Mailman 3 September 2014 - yt-users

rockstar exception message
by Bruno Villasenor 19 Sep '14

19 Sep '14

Hi all, I'm trying to run the RockstarHaloFinder via the HaloCatalog function on a TIPSY file. When I run the HaloCatalog function I get the following rockstar output: ######################################################################## P002 yt : [INFO ] 2014-09-15 19:36:11,382 Rockstar is using 1 readers and 1 writers P000 yt : [INFO ] 2014-09-15 19:36:11,382 The citation for the Rockstar halo finder can be found at P001 yt : [INFO ] 2014-09-15 19:36:11,382 Rockstar is using 1 readers and 1 writers P000 yt : [INFO ] 2014-09-15 19:36:11,382 http://adsabs.harvard.edu /abs/2013ApJ...762..109B P000 yt : [INFO ] 2014-09-15 19:36:11,383 Rockstar is using 1 readers and 1 writers P001 yt : [WARNING ] 2014-09-15 19:36:41,582 Total Particle Count: 4.862e+07 [ 0s] Accepting connections... [ 1s] Accepted all reader / writer connections. [ 1s] Verified all reader / writer connections. [ 1s] Transmitted all client connection info. [ 2s] Reading 1 blocks for snapshot 0... Exception yt.utilities.exceptions.YTFieldNotFound: YTFieldNotFound() in 'yt.analysis_modules.halo_finding.rockstar.rockstar_interface.rh_read_particles' ignored [ 2s] Transferring particles to writers... [ 2s] Analyzing for FoF groups... [ 2s] Transferring boundary particles between writers... [ 2s] Linking boundary particles... [ 3s] Analyzing for halos / subhalos... [ 3s] Loading merger tree information... [ 3s] Constructing merger tree... [ 3s] [Success] Done with snapshot 0. [ 3s] [Finished] ####################################################################### followed by the next YT output ####################################################################### P001 yt : [INFO ] 2014-09-15 19:36:44,986 Parameters: current_time = 2.44801700503e+17 s P001 yt : [INFO ] 2014-09-15 19:36:44,987 Parameters: domain_dimensions = [2 2 2] P000 yt : [INFO ] 2014-09-15 19:36:44,994 Parameters: current_time = 2.44801700503e+17 s P000 yt : [INFO ] 2014-09-15 19:36:44,994 Parameters: domain_dimensions = [2 2 2] P000 yt : [INFO ] 2014-09-15 19:36:44,994 Parameters: domain_left_edge = [ 0. 0. 0.] P000 yt : [INFO ] 2014-09-15 19:36:45,012 Parameters: domain_right_edge = [ 0.00207136 0.00207136 0.00207136] P000 yt : [INFO ] 2014-09-15 19:36:45,013 Parameters: cosmological_simulation = 1 P000 yt : [INFO ] 2014-09-15 19:36:45,014 Parameters: current_redshift = 0.6 P001 yt : [INFO ] 2014-09-15 19:36:44,987 Parameters: domain_left_edge = [ 0. 0. 0.] P000 yt : [INFO ] 2014-09-15 19:36:45,014 Parameters: omega_lambda = 0.699999988079 P000 yt : [INFO ] 2014-09-15 19:36:45,014 Parameters: omega_matter = 0.300000011921 P000 yt : [INFO ] 2014-09-15 19:36:45,014 Parameters: hubble_constant = 0.699999988079 P001 yt : [INFO ] 2014-09-15 19:36:45,014 Parameters: domain_right_edge = [ 0.00207136 0.00207136 0.00207136] P001 yt : [INFO ] 2014-09-15 19:36:45,014 Parameters: cosmological_simulation = 1 P001 yt : [INFO ] 2014-09-15 19:36:45,015 Parameters: current_redshift = 0.6 P001 yt : [INFO ] 2014-09-15 19:36:45,015 Parameters: omega_lambda = 0.699999988079 P001 yt : [INFO ] 2014-09-15 19:36:45,015 Parameters: omega_matter = 0.300000011921 P001 yt : [INFO ] 2014-09-15 19:36:45,015 Parameters: hubble_constant = 0.699999988079 P000 yt : [INFO ] 2014-09-15 19:36:45,070 Allocating for 0.000e+00 particles P001 yt : [INFO ] 2014-09-15 19:36:45,070 Allocating for 0.000e+00 particles P002 yt : [INFO ] 2014-09-15 19:36:45,070 Allocating for 0.000e+00 particles