Mailman 3 October 2016 - yt-users

Error in Rockstar Halo Finding
by Reju Sam John Oct. 26, 2016

Oct. 26, 2016

Hi all, I am trying to run Rockstar Halo Finding with the following code. from yt.mods import * from yt.analysis_modules.halo_finding.rockstar.api import RockstarHaloFinder #find all of our simulation files files = glob.glob("RD*/*hierarchy") #hopefully the file name order is chronological files.sort() print files ts = TimeSeriesData.from_filenames(files[:]) rh = RockstarHaloFinder(ts) rh.run() but I am getting the following error. File "rockstar_halo_finding.py", line 14, in <module> rh = RockstarHaloFinder(ts) File "/home/john/yt_new/yt-x86_64/src/yt-hg/yt/analysis_modules/halo_finding/rockstar/rockstar.py", line 220, in __init__ self.pool, self.workgroup = self.runner.setup_pool() File "/home/john/yt_new/yt-x86_64/src/yt-hg/yt/analysis_modules/halo_finding/rockstar/rockstar.py", line 102, in setup_pool (self.num_writers, "writers") ] File "/home/john/yt_new/yt-x86_64/src/yt-hg/yt/utilities/parallel_tools/parallel_analysis_interface.py", line 325, in from_sizes pool.add_workgroup(size, name = name) File "/home/john/yt_new/yt-x86_64/src/yt-hg/yt/utilities/parallel_tools/parallel_analysis_interface.py", line 293, in add_workgroup group = self.comm.comm.Get_group().Incl(ranks) AttributeError: 'NoneType' object has no attribute 'Get_group' could you please explain what is going wrong here ? Thank you. -- Reju Sam John

2 1

librockstar.so not loaded
by oleg burgueño Oct. 25, 2016

Oct. 25, 2016

Hi people from the yt mailing list, I'm trying to import to python the rockstar halo finder and it says that an import error occurred. I installed yt via the installation script with INST_CONDA=0, INST_YT_SOURCE=1, ROCKSTAR = 1 ImportError: dlopen(/Users/Oleg/yt-x86_64/src/yt-hg/yt/analysis_modules/halo_finding/rockstar/rockstar_interface.so, 2): Library not loaded: librockstar.so Referenced from: /Users/Oleg/yt-x86_64/src/yt-hg/yt/analysis_modules/halo_finding/rockstar/rockstar_interface.so Reason: image not found I'll appreciate any help Oleg

2 1

create_profile + particle_mass
by John Regan Oct. 21, 2016

Oct. 21, 2016

Hi All, I'm getting some strange results when I try to profile the particle distribution. I'm using the Enzo64 dataset pulled from the YTHub. I use the following very simple script but get values which are different by 50 orders of magnitude. I must be doing something very wrong with the create_profile routine but its not obvious prof = create_profile(sp, [("all", "particle_radius")], [("all", "particle_mass")], weight_field=None) Any ideas what's going wrong here? Looks at a minimum that the units are getting messed up? Cheers, John

2 2

RuntimeError: yt attempted to read outside the boundaries
by Slavin, Jonathan Oct. 20, 2016

Oct. 20, 2016

Hi all, I have a simulation on a 3D cartesian grid and when trying to get surfaces of various types I keep getting the error message: " RuntimeError: Error: yt attempted to read outside the boundaries of a non-periodic domain along dimension 0. Region left edge = -1.157125e+19 code_length, Region right edge = 1.7356875e+19 code_length Dataset left edge = 0.0 code_length, Dataset right edge = 9.257e+19 code_length This commonly happens when trying to compute ghost cells up to the domain boundary. Two possible solutions are to load a smaller region that does not border the edge or override the periodicity for this dataset. " So, I don't think I should override the periodicity for the dataset, since it is decidedly not periodic. I could load a smaller region, I suppose, but not without significant effort, since I really want to include the volume out to some radial distance from the lower left corner (0,0,0). I would need to define some slightly smaller octant, I guess. Anyway, shouldn't there be some way to specify to yt that it should calculate ghost zones via some given boundary condition? That is, if it really even needs to use ghost zones (which I'm not sure why it does). Regards, Jon -- ________________________________________________________ Jonathan D. Slavin Harvard-Smithsonian CfA jslavin(a)cfa.harvard.edu 60 Garden Street, MS 83 phone: (617) 496-7981 Cambridge, MA 02138-1516 cell: (781) 363-0035 USA ________________________________________________________

