<div dir="ltr">Hi all,<div><br></div><div>I'm trying to run the <span class="" id=":2b4.1" tabindex="-1">RockstarHaloFinder</span> via the <span class="" id=":2b4.2" tabindex="-1">HaloCatalog</span> function on a TIPSY file. </div><div>When I run the <span class="" id=":2b4.3" tabindex="-1">HaloCatalog</span> function I get the following <span class="" id=":2b4.4" tabindex="-1">rockstar</span> output:</div><div><br></div><div>########################################################################</div><div><div>P002 <span class="" id=":2b4.5" tabindex="-1">yt</span> : [INFO     ] 2014-09-15 19:36:11,382 <span class="" id=":2b4.6" tabindex="-1">Rockstar</span> is using 1 readers and 1 writers</div><div>P000 <span class="" id=":2b4.7" tabindex="-1">yt</span> : [INFO     ] 2014-09-15 19:36:11,382 The citation for the <span class="" id=":2b4.8" tabindex="-1">Rockstar</span> halo finder can be found at</div><div>P001 <span class="" id=":2b4.9" tabindex="-1">yt</span> : [INFO     ] 2014-09-15 19:36:11,382 <span class="" id=":2b4.10" tabindex="-1">Rockstar</span> is using 1 readers and 1 writers</div><div>P000 <span class="" id=":2b4.11" tabindex="-1">yt</span> : [INFO     ] 2014-09-15 19:36:11,382 http://<span class="" id=":2b4.12" tabindex="-1">adsabs</span>.<span class="" id=":2b4.13" tabindex="-1">harvard</span>.<span class="" id=":2b4.14" tabindex="-1">edu</span>/abs/2013ApJ...762..109B</div><div>P000 <span class="" id=":2b4.15" tabindex="-1">yt</span> : [INFO     ] 2014-09-15 19:36:11,383 <span class="" id=":2b4.16" tabindex="-1">Rockstar</span> is using 1 readers and 1 writers</div><div>P001 <span class="" id=":2b4.17" tabindex="-1">yt</span> : [WARNING  ] 2014-09-15 19:36:41,582 Total Particle Count: 4.862e+07</div><div>[     0s] Accepting connections...</div><div>[     1s] Accepted all reader / writer connections.</div><div>[     1s] Verified all reader / writer connections.</div><div>[     1s] Transmitted all client connection info.</div><div>[     2s] Reading 1 blocks for snapshot 0...</div><div>Exception <span class="" id=":2b4.18" tabindex="-1">yt</span>.utilities.exceptions.<span class="" id=":2b4.19" tabindex="-1">YTFieldNotFound</span>: <span class="" id=":2b4.20" tabindex="-1">YTFieldNotFound</span>() in 'yt.analysis_modules.halo_finding.<span class="" id=":2b4.21" tabindex="-1">rockstar</span>.<span class="" id=":2b4.22" tabindex="-1">rockstar</span>_interface.<span class="" id=":2b4.23" tabindex="-1">rh</span>_read_particles' ignored</div><div>[     2s] Transferring particles to writers...</div><div>[     2s] Analyzing for <span class="" id=":2b4.24" tabindex="-1">FoF</span> groups...</div><div>[     2s] Transferring boundary particles between writers...</div><div>[     2s] Linking boundary particles...</div><div>[     3s] Analyzing for halos / <span class="" id=":2b4.25" tabindex="-1">subhalos</span>...</div><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></div><div>#######################################################################</div><div><br></div><div>followed by the next  YT output</div><div><br></div><div>#######################################################################</div><div><div>P001 <span class="" id=":2b4.26" tabindex="-1">yt</span> : [INFO     ] 2014-09-15 19:36:44,986 Parameters: current_time              = 2.44801700503e+17 s</div><div>P001 <span class="" id=":2b4.27" tabindex="-1">yt</span> : [INFO     ] 2014-09-15 19:36:44,987 Parameters: domain_dimensions         = [2 2 2]</div><div>P000 <span class="" id=":2b4.28" tabindex="-1">yt</span> : [INFO     ] 2014-09-15 19:36:44,994 Parameters: current_time              = 2.44801700503e+17 s</div><div>P000 <span class="" id=":2b4.29" tabindex="-1">yt</span> : [INFO     ] 2014-09-15 19:36:44,994 Parameters: domain_dimensions         = [2 2 2]</div><div>P000 <span class="" id=":2b4.30" tabindex="-1">yt</span> : [INFO     ] 2014-09-15 19:36:44,994 Parameters: domain_left_edge          = [ 0.  