09-18 13:55:53,605 Parameters: hubble_constant = 0.699999988079</div><div>P000 yt : [INFO ] 2014-09-18 13:55:53,614 Allocating for 0.000e+00 particles</div><div>P002 yt : [INFO ] 2014-09-18 13:55:53,615 Allocating for 0.000e+00 particles</div><div>P001 yt : [INFO ] 2014-09-18 13:55:53,615 Allocating for 0.000e+00 particles</div><div>P000 yt : [WARNING ] 2014-09-18 13:55:53,618 No halos were found for galaxy.00300</div><div>P002 yt : [WARNING ] 2014-09-18 13:55:53,619 No halos were found for galaxy.00300</div><div>P000 yt : [INFO ] 2014-09-18 13:55:53,619 Saving halo catalog (0 halos) to halo_catalogs/catalog/catalog.</div><div>P002 yt : [INFO ] 2014-09-18 13:55:53,619 Saving halo catalog (0 halos) to halo_catalogs/catalog/catalog.</div><div>P001 yt : [WARNING ] 2014-09-18 13:55:53,623 No halos were found for galaxy.00300</div><div>P001 yt : [INFO ] 2014-09-18 13:55:53,623 Saving halo catalog (0 halos) to halo_catalogs/catalog/catalog.</div></div><div>###################################################</div><div><br></div><div><br></div><div>Thanks a lot for the quick fix.</div><div><br></div><div>There's something else, I don't understand why Rockstar is not finding any halos. (when I use "hop finder_method" it finds a bunch of them),</div><div>does the exception message below means that the finder is looking for something that I should be creating for a TipsyDataset?</div><div>########################################</div><span><div>Exception yt.utilities.exceptions.YTFieldNotFound: YTFieldNotFound() in 'yt.analysis_modules.halo_finding.rockstar.rockstar_interface.rh_read_particles' ignored<br></div></span><div>########################################</div><div><br></div><div>I'm an undergraduate student who just very recently started using yt, so if someone has any suggestion I will really appreciate it.</div><div><br></div><div>Thanks in advance.</div><div><br></div><div>Best Regards</div><div>Bruno</div><div><br></div><div><br></div></div><div class="gmail_extra"><br><div class="gmail_quote">2014-09-18 11:40 GMT-05:00 Nathan Goldbaum <span dir="ltr"><<a href="mailto:nathan12343@gmail.com" target="_blank">nathan12343@gmail.com</a>></span>:<div><div><br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Looks like Hillary just opened a PR to fix this:<div><br></div><div><a href="https://bitbucket.org/yt_analysis/yt/pull-request/1213/bugfix-catch-no-halos-found-error-before/diff" target="_blank">https://bitbucket.org/yt_analysis/yt/pull-request/1213/bugfix-catch-no-halos-found-error-before/diff</a></div><div><br></div><div>Bruno <span></span>if you could test this, that would be great. Let us know if you have any questions about how to locally test a pull request.<div><div><br><br>On Thursday, September 18, 2014, Matthew Turk <<a href="mailto:matthewturk@gmail.com" target="_blank">matthewturk@gmail.com</a>> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hi Bruno,<br>
<br>
On Mon, Sep 15, 2014 at 7:58 PM, Bruno Villasenor <<a>br1villasen@gmail.com</a>> wrote:<br>
> Hi all,<br>
><br>
> I'm trying to run the RockstarHaloFinder via the HaloCatalog function on a<br>
> TIPSY file.<br>
> When I run the HaloCatalog function I get the following rockstar output:<br>
><br>
> ########################################################################<br>
> P002 yt : [INFO ] 2014-09-15 19:36:11,382 Rockstar is using 1 readers<br>
> and 1 writers<br>
> P000 yt : [INFO ] 2014-09-15 19:36:11,382 The citation for the Rockstar<br>
> halo finder can be found at<br>
> P001 yt : [INFO ] 2014-09-15 19:36:11,382 Rockstar is using 1 readers<br>
> and 1 writers<br>
> P000 yt : [INFO ] 2014-09-15 19:36:11,382<br>
> <a href="http://adsabs.harvard.edu/abs/2013ApJ...762..109B" target="_blank">http://adsabs.harvard.edu/abs/2013ApJ...762..109B</a><br>
> P000 yt : [INFO ] 2014-09-15 19:36:11,383 Rockstar is using 1 readers<br>