Traceback (most recent call last): File "simple_rockstar.py", line 44, in <module> Traceback (most recent call last): File "simple_rockstar.py", line 44, in <module> Traceback (most recent call last): File "simple_rockstar.py", line 44, in <module> hc.create() File "/home/bruno/apps/yt-x86_64/src/yt-hg/yt /analysis_modules/halo_analysis/halo_catalog.py", line 297, in create hc.create() File "/home/bruno/apps/yt-x86_64/src/yt-hg/yt /analysis_modules/halo_analysis/halo_catalog.py", line 297, in create hc.create() File "/home/bruno/apps/yt-x86_64/src/yt-hg/yt /analysis_modules/halo_analysis/halo_catalog.py", line 297, in create self._run(save_halos, save_catalog, njobs=njobs, dynamic=dynamic) File "/home/bruno/apps/yt-x86_64/src/yt-hg/yt /utilities/parallel_tools/parallel_analysis_interface.py", line 248, in barrierize self._run(save_halos, save_catalog, njobs=njobs, dynamic=dynamic) self._run(save_halos, save_catalog, njobs=njobs, dynamic=dynamic) File "/home/bruno/apps/yt-x86_64/src/yt-hg/yt /utilities/parallel_tools/parallel_analysis_interface.py", line 248, in barrierize File "/home/bruno/apps/yt-x86_64/src/yt-hg/yt /utilities/parallel_tools/parallel_analysis_interface.py", line 248, in barrierize retval = func(*args, **kwargs) File "/home/bruno/apps/yt-x86_64/src/yt-hg/yt /analysis_modules/halo_analysis/halo_catalog.py", line 367, in _run self.halos_ds.index AttributeError: 'NoneType' object has no attribute 'index' retval = func(*args, **kwargs) File "/home/bruno/apps/yt-x86_64/src/yt-hg/yt /analysis_modules/halo_analysis/halo_catalog.py", line 367, in _run self.halos_ds.index retval = func(*args, **kwargs) AttributeError: 'NoneType' object has no attribute 'index' File "/home/bruno/apps/yt-x86_64/src/yt-hg/yt /analysis_modules/halo_analysis/halo_catalog.py", line 367, in _run self.halos_ds.index AttributeError: 'NoneType' object has no attribute 'index' ####################################################################################### It seems to me like rockstar is not finding anything (Exception message) and then when yt load and save to disk it fails. The simplest working version of my code is the next one: ####################################################################################### import yt from yt.mods import * from yt.analysis_modules.halo_analysis.api import HaloCatalog from yt.data_objects.particle_filters import add_particle_filter from mpi4py import MPI import numpy as np dataDir = "/home/bruno/Desktop/data/yt/" dataFile = 'DM.Only.tipsy/dwf1.6144.01280' ts = DatasetSeries([dataDir + dataFile]) data_ds = ts[0] #data_ds = yt.load( dataDir + dataFile ) data_ds.set_units( ) #Add symbol "Mpccm" data_ds.unit_registry.add( 'Mpccm', float(units.Mpc.in_cgs().v), units.dimensions.length) #Create particle filter to filter to filter a single mass particle type def low_mass(pfilter, data): filter = data["all", "Mass"] < 1.3e-12 * units.Msun return filter add_particle_filter("low_mass", function=low_mass, filtered_type='all', requires=["Mass"]) data_ds.add_particle_filter("low_mass") #Set cosmology parameters data_ds.hubble_constant = 0.7 data_ds.omega_matter = 0.3 data_ds.current_redshift = 0.6 data_ds.omega_lambda = 0.7 #Arguments for RockstarHoloFinder rockstar_kwargs = { 'particle_type': 'low_mass', 'force_res': 1e-4 #100pc } hc = HaloCatalog(data_ds=data_ds, finder_method='rockstar', finder_kwargs = rockstar_kwargs) hc.create() ################################################################## If someone has any suggestion I would really appreciate it. Thanks, Bruno