0.  0.]</div><div>P000 <span class="" id=":2b4.31" tabindex="-1">yt</span> : [INFO     ] 2014-09-15 19:36:45,012 Parameters: domain_right_edge         = [ 0.00207136  0.00207136  0.00207136]</div><div>P000 <span class="" id=":2b4.32" tabindex="-1">yt</span> : [INFO     ] 2014-09-15 19:36:45,013 Parameters: cosmological_simulation   = 1</div><div>P000 <span class="" id=":2b4.33" tabindex="-1">yt</span> : [INFO     ] 2014-09-15 19:36:45,014 Parameters: current_redshift          = 0.6</div><div>P001 <span class="" id=":2b4.34" tabindex="-1">yt</span> : [INFO     ] 2014-09-15 19:36:44,987 Parameters: domain_left_edge          = [ 0.  0.  0.]</div><div>P000 <span class="" id=":2b4.35" tabindex="-1">yt</span> : [INFO     ] 2014-09-15 19:36:45,014 Parameters: omega_lambda              = 0.699999988079</div><div>P000 <span class="" id=":2b4.36" tabindex="-1">yt</span> : [INFO     ] 2014-09-15 19:36:45,014 Parameters: omega_matter              = 0.300000011921</div><div>P000 <span class="" id=":2b4.37" tabindex="-1">yt</span> : [INFO     ] 2014-09-15 19:36:45,014 Parameters: <span class="" id=":2b4.38" tabindex="-1">hubble</span>_constant           = 0.699999988079</div><div>P001 <span class="" id=":2b4.39" tabindex="-1">yt</span> : [INFO     ] 2014-09-15 19:36:45,014 Parameters: domain_right_edge         = [ 0.00207136  0.00207136  0.00207136]</div><div>P001 <span class="" id=":2b4.40" tabindex="-1">yt</span> : [INFO     ] 2014-09-15 19:36:45,014 Parameters: cosmological_simulation   = 1</div><div>P001 <span class="" id=":2b4.41" tabindex="-1">yt</span> : [INFO     ] 2014-09-15 19:36:45,015 Parameters: current_redshift          = 0.6</div><div>P001 <span class="" id=":2b4.42" tabindex="-1">yt</span> : [INFO     ] 2014-09-15 19:36:45,015 Parameters: omega_lambda              = 0.699999988079</div><div>P001 <span class="" id=":2b4.43" tabindex="-1">yt</span> : [INFO     ] 2014-09-15 19:36:45,015 Parameters: omega_matter              = 0.300000011921</div><div>P001 <span class="" id=":2b4.44" tabindex="-1">yt</span> : [INFO     ] 2014-09-15 19:36:45,015 Parameters: <span class="" id=":2b4.45" tabindex="-1">hubble</span>_constant           = 0.699999988079</div><div>P000 <span class="" id=":2b4.46" tabindex="-1">yt</span> : [INFO     ] 2014-09-15 19:36:45,070 Allocating for 0.000e+00 particles</div><div>P001 <span class="" id=":2b4.47" tabindex="-1">yt</span> : [INFO     ] 2014-09-15 19:36:45,070 Allocating for 0.000e+00 particles</div><div>P002 <span class="" id=":2b4.48" tabindex="-1">yt</span> : [INFO     ] 2014-09-15 19:36:45,070 Allocating for 0.000e+00 particles</div><div><span class="" id=":2b4.49" tabindex="-1">Traceback</span> (most recent call last):</div><div>  File "simple_<span class="" id=":2b4.50" tabindex="-1">rockstar</span>.<span class="" id=":2b4.51" tabindex="-1">py</span>", line 44, in <module></div><div><span class="" id=":2b4.52" tabindex="-1">Traceback</span> (most recent call last):</div><div>  File "simple_<span class="" id=":2b4.53" tabindex="-1">rockstar</span>.<span class="" id=":2b4.54" tabindex="-1">py</span>", line 44, in <module></div><div><span class="" id=":2b4.55" tabindex="-1">Traceback</span> (most recent call last):</div><div>  File "simple_<span class="" id=":2b4.56" tabindex="-1">rockstar</span>.<span class="" id=":2b4.57" tabindex="-1">py</span>", line 44, in <module></div><div>    <span class="" id=":2b4.58" tabindex="-1">hc</span>.create()</div><div>  File "/home/<span class="" id=":2b4.59" tabindex="-1">bruno</span>/apps/<span class="" id=":2b4.60" tabindex="-1">yt</span>-x86_64/<span class="" id=":2b4.61" tabindex="-1">src</span>/<span class="" id=":2b4.62" tabindex="-1">yt</span>-<span class="" id=":2b4.63" tabindex="-1">hg</span>/<span class="" id=":2b4.64" tabindex="-1">yt</span>/analysis_modules/halo_analysis/halo_catalog.