Mailman 3 July 2018 - yt-users

Saving transparent pdfs
by Logan Harbour 26 Jul '18

26 Jul '18

I'm having some trouble saving pdfs that are transparent using .save() with any of the PlotContainer inherited classes. Typically when I have access to the entire figure, plt.savefig has an optional argument Transparent=True that returns the desired result. I've tried to get the underlying figure with my SlicePlot for example, but I also have additional annotations (contours) and I'm not sure how to add these to the underlying figure in order to use plt.savefig. I see that the save function in PlotContainer creates a FigureCanvasPdf object which then calls print_figure (which calls print_pdf). This function does not have an argument for transparency. Thoughts?

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Re: Questions about YT and Dask
by Nathan Goldbaum 25 Jul '18

25 Jul '18

We use mpi4py for parallelism: https://yt-project.org/doc/analyzing/parallel_computation.html We are experimenting with using dark for some things, but yt predates dask and has its own capabilities for out of core and parallel computation. Deeper integration with dask is amethyst g we might explore in the future but we have no current concrete plans. Also please direct questions like this to the mailing list (cc’d) rather than to the mailing list admins. On Tue, Jul 24, 2018 at 7:07 PM Aaron Chu <xweichu(a)ucsc.edu> wrote: > Dear teams, > > We're working on a project which needs yt lib to access boxlib data such > as Amex. And we consider to distribute the computation across multiple > nodes. Is there a way that yt can be used with distributed computation > framework like dask(https://dask.pydata.org/en/latest/)? Or any features > are under development to support Dask? > > Appreciate your time. Thanks. > > > -- > Best Regards, > Aaron Chu >

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Configuring ytini on the Mac
by bach44＠gmail.com 24 Jul '18

24 Jul '18

Hi novice Python user trying to get ytini (Houdini for Astronomy) up and running on my Mac. Followed instructions, using miniconda and then installed the yt package. Confirmed that it is correctly installed. But from within Houdini's Python shell when I try and do an import yt I get a package not found error. I assume my pathing is wrong. The install directions here http://ytini.com/getstarted.html suggest modifying your .bash_profile which I've done after first making necessary changes. But the directions assume there is a yt-conda directory /Users/<userfoo>/yt-conda/bin and also a yt-conda/sbin directory /Users/<userfoo>/yt-conda/sbin but I have neither. Only the following /Users/<userfoo>/miniconda3/bin What changes should I make to my pathing to make Houdini recognize the yt package install? Thanks!

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Issue with contours and Exodus output
by Logan Harbour 24 Jul '18

24 Jul '18

I have a simplified example of a 2x2x2 cuboid mesh with constant values on each element, stored in the variable group_0 in Exodus format (this is all done with MOOSE). My environment is Yt 3.4.1 and Python 3.6.5. If I do a SlicePlot and try to use annotate_contour, I end up with an indexing error. I've tried to follow the traceback but frankly I'm not well versed enough with Yt to make any sense of it. Interestingly, if I instead attempt to plot a 2x2x1 mesh cut in the z-plane, the contours will plot without issue. I've uploaded the full output, the simple (4 line) example, and my Exodus file: http://use.yt/upload/078c018a Thank you in advance for the assistance.

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Rockstar force_res attribute issue
by sflarkin＠ucsc.edu 21 Jul '18

21 Jul '18

Hello all, In the rockstar call function if you dont supply a force_res for your simulation, it runs the call if force_res is None: tds = ts[-1] # Cache a reference self.force_res = tds.index.get_smallest_dx().in_units("Mpc/h") # We have to delete now to wipe the index del tds in the runrockstar.py file in yt. However, I get an error File "./runrockstar.py", line 266, in <module> num_readers=args['num_readers']) File "./runrockstar.py", line 198, in run_rockstar particle_mass=dm_min_mass) File "/home1/sflarkin/build/yt/yt/analysis_modules/halo_finding/rockstar/rockstar.py", line 221, in __init__ self.force_res = tds.index.get_smallest_dx().in_units("Mpc/h") P014 yt : [ERROR ] 2018-07-20 13:58:08,873 AttributeError: 'numpy.float64' object has no attribute 'in_units' I am not sure what is causing this, I have been looking in my fields for a problem but do not see any.