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Rollback to yt version 2.x problem
by trobolo dinni 18 Sep '14

18 Sep '14

Dear yt users, recently I updated yt with the update command from version 2 to version 3, but (my error) I did not notice all the changes that had been made from one to the other version. I tried to rollback to version 2.x following the method suggested in this page of the website http://yt-project.org/docs/dev/installing.html for the installation made via the user_script, but when I launche the command python setup.py develop I get the following error: *(yt-x86_64)cthulhu@42828678:~/yt-x86_64/src/yt-hg$ python setup.py develop* *PNG_LOCATION: png.cfg: /home/cthulhu/yt-x86_64/include, /home/cthulhu/yt-x86_64/lib* *FTYPE_LOCATION: FTYPE found via ctypes in: /home/cthulhu/yt-x86_64/include, /home/cthulhu/yt-x86_64/lib* *HDF5_LOCATION: HDF5 found via ctypes in: /home/cthulhu/yt-x86_64/include, /home/cthulhu/yt-x86_64/lib* *running develop* *running build_scripts* *running egg_info* *running build_src* *running build_forthon* *Building package fKD* *Traceback (most recent call last):* * File "/home/cthulhu/yt-x86_64/bin/Forthon", line 2, in <module>* * import Forthon.Forthon_builder* * File "/home/cthulhu/yt-x86_64/lib/python2.7/site-packages/Forthon/Forthon_builder.py", line 88, in <module>* * raise Exception('Main fortran file can not be found, please specify using the fortranfile option')* *Exception: Main fortran file can not be found, please specify using the fortranfile option* *Traceback (most recent call last):* * File "setup.py", line 281, in <module>* * setup_package()* * File "setup.py", line 276, in setup_package* * 'build_src': my_build_src, 'install_data': my_install_data},* * File "/home/cthulhu/yt-x86_64/lib/python2.7/site-packages/numpy/distutils/core.py", line 169, in setup* * return old_setup(**new_attr)* * File "/home/cthulhu/yt-x86_64/lib/python2.7/distutils/core.py", line 151, in setup* * dist.run_commands()* * File "/home/cthulhu/yt-x86_64/lib/python2.7/distutils/dist.py", line 953, in run_commands* * self.run_command(cmd)* * File "/home/cthulhu/yt-x86_64/lib/python2.7/distutils/dist.py", line 972, in run_command* * cmd_obj.run()* * File "/home/cthulhu/yt-x86_64/lib/python2.7/site-packages/distribute-0.6.32-py2.7.egg/setuptools/command/develop.py", line 27, in run* * self.install_for_development()* * File "/home/cthulhu/yt-x86_64/lib/python2.7/site-packages/numpy/distutils/command/develop.py", line 17, in install_for_development* * old_develop.install_for_development(self)* * File "/home/cthulhu/yt-x86_64/lib/python2.7/site-packages/distribute-0.6.32-py2.7.egg/setuptools/command/develop.py", line 110, in install_for_development* * self.run_command('egg_info')* * File "/home/cthulhu/yt-x86_64/lib/python2.7/distutils/cmd.py", line 326, in run_command* * self.distribution.run_command(command)* * File "/home/cthulhu/yt-x86_64/lib/python2.7/distutils/dist.py", line 972, in run_command* * cmd_obj.run()* * File "/home/cthulhu/yt-x86_64/lib/python2.7/site-packages/numpy/distutils/command/egg_info.py", line 10, in run* * self.run_command("build_src")* * File "/home/cthulhu/yt-x86_64/lib/python2.7/distutils/cmd.py", line 326, in run_command* * self.distribution.run_command(command)* * File "/home/cthulhu/yt-x86_64/lib/python2.7/distutils/dist.py", line 972, in run_command* * cmd_obj.run()* * File "setup.py", line 192, in run* * self.run_command("build_forthon")* * File "/home/cthulhu/yt-x86_64/lib/python2.7/distutils/cmd.py", line 326, in run_command* * self.distribution.run_command(command)* * File "/home/cthulhu/yt-x86_64/lib/python2.7/distutils/dist.py", line 972, in run_command* * cmd_obj.run()* * File "setup.py", line 62, in run* * subprocess.check_call(cmd, shell=False)* * File "/home/cthulhu/yt-x86_64/lib/python2.7/subprocess.py", line 540, in check_call* * raise CalledProcessError(retcode, cmd)* *subprocess.CalledProcessError: Command '['/home/cthulhu/yt-x86_64/bin/Forthon', '-F', 'gfortran', '--compile_first', 'fKD_source', '--no2underscores', '--fopt', "'-O3'", 'fKD', 'fKD_source.f90']' returned non-zero exit status 1* I would like to ask some suggestions on how to solve the problem. Thanks, Roberto