<span class="" id=":2b4.65" tabindex="-1">py</span>", line 297, in create</div><div>    <span class="" id=":2b4.66" tabindex="-1">hc</span>.create()</div><div>  File "/home/<span class="" id=":2b4.67" tabindex="-1">bruno</span>/apps/<span class="" id=":2b4.68" tabindex="-1">yt</span>-x86_64/<span class="" id=":2b4.69" tabindex="-1">src</span>/<span class="" id=":2b4.70" tabindex="-1">yt</span>-<span class="" id=":2b4.71" tabindex="-1">hg</span>/<span class="" id=":2b4.72" tabindex="-1">yt</span>/analysis_modules/halo_analysis/halo_catalog.<span class="" id=":2b4.73" tabindex="-1">py</span>", line 297, in create</div><div>    <span class="" id=":2b4.74" tabindex="-1">hc</span>.create()</div><div>  File "/home/<span class="" id=":2b4.75" tabindex="-1">bruno</span>/apps/<span class="" id=":2b4.76" tabindex="-1">yt</span>-x86_64/<span class="" id=":2b4.77" tabindex="-1">src</span>/<span class="" id=":2b4.78" tabindex="-1">yt</span>-<span class="" id=":2b4.79" tabindex="-1">hg</span>/<span class="" id=":2b4.80" tabindex="-1">yt</span>/analysis_modules/halo_analysis/halo_catalog.<span class="" id=":2b4.81" tabindex="-1">py</span>", line 297, in create</div><div>    self._run(save_halos, save_catalog, <span class="" id=":2b4.82" tabindex="-1">njobs</span>=<span class="" id=":2b4.83" tabindex="-1">njobs</span>, dynamic=dynamic)</div><div>  File "/home/<span class="" id=":2b4.84" tabindex="-1">bruno</span>/apps/<span class="" id=":2b4.85" tabindex="-1">yt</span>-x86_64/<span class="" id=":2b4.86" tabindex="-1">src</span>/<span class="" id=":2b4.87" tabindex="-1">yt</span>-<span class="" id=":2b4.88" tabindex="-1">hg</span>/<span class="" id=":2b4.89" tabindex="-1">yt</span>/utilities/parallel_tools/parallel_analysis_interface.<span class="" id=":2b4.90" tabindex="-1">py</span>", line 248, in <span class="" id=":2b4.91" tabindex="-1">barrierize</span></div><div>    self._run(save_halos, save_catalog, <span class="" id=":2b4.92" tabindex="-1">njobs</span>=<span class="" id=":2b4.93" tabindex="-1">njobs</span>, dynamic=dynamic)</div><div>    self._run(save_halos, save_catalog, <span class="" id=":2b4.94" tabindex="-1">njobs</span>=<span class="" id=":2b4.95" tabindex="-1">njobs</span>, dynamic=dynamic)</div><div>  File "/home/<span class="" id=":2b4.96" tabindex="-1">bruno</span>/apps/<span class="" id=":2b4.97" tabindex="-1">yt</span>-x86_64/<span class="" id=":2b4.98" tabindex="-1">src</span>/<span class="" id=":2b4.99" tabindex="-1">yt</span>-<span class="" id=":2b4.100" tabindex="-1">hg</span>/<span class="" id=":2b4.101" tabindex="-1">yt</span>/utilities/parallel_tools/parallel_analysis_interface.<span class="" id=":2b4.102" tabindex="-1">py</span>", line 248, in <span class="" id=":2b4.103" tabindex="-1">barrierize</span></div><div>  File "/home/<span class="" id=":2b4.104" tabindex="-1">bruno</span>/apps/<span class="" id=":2b4.105" tabindex="-1">yt</span>-x86_64/<span class="" id=":2b4.106" tabindex="-1">src</span>/<span class="" id=":2b4.107" tabindex="-1">yt</span>-<span class="" id=":2b4.108" tabindex="-1">hg</span>/<span class="" id=":2b4.109" tabindex="-1">yt</span>/utilities/parallel_tools/parallel_analysis_interface.<span class="" id=":2b4.110" tabindex="-1">py</span>", line 248, in <span class="" id=":2b4.111" tabindex="-1">barrierize</span></div><div>    <span class="" id=":2b4.112" tabindex="-1">retval</span> = <span class="" id=":2b4.113" tabindex="-1">func</span>(*<span class="" id=":2b4.114" tabindex="-1">args</span>, **<span class="" id=":2b4.115" tabindex="-1">kwargs</span>)</div><div>  File "/home/<span class="" id=":2b4.116" tabindex="-1">bruno</span>/apps/<span class="" id=":2b4.117" tabindex="-1">yt</span>-x86_64/<span class="" id=":2b4.118" tabindex="-1">src</span>/<span class="" id=":2b4.119" tabindex="-1">yt</span>-<span class="" id=":2b4.120" tabindex="-1">hg</span>/<span class="" id=":2b4.121" tabindex="-1">yt</span>/analysis_modules/halo_analysis/halo_catalog.