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Writing FITS Image
by Prateek Gupta 20 Jul '18

20 Jul '18

Hello, yt-users, I am using yt.FITSProjection to write the field projection to a FITS file. As stated in the documentation, it always makes projections of the width of domain size. But I need to make the FITS projection plot with defined width or arbitrary box size. Is there any way to do so? I tried with Geometry Data objects as it contains the data set as a whole but problem is that it doesn't have the coordinates attribute. Is there any way to take out the coordinate info also, or create a small dataset of ENZO simulation (cube of small size). Thanks, -Prateek

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Running a Dev Fork
by sflarkin＠ucsc.edu 20 Jul '18

20 Jul '18

Hello all, I am attempting to run a yt fork I made to fix the issue I noted yesterday. I installed the fork and rockstar support using the conda based install method listed on the install guide, but I can't run any scripts using this new version, as It wont override my default python program. I was wondering the correct way to do this? Thanks

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Running Rockstar Help
by sflarkin＠ucsc.edu 18 Jul '18

18 Jul '18

Hey All, I am having a problem running rockstar with yt. I am updating a python 2 code that was used to run the same simulations I am running, but am getting 2 errors when running it. The first error occurs in this section of code: if MPI.COMM_WORLD.Get_rank()==0: print() print('Beginning Rockstar analysis in ', sim_dir) print('Placing output in ', out_dir) # Generate data series snap_base = sim_dir+ '/' + snap_base + '*' ts = yt.DatasetSeries(snap_base) if len(ts) > 1: first_snap = ts[0] last_snap = ts[-1] if MPI.COMM_WORLD.Get_rank()==0: print('first snapshot: ', first_snap.basename) print('last snapshot: ', last_snap.basename) else: last_snap = ts[0] if MPI.COMM_WORLD.Get_rank()==0: print('snapshot: ', last_snap.basename) # Create particle union if needed particle_type = particle_types[0] ad = last_snap.all_data() particle_masses = yt.np.unique(ad[(particle_type, 'particle_mass')].in_units('Msun/h')) total_particles = ad.quantities.total_quantity((particle_type, "particle_ones")) if MPI.COMM_WORLD.Get_rank()==0: print('Using particle(s) ', particle_types, ' with mass(es) ', particle_masses) print() When the script gets to the total_particles = ad.quantities...., I get this error: File "./runrockstar.py", line 269, in <module> num_readers=args['num_readers']) File "./runrockstar.py", line 149, in run_rockstar particle_masses = yt.np.unique(ad[(particle_type, 'particle_mass')].in_units('Msun/h')) File "/home1/sflarkin/build/yt-conda/src/yt-git/yt/data_objects/data_containers.py", line 282, in __getitem__ self.get_data(f) File "/home1/sflarkin/build/yt-conda/src/yt-git/yt/data_objects/data_containers.py", line 1334, in get_data particles, self, self._current_chunk) File "/home1/sflarkin/build/yt-conda/src/yt-git/yt/geometry/geometry_handler.py", line 227, in _read_particle_fields fields_to_read) File "/home1/sflarkin/build/yt-conda/src/yt-git/yt/utilities/io_handler.py", line 199, in _read_particle_selection psize = self._count_particles_chunks(chunks, ptf, selector) File "/home1/sflarkin/build/yt-conda/src/yt-git/yt/utilities/io_handler.py", line 170, in _count_particles_chunks for ptype, (x, y, z) in self._read_particle_coords(chunks, ptf): File "/home1/sflarkin/build/yt-conda/src/yt-git/yt/frontends/art/io.py", line 102, in _read_particle_coords x = self._get_field((ptype, "particle_position_x")) File "/home1/sflarkin/build/yt-conda/src/yt-git/yt/frontends/art/io.py", line 139, in _get_field tr[field] = rp([ax])[0]/dd - off File "/home1/sflarkin/build/yt-conda/src/yt-git/yt/frontends/art/io.py", line 134, in <lambda> idxb=idxb, fields=ax) File "/home1/sflarkin/build/yt-conda/src/yt-git/yt/frontends/art/io.py", line 458, in read_particles ranges = get_ranges(skip, count, field, **kwargs) File "/home1/sflarkin/build/yt-conda/src/yt-git/yt/frontends/art/io.py", line 425, in get_ranges for page in range(num_pages): P001 yt : [ERROR ] 2018-07-17 15:24:08,955 TypeError: 'float' object cannot be interpreted as an integer P001 yt : [ERROR ] 2018-07-17 15:24:08,955 Error occured on rank 1. I am not sure why this is occuring, and if I am missing something obvious. The other error occurs when attempting to clear the cache, done as follows: if len(ts) > 1 : del first_snap del last_snap _cached_datasets.clear() but _cached_datasets is said as not defined, despite being called by an earlier call of: from yt.data_objects.static_output import _cached_datasets I am wondering if this is the correct way to go about that? Thanks

