yt-users

yt-users@python.org

2791 discussions

[ANN] yt 4.1.2
by Clément Robert 19 Nov '22

19 Nov '22

Announcing yt 4.1.2 ! This is a bugfix release with no new features, all users are encouraged to upgrade. See the release notes for details https://github.com/yt-project/yt/releases/tag/yt-4.1.2 Clément, for the yt dev team

1 0

ytree 3.2 released!
by Britton Smith 18 Nov '22

18 Nov '22

HI everyone, ytree 3.2.0 is released! ytree is an extension of yt for analyzing merger trees. This release includes the addition of two new frontends for Gadget4 and the newer AHF format as well as some enhancements to the documentation and bugfixes for the older AHF format. See below for detailed information. Thanks as always to the wonderful yt community. Britton New Features - Add Gadget4 frontend. #138 <https://github.com/ytree-project/ytree/pull/138> - Update AHF frontend for new format #154 <https://github.com/ytree-project/ytree/pull/154> Minor Enhancements - Add plotting examples and improve examples documentation. #142 <https://github.com/ytree-project/ytree/pull/142> - Update installation instructions to include conda option. #135 <https://github.com/ytree-project/ytree/pull/135> Bugfixes - Fix two AHF frontend issues. #149 <https://github.com/ytree-project/ytree/pull/149> Infrastructure Updates - Drop python 3.7 support and update circle images. #150 <https://github.com/ytree-project/ytree/pull/150> - Add script to fix filename in junit output. #152 <https://github.com/ytree-project/ytree/pull/152> - Fix flake8 errors. #144 <https://github.com/ytree-project/ytree/pull/144> ytree can be installed with pip or conda: pip install ytree conda install ytree Full documentation can be found at https://ytree.readthedocs.io/ Full Changelog: ytree-3.1.2...ytree-3.2.0 <https://github.com/ytree-project/ytree/compare/ytree-3.1.2...ytree-3.2.0>

1 0

problem creating point object
by Slavin, Jonathan 18 Oct '22

18 Oct '22

Hi, I have some FLASH data from a 2-D simulation (cylindrical symmetry, R-Z) and I was trying to get point objects following the approach on the web page: https://yt-project.org/doc/analyzing/objects.html?highlight=interpolate There it indicates that you can do something like: ds = yt.load(file) pt = ds.r[(10.0, "km"), (200, "m"), (1.0, "km")] In my case I just give 0 for the last value since it doesn't matter in 2D. However if I try that I get the error message: --------------------------------------------------------------------------- YTDimensionalityError Traceback (most recent call last) Cell In [4], line 1 ----> 1 pt = ds.r[(rinit,'pc'), (zinit,'pc'), (0.,'pc')] File /export/slavin/anaconda3/envs/py38/lib/python3.8/site-packages/yt/data_objects/region_expression.py:67, in RegionExpression.__getitem__(self, item) 61 item.insert(idx, slice(None)) 63 if len(item) != self.ds.dimensionality: 64 # Not the right specification, and we don't want to do anything 65 # implicitly. Note that this happens *after* the implicit expansion 66 # of a single slice. ---> 67 raise YTDimensionalityError(len(item), self.ds.dimensionality) 69 # OK, now we need to look at our slices. How many are a specific 70 # coordinate? 72 nslices = sum(isinstance(v, slice) for v in item) YTDimensionalityError: Dimensionality specified was 3 but we need 2 So I thought this might be due to the data being 2D. Then I tried pt = ds.r[(rinit,'pc'), (zinit,'pc')] but that leads to a TypeError - the message ends with: File /export/slavin/anaconda3/envs/py38/lib/python3.8/site-packages/yt/funcs.py:1119, in validate_3d_array(obj) 1117 def validate_3d_array(obj): 1118 if not is_sequence(obj) or len(obj) != 3: -> 1119 raise TypeError( 1120 "Expected an array of size (3,), received '%s' of " 1121 "length %s" % (str(type(obj)).split("'")[1], len(obj)) 1122 ) TypeError: Expected an array of size (3,), received 'list' of length 2 So is there any way around this? (By the way, I'm using yt 4.1.1 and got the same issue with 4.0.5.) Thanks in advance for any help. Regards, Jon -- Jonathan D. Slavin (he/him) Astrophysicist - High Energy Astrophysics Division Center for Astrophysics | Harvard & Smithsonian Office: (617) 496-7981 | Cell: (781) 363-0035 60 Garden Street | MS 04 | Cambridge, MA 02138

3 4

ANN: yt 4.1.1 is available
by Clément Robert 18 Oct '22

18 Oct '22

yt 4.1.1 is out ! It fixes a couple important bugs that were discovered after the 4.1.0 release, including the octree memory leak recently discussed on the user mailing list. See the release notes on github for details : https://github.com/yt-project/yt/releases/tag/yt-4.1.1 Happy analysis! Clément, on behalf of the yt team