<span class="" id=":2b4.122" tabindex="-1">py</span>", line 367, in _run</div><div>    self.halos_<span class="" id=":2b4.123" tabindex="-1">ds</span>.index</div><div><span class="" id=":2b4.124" tabindex="-1">AttributeError</span>: 'NoneType' object has no attribute 'index'</div><div>    <span class="" id=":2b4.125" tabindex="-1">retval</span> = <span class="" id=":2b4.126" tabindex="-1">func</span>(*<span class="" id=":2b4.127" tabindex="-1">args</span>, **<span class="" id=":2b4.128" tabindex="-1">kwargs</span>)</div><div>  File "/home/<span class="" id=":2b4.129" tabindex="-1">bruno</span>/apps/<span class="" id=":2b4.130" tabindex="-1">yt</span>-x86_64/<span class="" id=":2b4.131" tabindex="-1">src</span>/<span class="" id=":2b4.132" tabindex="-1">yt</span>-<span class="" id=":2b4.133" tabindex="-1">hg</span>/<span class="" id=":2b4.134" tabindex="-1">yt</span>/analysis_modules/halo_analysis/halo_catalog.<span class="" id=":2b4.135" tabindex="-1">py</span>", line 367, in _run</div><div>    self.halos_<span class="" id=":2b4.136" tabindex="-1">ds</span>.index</div><div>    <span class="" id=":2b4.137" tabindex="-1">retval</span> = <span class="" id=":2b4.138" tabindex="-1">func</span>(*<span class="" id=":2b4.139" tabindex="-1">args</span>, **<span class="" id=":2b4.140" tabindex="-1">kwargs</span>)</div><div><span class="" id=":2b4.141" tabindex="-1">AttributeError</span>: 'NoneType' object has no attribute 'index'</div><div>  File "/home/<span class="" id=":2b4.142" tabindex="-1">bruno</span>/apps/<span class="" id=":2b4.143" tabindex="-1">yt</span>-x86_64/<span class="" id=":2b4.144" tabindex="-1">src</span>/<span class="" id=":2b4.145" tabindex="-1">yt</span>-<span class="" id=":2b4.146" tabindex="-1">hg</span>/<span class="" id=":2b4.147" tabindex="-1">yt</span>/analysis_modules/halo_analysis/halo_catalog.<span class="" id=":2b4.148" tabindex="-1">py</span>", line 367, in _run</div><div>    self.halos_<span class="" id=":2b4.149" tabindex="-1">ds</span>.index</div><div><span class="" id=":2b4.150" tabindex="-1">AttributeError</span>: 'NoneType' object has no attribute 'index'</div></div><div>#######################################################################################</div><div><br></div><div>It seems to me like <span class="" id=":2b4.151" tabindex="-1">rockstar</span> is not finding anything (Exception message) and  then when <span class="" id=":2b4.152" tabindex="-1">yt</span> load and save to disk it fails.</div><div>The simplest working version of my code is the next one:</div><div><br></div><div>#######################################################################################</div><div><div>import <span class="" id=":2b4.153" tabindex="-1">yt</span></div><div>from <span class="" id=":2b4.154" tabindex="-1">yt</span>.mods import *</div><div>from <span class="" id=":2b4.155" tabindex="-1">yt</span>.analysis_modules.halo_analysis.api import <span class="" id=":2b4.156" tabindex="-1">HaloCatalog</span></div><div>from <span class="" id=":2b4.157" tabindex="-1">yt</span>.data_objects.particle_filters import add_particle_filter</div><div>from mpi4py import <span class="" id=":2b4.158" tabindex="-1">MPI</span></div><div>import <span class="" id=":2b4.159" tabindex="-1">numpy</span> as <span class="" id=":2b4.160" tabindex="-1">np</span></div><div><br></div><div><span class="" id=":2b4.161" tabindex="-1">dataDir</span> = "/home/<span class="" id=":2b4.162" tabindex="-1">bruno</span>/Desktop/data/<span class="" id=":2b4.163" tabindex="-1">yt</span>/"</div><div><span