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Carpool out of Chicago for the Oct Workshop?
by Jill Naiman 16 Sep '14

16 Sep '14

Hi All! Is anybody driving out of Chicago on the 15th (or 16th) for the yt conference? Its about $200 cheaper of a flight to Chicago than Urbana, so if anybody wants a road trip buddy please feel free to drop me a line in the next day or so. See you all there! -Jill -- Jill P. Naiman, Ph.D. Harvard-Smithsonian Center for Astrophysics jnaiman(a)ucolick.org www.astroblend.com www.avriot.com

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self.recv_points Error When Parallelizing Two Point function
by Piyanat Kittiwisit 16 Sep '14

16 Sep '14

Hi everyone, I ran into a ValueError("self.recv_points is no good!”) when trying to run a TPF script with mpi. I take a look into the TPF source codes, and the issue seems to be related to the comm_size parameters building a TPF object. I tried to vary the value but nothing change. Has anyone run into this issue before? You can see my test script and the output dump in this gist https://gist.github.com/piyanatk/5d6692f0adf01b70ea18. Thanks, -Piyanat

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Point Pairs in the Two Point Function
by Piyanat Kittiwisit 16 Sep '14

16 Sep '14

Hello, I have some questions regarding the two point function in yt-2.6. 1) If my volume is a generic data on a rectangular grid, would the random point pairs be on a regular grid, or would they be truly random on a spherical grid an interpolated/averaged from the nearest neighborhoods on a rectangular grid? 2) If the former is true in 1), does it meant that you have to pick total_values that will not exceed the number of point pairs within your distance? -Piyanat

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FRB question
by David Collins 16 Sep '14

16 Sep '14

Hi, Everybody-- I have a dumb question about getting fixed resolution buffers working in yt3.0. I'm trying the following: >>> slice = ds.slice(0,[0.5]*3) >>> frb = slice.to_frb((1.0,'unitary'),[512,512]) but accessing data in the frb is causing things to choke. Any idea what I might be doing wrong? Thanks! >>> frb['density'] yt : [INFO ] 2014-09-16 09:29:47,060 Making a fixed resolution buffer of (density) 512 by 512 Traceback (most recent call last): File "<stdin>", line 1, in <module> File "/home/dcollins4096/local-yt-2014-08-27/src/yt-hg/yt/visualization/fixed_resolution.py", line 127, in __getitem__ int(self.antialias)) File "/home/dcollins4096/local-yt-2014-08-27/src/yt-hg/yt/geometry/cartesian_coordinates.py", line 54, in pixelize antialias, dimension, periodic) File "/home/dcollins4096/local-yt-2014-08-27/src/yt-hg/yt/geometry/cartesian_coordinates.py", line 67, in _ortho_pixelize buff = _MPL.Pixelize(data_source['px'], data_source['py'], File "/home/dcollins4096/local-yt-2014-08-27/src/yt-hg/yt/data_objects/data_containers.py", line 237, in __getitem__ self.ds.arr(self._generate_container_field(f)) File "/home/dcollins4096/local-yt-2014-08-27/src/yt-hg/yt/data_objects/selection_data_containers.py", line 231, in _generate_container_field self.index._identify_base_chunk(self) File "/home/dcollins4096/local-yt-2014-08-27/src/yt-hg/yt/geometry/grid_geometry_handler.py", line 280, in _identify_base_chunk gi = dobj.selector.select_grids(self.grid_left_edge, File "/home/dcollins4096/local-yt-2014-08-27/src/yt-hg/yt/data_objects/data_containers.py", line 546, in selector self._selector = sclass(self) File "selection_routines.pyx", line 974, in yt.geometry.selection_routines.SliceSelector.__init__ (yt/geometry/selection_routines.c:22578) TypeError: a float is required

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Notes for the first yt team coordinator meeting
by Nathan Goldbaum 15 Sep '14

15 Sep '14

Hi all, We just finished up our first monthly scheduled meeting. For more details about our governance and management plan going forward, YTEP-1776 [0], which was hashed out as a community discussion last month. The notes for the meeting are available in a google doc [1]. If you have any questions, comments, or suggestions please feel free to reply to this thread. We've preliminarily scheduled the next meeting to happen during the yt development workshop at NCSA next month. -Nathan [0] http://ytep.readthedocs.org/en/latest/YTEPs/YTEP-1776.html [1] https://docs.google.com/document/d/1SqXetAVp5IhHH4SdLRwXUyfdQgbiRHCo9m2ydZJ…