2 1

Derived fields for generic array data
by Will Barnes Oct. 20, 2016

Oct. 20, 2016

Hi yt users, I have a question about derived fields in a dataset loaded from generic array data. I’ve created a dataset from a three dimensional Numpy array and traced some streamlines (say N of them) through the volume (this is a 3D magnetic field) such that I now have a set of N fieldlines. External to the dataset, I then have N Numpy arrays corresponding to each of the N streamlines, each the same length of the corresponding streamline, that represent the density as a function of the position along the streamline. What I’d like to do is create a new derived field (“density”) where the values from each of my external numpy arrays are mapped to the corresponding coordinate (as determined by the streamlines) and then “density” is zero everywhere else. I’ve read the documentation about creating derived fields and adding fields to a dataset, but it is not clear to me how to use external information (e.g. my set of N arrays) to create a new or derived field as all the examples show only how to use already existing fields in the dataset to create a new field. This seems like a relatively simple thing so perhaps I am just missing something or not quite understanding how a new field is added to a dataset? Since my explanation above is a bit confusing, I’ve included a code snippet below that hopefully illustrates a bit better what I’d like to do. Thanks! Will Barnes ``` # create 3d numpy array arr = np.random.random(size=(64,64,64)) # load generic data into a dataset data = dict(density = (arr, "g/cm**3")) bbox = np.array([[-1.5, 1.5], [-1.5, 1.5], [-1.5, 1.5]]) ds = yt.load_uniform_grid(data, arr.shape, length_unit="Mpc", bbox=bbox, nprocs=64) # set seed points c = ds.domain_center N = 100 scale = ds.domain_width[0] pos_dx = np.random.random((N,3))*scale-scale/2. pos = c+pos_dx # Create streamlines streamlines = Streamlines(ds, pos, 'velocity_x', 'velocity_y', 'velocity_z',length=1.0*Mpc, get_magnitude=True) streamlines.integrate_through_volume() # create a density field in ds initialized as 0 everywhere # for each streamline in streamlines, find coordinates from streamline and add the appropriate density value to the coordinates ```