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Running Rockstar Help
by Sean Larkin 18 Jul '18

18 Jul '18

I am having a problem running rockstar with yt. I am updating a python 2 code that was used to run the same simulations I am running, but am getting 2 errors when running it. The first error occurs in this section of code: if MPI.COMM_WORLD.Get_rank()==0: print() print('Beginning Rockstar analysis in ', sim_dir) print('Placing output in ', out_dir) # Generate data series snap_base = sim_dir+ '/' + snap_base + '*' ts = yt.DatasetSeries(snap_base) if len(ts) > 1: first_snap = ts[0] last_snap = ts[-1] if MPI.COMM_WORLD.Get_rank()==0: print('first snapshot: ', first_snap.basename) print('last snapshot: ', last_snap.basename) else: last_snap = ts[0] if MPI.COMM_WORLD.Get_rank()==0: print('snapshot: ', last_snap.basename) # Create particle union if needed particle_type = particle_types[0] ad = last_snap.all_data() particle_masses = yt.np.unique(ad[(particle_type, 'particle_mass')].in_units('Msun/h')) total_particles = ad.quantities.total_quantity((particle_type, "particle_ones")) if MPI.COMM_WORLD.Get_rank()==0: print('Using particle(s) ', particle_types, ' with mass(es) ', particle_masses) print() When the script gets to the total_particles = ad.quantities...., I get this error: File "./runrockstar.py", line 269, in <module> num_readers=args['num_readers']) File "./runrockstar.py", line 149, in run_rockstar particle_masses = yt.np.unique(ad[(particle_type, 'particle_mass')].in_units('Msun/h')) File "/home1/sflarkin/build/yt-conda/src/yt-git/yt/data_objects/data_containers.py", line 282, in __getitem__ self.get_data(f) File "/home1/sflarkin/build/yt-conda/src/yt-git/yt/data_objects/data_containers.py", line 1334, in get_data particles, self, self._current_chunk) File "/home1/sflarkin/build/yt-conda/src/yt-git/yt/geometry/geometry_handler.py", line 227, in _read_particle_fields fields_to_read) File "/home1/sflarkin/build/yt-conda/src/yt-git/yt/utilities/io_handler.py", line 199, in _read_particle_selection psize = self._count_particles_chunks(chunks, ptf, selector) File "/home1/sflarkin/build/yt-conda/src/yt-git/yt/utilities/io_handler.py", line 170, in _count_particles_chunks for ptype, (x, y, z) in self._read_particle_coords(chunks, ptf): File "/home1/sflarkin/build/yt-conda/src/yt-git/yt/frontends/art/io.py", line 102, in _read_particle_coords x = self._get_field((ptype, "particle_position_x")) File "/home1/sflarkin/build/yt-conda/src/yt-git/yt/frontends/art/io.py", line 139, in _get_field tr[field] = rp([ax])[0]/dd - off File "/home1/sflarkin/build/yt-conda/src/yt-git/yt/frontends/art/io.py", line 134, in <lambda> idxb=idxb, fields=ax) File "/home1/sflarkin/build/yt-conda/src/yt-git/yt/frontends/art/io.py", line 458, in read_particles ranges = get_ranges(skip, count, field, **kwargs) File "/home1/sflarkin/build/yt-conda/src/yt-git/yt/frontends/art/io.py", line 425, in get_ranges for page in range(num_pages): P001 yt : [ERROR ] 2018-07-17 15:24:08,955 TypeError: 'float' object cannot be interpreted as an integer P001 yt : [ERROR ] 2018-07-17 15:24:08,955 Error occured on rank 1. I am not sure why this is occuring, and if I am missing something obvious. The other error occurs when attempting to clear the cache, done as follows: if len(ts) > 1 : del first_snap del last_snap _cached_datasets.clear() but _cached_datasets is said as not defined, despite being called by an earlier call of: from yt.data_objects.static_output import _cached_datasets I am wondering if this is the correct way to go about that? Thanks

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John Hunter Plotting Contest
by Nathan Goldbaum 12 Jul '18

12 Jul '18

Hi all, I'm here at the scipy conference this week where they just announced the winners of the John Hunter Excellence in Plotting Contest. This year the second prize winner was Enrico Garaldi, who made a very nice visualization of a cosmological RAMSES simulation using yt to extract the data and matplotlib to make the plot. You can see more details about this plot here: http://droettboom.com/jhepc2018-judge-packet/entry19.html Congratulations Enrico and congratulations to the other winners and honorable mentions as well. -Nathan

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