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YT-3.0 - quick question - teething problems....
by John Regan 15 Sep '14

15 Sep '14

Hi All, I'm having some teething problems with 3.0. It seems that I have a conflict somewhere but I can't see where. For example I have a very simple script which is doing weird things #Simple simple script import yt filename = "....../RD0000/RD0000" ds = yt.load(filename) This fails with: File "test.py", line 6, in <module> ds = yt.load(filename) AttributeError: 'module' object has no attribute 'load' If instead I change the script to be: #Simple simple script from yt.mods import * filename = "......../RD0000/RD0000" ds = load(filename) sp = ds.h.sphere('max', (10, 'kpc')) prof1d = ProfilePlot(sphere, "radius", "H2I_Fraction") This now loads the file but fails on: File "test.py", line 9, in <module> prof1d = ProfilePlot(sphere, "radius", "H2I_Fraction") NameError: name 'ProfilePlot' is not defined Any ideas what's happening here? Cheers, John (yt-x86_64)[regan@taito-login3 RT]$ yt instinfo yt module located at: /homeappl/home/regan/appl_taito/YT/Dev-3.0/yt-3.0 The current version of the code is: --- 38fff02747ca --- This installation CAN be automatically updated. yt dependencies were last updated on Mon Sep 15 12:40:51 EEST 2014 (yt-x86_64)[regan@taito-login3 RT]$ which pyyt /homeappl/home/regan/appl_taito/YT/Dev-3.0/yt-3.0/doc/yt-x86_64/bin/pyyt

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TIPSY and rockstar in yt
by Bruno Villasenor Alvarez 13 Sep '14

13 Sep '14

Hi everyone, I just started using YT and I find it to be great, thanks for making such a useful tool publicly available. Now my question, Is the rockstar finder method in the HaloCatalog function compatible with TIPSY files? Im trying to pass the TIPSY_LENGTH_CONVERSION and TIPSY_VELOCITY_CONVERSION as kwargs and it doesn't recognize them as valid. Any suggestions? Thanks in advance. Bruno

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Fwd: Blue Waters Advanced User Workshop and yt development workshop
by Matthew Turk 12 Sep '14

12 Sep '14

Hi everyone, As noted below, there's going to be a development workshop for yt at NCSA at University of Illinois Urbana-Champaign, on October 16 and 17. This is going to be a dev workshop, but *everyone* is invited (whether you use Blue Waters or not!). There isn't yet a set schedule, but I hope we can spend time on solidifying support for newer frontends, attaching to running simulations, and hopefully even converting the n-body codes to forest-of-octree from the current implementation. I'm also thinking it might be a good idea to block off an afternoon *just* for converting any analysis modules or analysis code that works on yt 2 but not yt 3. In the next few days I will have information about funding for attendance; please write to me to let me know if you'd like travel support. I can't guarantee anything yet, but I am hoping to have some positive information soon. Hope to see lots of people there! -Matt ---------- Forwarded message ---------- From: <help+bw(a)ncsa.illinois.edu> Date: Mon, Sep 1, 2014 at 3:16 PM Subject: Blue Waters Advanced User Workshop and yt development workshop To: Blue Waters Announcements <noreply(a)ncsa.illinois.edu> We are pleased to announce a three-day, hands-on oriented advanced user workshop about using Blue Waters to its fullest potential. Representatives from Cray, Allinea, PGI and NVIDIA will be on-site to present material and interact with attendees so bring your own code. This work shop is targeting existing or recently allocated, advanced users of Blue Waters. In conjunction with the Blue Waters Advanced User workshop, we are pleased to invite people who are interested in participating in development of the yt project (yt-project.org) to a two-day hands-on development workshop, focusing on parallel and in situ analysis, stabilizing existing data format front-ends, and expanding the capabilities of yt to take advantage of supercomputing resources. Blue Waters Advanced User workshop https://bluewaters.ncsa.illinois.edu/blue-waters-advanced-user-workshop-oct… yt development workshop https://bluewaters.ncsa.illinois.edu/yt-development-workshop-oct-16-17-2014 We hope to see you here.

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