3 2

Problem loading FLASH2.5 data
by Philipp Girichidis Oct. 20, 2016

Oct. 20, 2016

Dear YT users, I upgraded my version of YT from an older version that still installed the libraries on its own (version downloaded 2016/06/21) to a more recent version using yt-conda. With the new version I cannot read old FLASH2.5 data any more. The previous version of yt gave me the correct output yt : [INFO ] 2016-09-09 16:37:59,285 Parameters: current_time = 1260000000.0 yt : [INFO ] 2016-09-09 16:37:59,286 Parameters: domain_dimensions = [8 8 8] yt : [INFO ] 2016-09-09 16:37:59,289 Parameters: domain_left_edge = [ -4.00000000e+17 -4.00000000e+17 -4.00000000e+17] yt : [INFO ] 2016-09-09 16:37:59,290 Parameters: domain_right_edge = [ 4.00000000e+17 4.00000000e+17 4.00000000e+17] yt : [INFO ] 2016-09-09 16:37:59,291 Parameters: cosmological_simulation = 0.0 the new version does not read some of the numbers properly, yt : [INFO ] 2016-09-09 16:39:11,692 Parameters: current_time = 1.06099789548e-313 yt : [INFO ] 2016-09-09 16:39:11,692 Parameters: domain_dimensions = [1104332420 0 1102957925] yt : [INFO ] 2016-09-09 16:39:11,693 Parameters: domain_left_edge = [ -4.00000000e+17 -4.00000000e+17 -4.00000000e+17] yt : [INFO ] 2016-09-09 16:39:11,694 Parameters: domain_right_edge = [ 4.00000000e+17 4.00000000e+17 4.00000000e+17] yt : [INFO ] 2016-09-09 16:39:11,695 Parameters: cosmological_simulation = 0.0 The time value as well as the dimensions are messed up and thus yt crashes with a memory error at some point. To me it looks like a conversion problem between big and little endian or some similar conversion problem between single and double precision. I tried various combinations of MAC and linux and the problem does not seem to operating system dependent. Quite a few functions have changed in terms of reading particle data, but the simulation does not contain particles. I tried to find the part of the code that reads the domain_dimensions and looked at file yt-conda/lib/python2.7/site-packages/yt/frontends/flash/data_structures.py where in line 99ff the block dimensions are read. But this part of the code is not executed (checked with print statements in iyt). Loading the hdf5 file with h5py and using the code in line 104 gives me the correct numbers, but I guess yt reads the data from somewhere else? Any hints on how the hierarchy of reading data is organized or where to search? I know FLASH2.5 is very old but we still have a lot of (quite expensive) F2.5 data. With best regards, Philipp Girichidis

7 10

error while trying to find abundances through checkpoint files
by tazkera haque Oct. 18, 2016

Oct. 18, 2016

HI people, I am using yt 3.3.1 and submitting my SLURM script to stampede. I was using this script to find abundances of C, O etc through checkpoint files in FLASH. while my script worked fine with old yt (3.1) , suddenly it crashed today and returned me the following error: *yt : [INFO ] 2016-10-17 23:22:24,295 Parameters: current_time = 28.1847530806* *yt : [INFO ] 2016-10-17 23:22:24,295 Parameters: domain_dimensions = [128 128 128]* *yt : [INFO ] 2016-10-17 23:22:24,296 Parameters: domain_left_edge = [ -2.80000000e+10 -2.80000000e+10 -2.80000000e+10]* *yt : [INFO ] 2016-10-17 23:22:24,296 Parameters: domain_right_edge = [ 2.80000000e+10 2.80000000e+10 2.80000000e+10]* *yt : [INFO ] 2016-10-17 23:22:24,296 Parameters: cosmological_simulation = 0.0* *Executin lessg abundance.py* *Traceback (most recent call last):* * File "abundance2.py", line 304, in <module>* * main(chkFilenames_own)* * File "abundance2.py", line 59, in main* * pf = yt.load(filenames[n])* * File "/work/03858/thaque56/sw/yt-new-3.3/yt-conda/lib/python2.7/site-packages/yt/convenience.py", line 79, in load* * if c._is_valid(*args, **kwargs): candidates.append(n)* * File "/work/03858/thaque56/sw/yt-new-3.3/yt-conda/lib/python2.7/site-packages/yt/frontends/flash/data_structures.py", line 478, in _is_valid* * if "bounding box" not in fileh["/"].keys() \* * File "/work/03858/thaque56/sw/yt-new-3.3/yt-conda/lib/python2.7/site-packages/h5py/_hl/base.py", line 368, in keys* * return list(self)* * File "h5py/_objects.pyx", line 54, in h5py._objects.with_phil.wrapper (/home/ilan/minonda/conda-bld/work/h5py/_objects.c:2696)* * File "h5py/_objects.pyx", line 55, in h5py._objects.with_phil.wrapper (/home/ilan/minonda/conda-bld/work/h5py/_objects.c:2654)* * File "/work/03858/thaque56/sw/yt-new-3.3/yt-conda/lib/python2.7/site-packages/h5py/_hl/group.py", line 303, in __len__* * return self.id.get_num_objs()* * File "h5py/_objects.pyx", line 54, in h5py._objects.with_phil.wrapper (/home/ilan/minonda/conda-bld/work/h5py/_objects.c:2696)* * File "h5py/_objects.pyx", line 55, in h5py._objects.with_phil.wrapper (/home/ilan/minonda/conda-bld/work/h5py/_objects.c:2654)* * File "h5py/h5g.pyx", line 321, in h5py.h5g.GroupID.get_num_objs (/home/ilan/minonda/conda-bld/work/h5py/h5g.c:4194)* *RuntimeError: Can't determine (Bad symbol table node signature)* *[c560-102.stampede.tacc.utexas.edu:mpispawn_0][child_handler] MPI process (rank: 0, pid: 22137) exited with status 1* *TACC: MPI job exited with code: 1* *TACC: Shutdown complete. Exiting.* I was wondering if there is something wrong with my code or the new yt. I am also attaching my code here to look at. Thanks in advance Best Tazkera