class="" id=":2b4.164" tabindex="-1">dataFile</span> = 'DM.Only.tipsy/dwf1.6144.01280'</div><div>ts = <span class="" id=":2b4.165" tabindex="-1">DatasetSeries</span>([<span class="" id=":2b4.166" tabindex="-1">dataDir</span> + <span class="" id=":2b4.167" tabindex="-1">dataFile</span>])</div><div>data_<span class="" id=":2b4.168" tabindex="-1">ds</span> = ts[0]</div><div>#data_<span class="" id=":2b4.169" tabindex="-1">ds</span> = <span class="" id=":2b4.170" tabindex="-1">yt</span>.load( <span class="" id=":2b4.171" tabindex="-1">dataDir</span> + <span class="" id=":2b4.172" tabindex="-1">dataFile</span> )</div><div>data_<span class="" id=":2b4.173" tabindex="-1">ds</span>.set_units( )</div><div><br></div><div>#Add symbol "<span class="" id=":2b4.174" tabindex="-1">Mpccm</span>"</div><div>data_<span class="" id=":2b4.175" tabindex="-1">ds</span>.unit_registry.add( 'Mpccm',</div><div><span class="" style="white-space:pre">                        </span>  float(units.<span class="" id=":2b4.176" tabindex="-1">Mpc</span>.in_<span class="" id=":2b4.177" tabindex="-1">cgs</span>().v), </div><div><span class="" style="white-space:pre">                  </span>  units.dimensions.length)</div><div><br></div><div>#Create particle filter to filter to filter a single mass particle <span class="" id=":2b4.182" tabindex="-1">type</span></div><div>def low_mass(<span class="" id=":2b4.186" tabindex="-1">pfilter</span>, data):</div><div>    filter = data["all", "Mass"] < 1.3e-12 * units.<span class="" id=":2b4.190" tabindex="-1">Msun</span></div><div>    return filter</div><div>add_particle_filter("low_mass", function=low_mass, </div><div>                    filtered_type='all',</div><div>                    requires=["Mass"])</div><div>data_<span class="" id=":2b4.201" tabindex="-1">ds</span>.add_particle_filter("low_mass")</div><div><br></div><div>#Set cosmology <span class="" id=":2b4.206" tabindex="-1">parameters</span></div><div>data_<span class="" id=":2b4.207" tabindex="-1">ds</span>.<span class="" id=":2b4.208" tabindex="-1">hubble</span>_constant = 0.7  </div><div>data_<span class="" id=":2b4.210" tabindex="-1">ds</span>.omega_matter = 0.<span class="" id=":2b4.211" tabindex="-1">3</span></div><div>data_<span class="" id=":2b4.212" tabindex="-1">ds</span>.current_redshift = 0.6</div><div>data_<span class="" id=":2b4.213" tabindex="-1">ds</span>.omega_lambda = 0.<span class="" id=":2b4.214" tabindex="-1">7</span></div><div><br></div><div>#Arguments for <span class="" id=":2b4.216" tabindex="-1">RockstarHoloFinder</span></div><div><span class="" id=":2b4.217" tabindex="-1">rockstar</span>_<span class="" id=":2b4.218" tabindex="-1">kwargs</span> = {</div><div>'particle_type': 'low_mass',</div><div>'force_res': 1e-4  #<span class="" id=":2b4.226" tabindex="-1">100pc</span></div><div>}</div><div><br></div><div><span class="" id=":2b4.227" tabindex="-1">hc</span> = <span class="" id=":2b4.228" tabindex="-1">HaloCatalog</span>(data_<span class="" id=":2b4.229" tabindex="-1">ds</span>=data_<span class="" id=":2b4.230" tabindex="-1">ds</span>, </div><div><span class="" style="white-space:pre">             </span> finder_method='rockstar', </div><div><span class="" style="white-space:pre">               </span> finder_<span class="" id=":2b4.233" tabindex="-1">kwargs</span> = <span class="" id=":2b4.234" tabindex="-1">rockstar</span>_<span class="" id=":2b4.235" tabindex="-1">kwargs</span>)</div><div><span class="" id=":2b4.236" tabindex="-1">hc</span>.create()</div></div><div>##################################################################</div><div><br></div><div>If someone has any suggestion  I would really appreciate it.</div><div><br></div><div>Thanks,</div><div><span class="" id=":2b4.245" tabindex="-1">Bruno</span></div></div>