> and 1 writers<br>
> P001 yt : [WARNING ] 2014-09-15 19:36:41,582 Total Particle Count:<br>
> 4.862e+07<br>
> [ 0s] Accepting connections...<br>
> [ 1s] Accepted all reader / writer connections.<br>
> [ 1s] Verified all reader / writer connections.<br>
> [ 1s] Transmitted all client connection info.<br>
> [ 2s] Reading 1 blocks for snapshot 0...<br>
> Exception yt.utilities.exceptions.YTFieldNotFound: YTFieldNotFound() in<br>
> 'yt.analysis_modules.halo_finding.rockstar.rockstar_interface.rh_read_particles'<br>
> ignored<br>
> [ 2s] Transferring particles to writers...<br>
> [ 2s] Analyzing for FoF groups...<br>
> [ 2s] Transferring boundary particles between writers...<br>
> [ 2s] Linking boundary particles...<br>
> [ 3s] Analyzing for halos / subhalos...<br>
> [ 3s] Loading merger tree information...<br>
> [ 3s] Constructing merger tree...<br>
> [ 3s] [Success] Done with snapshot 0.<br>
> [ 3s] [Finished]<br>
> #######################################################################<br>
><br>
> followed by the next YT output<br>
><br>
> #######################################################################<br>
> P001 yt : [INFO ] 2014-09-15 19:36:44,986 Parameters: current_time<br>
> = 2.44801700503e+17 s<br>
> P001 yt : [INFO ] 2014-09-15 19:36:44,987 Parameters: domain_dimensions<br>
> = [2 2 2]<br>
> P000 yt : [INFO ] 2014-09-15 19:36:44,994 Parameters: current_time<br>
> = 2.44801700503e+17 s<br>
> P000 yt : [INFO ] 2014-09-15 19:36:44,994 Parameters: domain_dimensions<br>
> = [2 2 2]<br>
> P000 yt : [INFO ] 2014-09-15 19:36:44,994 Parameters: domain_left_edge<br>
> = [ 0. 0. 0.]<br>
> P000 yt : [INFO ] 2014-09-15 19:36:45,012 Parameters: domain_right_edge<br>
> = [ 0.00207136 0.00207136 0.00207136]<br>
> P000 yt : [INFO ] 2014-09-15 19:36:45,013 Parameters:<br>
> cosmological_simulation = 1<br>
> P000 yt : [INFO ] 2014-09-15 19:36:45,014 Parameters: current_redshift<br>
> = 0.6<br>
> P001 yt : [INFO ] 2014-09-15 19:36:44,987 Parameters: domain_left_edge<br>
> = [ 0. 0. 0.]<br>
> P000 yt : [INFO ] 2014-09-15 19:36:45,014 Parameters: omega_lambda<br>
> = 0.699999988079<br>
> P000 yt : [INFO ] 2014-09-15 19:36:45,014 Parameters: omega_matter<br>
> = 0.300000011921<br>
> P000 yt : [INFO ] 2014-09-15 19:36:45,014 Parameters: hubble_constant<br>
> = 0.699999988079<br>
> P001 yt : [INFO ] 2014-09-15 19:36:45,014 Parameters: domain_right_edge<br>
> = [ 0.00207136 0.00207136 0.00207136]<br>
> P001 yt : [INFO ] 2014-09-15 19:36:45,014 Parameters:<br>
> cosmological_simulation = 1<br>
> P001 yt : [INFO ] 2014-09-15 19:36:45,015 Parameters: current_redshift<br>
> = 0.6<br>
> P001 yt : [INFO ] 2014-09-15 19:36:45,015 Parameters: omega_lambda<br>
> = 0.699999988079<br>
> P001 yt : [INFO ] 2014-09-15 19:36:45,015 Parameters: omega_matter<br>
> = 0.300000011921<br>
> P001 yt : [INFO ] 2014-09-15 19:36:45,015 Parameters: hubble_constant<br>
> = 0.699999988079<br>
> P000 yt : [INFO ] 2014-09-15 19:36:45,070 Allocating for 0.000e+00<br>
> particles<br>
> P001 yt : [INFO ] 2014-09-15 19:36:45,070 Allocating for 0.000e+00<br>
> particles<br>
> P002 yt : [INFO ] 2014-09-15 19:36:45,070 Allocating for 0.000e+00<br>
> particles<br>
> Traceback (most recent call last):<br>
> File "simple_rockstar.py", line 44, in <module><br>
> Traceback (most recent call last):<br>
> File "simple_rockstar.py", line 44, in <module><br>
> Traceback (most recent call last):<br>
> File "simple_rockstar.py", line 44, in <module><br>
> hc.create()<br>
> File<br>
> "/home/bruno/apps/yt-x86_64/src/yt-hg/yt/analysis_modules/halo_analysis/halo_catalog.py",<br>
> line 297, in create<br>
> hc.create()<br>
> File<br>
> "/home/bruno/apps/yt-x86_64/src/yt-hg/yt/analysis_modules/halo_analysis/halo_catalog.py",<br>
> line 297, in create<br>
> hc.create()<br>
> File<br>