3 9

Re: [yt-users] yt-users Digest, Vol 104, Issue 17
by Slavin, Jonathan Oct. 18, 2016

Oct. 18, 2016

Hi Nathan, Yes, if I could define the surface in terms of field values, things would be easier. Unfortunately I can't really do that. The thing is I want to define the outer shock wave in a simulation via a pressure criterion, which can work, but then there are regions in my simulation inside the shock that have pressure values below the cutoff value, which would then not be included in the volume. Jon On Tue, Oct 18, 2016 at 4:33 PM, <yt-users-request(a)lists.spacepope.org> wrote: > If you can define your surface in terms of field values, you can use a > cut_region data object: > > http://yt-project.org/doc/analyzing/filtering.html#cut-regions > > http://yt-project.org/doc/reference/api/generated/yt. > data_objects.selection_data_containers.YTCutRegion.html# > yt.data_objects.selection_data_containers.YTCutRegion > > I don't think there is a way to create a data object from a triangulated > surface. In principle it would be possible to add by creating a new data > object and adding new hooks to cython geometric selector API, but that has > not yet been implemented. > > -Nathan > -- ________________________________________________________ Jonathan D. Slavin Harvard-Smithsonian CfA jslavin(a)cfa.harvard.edu 60 Garden Street, MS 83 phone: (617) 496-7981 Cambridge, MA 02138-1516 cell: (781) 363-0035 USA ________________________________________________________

1 0

finding grid points within a volume
by Slavin, Jonathan Oct. 18, 2016

Oct. 18, 2016

Hi all, I'm looking for a way to find all the grid points in a volume, or really within a surface. I can get the surface using skimage.measure.marching_cubes (or I guess from the surface method of a data source). That is, it provides vertices that define a surface. What I then want to know is which grid points for an array that covers the simulation volume (fixed resolution array) are within that volume. It appears that yt is set up to calculate the flux across an isocontour, but I don't see anything related to the volume within it. Any help would be appreciated. Regards, Jon -- ________________________________________________________ Jonathan D. Slavin Harvard-Smithsonian CfA jslavin(a)cfa.harvard.edu 60 Garden Street, MS 83 phone: (617) 496-7981 Cambridge, MA 02138-1516 cell: (781) 363-0035 USA ________________________________________________________

2 1

Data Objects across simulation files
by Jason Galyardt Oct. 18, 2016

Oct. 18, 2016

Dear yt-users, Does anyone know whether it's possible to define a data object using one simulation file (an AMR grid simulation -- FLASH) and then apply that physical selection region to another simulation file (representing a different time in the same simulation)? For example, I'd like construct a cut_region data object using, say, temperature and density to select a particular feature at time t_n; I would then like to look at the gas in this same physical region at time t_m, where t_m < t_n. I assume that this would require somehow converting a collection of cells making up the cut_region from time t_n to a description of a (complex) geometrical selection, then applying this geometrical selection to the data file from time t_m. The caveat here is that the cells in the selected region may have time-varying levels of refinement. This seems like a non-trivial feature to implement, so I thought I'd ask whether it's already available. Cheers, Jason ------ Jason Galyardt University of Georgia

3 2