> "/home/bruno/apps/yt-x86_64/src/yt-hg/yt/analysis_modules/halo_analysis/halo_catalog.py",<br>
> line 297, in create<br>
> self._run(save_halos, save_catalog, njobs=njobs, dynamic=dynamic)<br>
> File<br>
> "/home/bruno/apps/yt-x86_64/src/yt-hg/yt/utilities/parallel_tools/parallel_analysis_interface.py",<br>
> line 248, in barrierize<br>
> self._run(save_halos, save_catalog, njobs=njobs, dynamic=dynamic)<br>
> self._run(save_halos, save_catalog, njobs=njobs, dynamic=dynamic)<br>
> File<br>
> "/home/bruno/apps/yt-x86_64/src/yt-hg/yt/utilities/parallel_tools/parallel_analysis_interface.py",<br>
> line 248, in barrierize<br>
> File<br>
> "/home/bruno/apps/yt-x86_64/src/yt-hg/yt/utilities/parallel_tools/parallel_analysis_interface.py",<br>
> line 248, in barrierize<br>
> retval = func(*args, **kwargs)<br>
> File<br>
> "/home/bruno/apps/yt-x86_64/src/yt-hg/yt/analysis_modules/halo_analysis/halo_catalog.py",<br>
> line 367, in _run<br>
> self.halos_ds.index<br>
> AttributeError: 'NoneType' object has no attribute 'index'<br>
> retval = func(*args, **kwargs)<br>
> File<br>
> "/home/bruno/apps/yt-x86_64/src/yt-hg/yt/analysis_modules/halo_analysis/halo_catalog.py",<br>
> line 367, in _run<br>
> self.halos_ds.index<br>
> retval = func(*args, **kwargs)<br>
> AttributeError: 'NoneType' object has no attribute 'index'<br>
> File<br>
> "/home/bruno/apps/yt-x86_64/src/yt-hg/yt/analysis_modules/halo_analysis/halo_catalog.py",<br>
> line 367, in _run<br>
> self.halos_ds.index<br>
> AttributeError: 'NoneType' object has no attribute 'index'<br>
<br>
This does indeed look like an internal error. It looks to me like the<br>
halos_ds is not being created -- even if R* finds something, I think<br>
this should be created. Britton and/or Hilary, have you seen this<br>
error before?<br>
<br>
-Matt<br>
<br>
> #######################################################################################<br>
><br>
> It seems to me like rockstar is not finding anything (Exception message) and<br>
> then when yt load and save to disk it fails.<br>
> The simplest working version of my code is the next one:<br>
><br>
> #######################################################################################<br>
> import yt<br>
> from yt.mods import *<br>
> from yt.analysis_modules.halo_analysis.api import HaloCatalog<br>
> from yt.data_objects.particle_filters import add_particle_filter<br>
> from mpi4py import MPI<br>
> import numpy as np<br>
><br>
> dataDir = "/home/bruno/Desktop/data/yt/"<br>
> dataFile = 'DM.Only.tipsy/dwf1.6144.01280'<br>
> ts = DatasetSeries([dataDir + dataFile])<br>
> data_ds = ts[0]<br>
> #data_ds = yt.load( dataDir + dataFile )<br>
> data_ds.set_units( )<br>
><br>
> #Add symbol "Mpccm"<br>
> data_ds.unit_registry.add( 'Mpccm',<br>
> float(units.Mpc.in_cgs().v),<br>
> units.dimensions.length)<br>
><br>
> #Create particle filter to filter to filter a single mass particle type<br>
> def low_mass(pfilter, data):<br>
> filter = data["all", "Mass"] < 1.3e-12 * units.Msun<br>
> return filter<br>
> add_particle_filter("low_mass", function=low_mass,<br>
> filtered_type='all',<br>
> requires=["Mass"])<br>
> data_ds.add_particle_filter("low_mass")<br>
><br>
> #Set cosmology parameters<br>
> data_ds.hubble_constant = 0.7<br>
> data_ds.omega_matter = 0.3<br>
> data_ds.current_redshift = 0.6<br>
> data_ds.omega_lambda = 0.7<br>
><br>
> #Arguments for RockstarHoloFinder<br>
> rockstar_kwargs = {<br>
> 'particle_type': 'low_mass',<br>
> 'force_res': 1e-4 #100pc<br>
> }<br>
><br>
> hc = HaloCatalog(data_ds=data_ds,<br>
> finder_method='rockstar',<br>
> finder_kwargs = rockstar_kwargs)<br>
> hc.create()<br>
> ##################################################################<br>
><br>
> If someone has any suggestion I would really appreciate it.<br>
><br>
> Thanks,<br>
> Bruno<br>
><br>
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