1 0

Potential memory leak in Ramses frontend
by Anne Noer Kolborg 12 Oct '22

12 Oct '22

Dear yt community, I am have encountered an out-of-memory problem (potential memory leak) when using yt to load and process several Ramses outputs in a row. Each simulation output is approximately 3 GB, but the RAM usage easily exceeds 16 GB in ~30 mins of computation time (single threaded computation time). When allocated more RAM the computation continues for longer but ultimately always runs out the memory before the end of the data-processing. I have created a minimal working example that triggers this problem. It is uploaded here: http://paste.yt-project.org/show/404/ <http://paste.yt-project.org/show/404/> Log of the memory usage over time while running that script is here: http://paste.yt-project.org/show/406/ <http://paste.yt-project.org/show/405/> As you can see the total memory usage simply grows for each round of the loop. I suspect that the memory allocated to the dataset does not get cleared. Simulation output to test the code is uploaded here: http://use.yt/upload/1ace6072 <http://use.yt/upload/1ace6072> The del and clear_data() statements in line 18 and 19 do not impact the memory usage when commented in. I tested the same bit of code using the “HiresIsolatedGalaxy” Enzo dataset from the sample datasets (https://yt-project.org/data/ <https://yt-project.org/data/>). It is similar in size to the outputs I am trying to process and runs without issues. Therefore, I suspect it might be the ramses frontend causing the memory leak. Any advice or pointers on how to debug this further, alternative ways to handle this or suggestions for how to use yt more efficiently are most welcome! Best regards, Anne Version lists: Yt version 4.1.dev, changeset = 39949fb6bfba. (cloned from GitHub about a week ago) - the stable version 4.0.1 also produces the same issue. Python version 3.8.12 Gcc 4.8.5 CentOS Linux release 7.9.2009 // Linux 3.10.0 (x86-64 architecture)

5 7

Quiver Keys in annotate velocity
by daniellin456＠gmail.com 10 Oct '22

10 Oct '22

Hi, Is that possible to add quiver key in the plot when using the annotate_velocity? Thank you

2 1

ANN: yt 4.1.0 is available
by Clément Robert 07 Oct '22

07 Oct '22

yt 4.1.0 is out ! This release represents more than a year worth of work form 30 contributors, and contains many improvements as well as new features. See the release notes on github for details : https://github.com/yt-project/yt/releases/tag/yt-4.1.0 Happy analysis! Clément, on behalf of the yt team

1 0

_fill_fields raise RuntimeError in Derived fields
by hyf＠stu.pku.edu.cn 04 Oct '22

04 Oct '22

Hi Everyone, I met RuntimeError when I tried to plot Derived fields, such as vorticity field derived from velocity field It seems that "tot" calculated from the function "fill_region" raising the "RuntimeError" (See the corresponding yt source code part below) I wonder how to fix up this error and will appreciate if anyone can help me~ -------------------------------------------------------- Here is the plotting vorticity field code PART ONE function 144 def vort_z_func(field, data): 145 return ( 146 + data['boxlib', 'v_gradient_x'] 147 - data['boxlib', 'u_gradient_y'] 148 ) PART TWO main 59 u_gradient = ds.add_gradient_fields(("boxlib","u")) 60 v_gradient = ds.add_gradient_fields(("boxlib","v")) 61 62 derived_fields = [ # field name, units, displayname 63 ('vort_z', '1 / cm', 'Vorticity in z direction') 64 ] 65 for name, unitstr, dispname in derived_fields: 66 ds.add_field( 67 ('boxlib', name), 68 units = unitstr, 69 function = eval(name + '_func'), 70 sampling_type = 'cell', 71 display_name = dispname 72 ) 73 ds.periodicity = (True, True, True) 74 slc = yt.SlicePlot(ds, 'z', 'vort_z', width=((chang,'cm'),(kuan,'cm')),center=([xcent,ycent,0.001],'cm')) -------------------------------------------------------------------------------------------------- Here is the error info: 1084 File "vorfield.py", line 143, in <module> 1085 slc = yt.SlicePlot(ds, 'z', 'vort_z', width=((chang,'cm'),(kuan,'cm')),center=([xcent,ycent,0.001],'cm')) 1086 File "/WORK/anaconde/envs/test/lib/python3.8/site-packages/yt/visualization/plot_window.py", line 1986, in SlicePlot 1087 return AxisAlignedSlicePlot(ds, normal, fields, *args, **kwargs) 1088 File "/WORK/anaconde/envs/test/lib/python3.8/site-packages/yt/visualization/plot_window.py", line 1282, in __init__ 1089 slc.get_data(fields) 1090 File "/WORK/anaconde/envs/test/lib/python3.8/site-packages/yt/data_objects/data_containers.py", line 1583, in get_data 1091 self._generate_fields(fields_to_generate) 1092 File "/WORK/anaconde/envs/test/lib/python3.8/site-packages/yt/data_objects/data_containers.py", line 1603, in _generate_fields 1093 fd = self._generate_field(field) 1094 File "/WORK/anaconde/envs/test/lib/python3.8/site-packages/yt/data_objects/data_containers.py", line 293, in _generate_field 1095 tr = self._generate_fluid_field(field) 1096 File "/WORK/anaconde/envs/test/lib/python3.8/site-packages/yt/data_objects/data_containers.py", line 311, in _generate_fluid_field 1097 rv = self._generate_spatial_fluid(field, ngt_exception.ghost_zones) 1098 File "/WORK/anaconde/envs/test/lib/python3.8/site-packages/yt/data_objects/data_containers.py", line 341, in _generate_spatial_fluid 1099 gz[field][ngz:-ngz, ngz:-ngz, ngz:-ngz], 1100 File "/WORK/anaconde/envs/test/lib/python3.8/site-packages/yt/data_objects/data_containers.py", line 256, in __getitem__ 1101 self.get_data(f) 1102 File "/WORK/anaconde/envs/test/lib/python3.8/site-packages/yt/data_objects/construction_data_containers.py", line 691, in get_data 1103 if len(fill) > 0: self._fill_fields(fill) 1104 File "/WORK/anaconde/envs/test/lib/python3.8/site-packages/yt/data_objects/construction_data_containers.py", line 1060, in _fill_fields 1105 raise RuntimeError --------------------------------------------------------------------------------------------------- Here is the corresponding yt source code part 1053 for chunk in ls.data_source.chunks(fields, "io"): 1054 chunk[fields[0]] 1055 input_fields = [chunk[field] for field in fields] 1056 tot -= fill_region(input_fields, ls.fields, ls.current_level, 1057 ls.global_startindex, chunk.icoords, 1058 chunk.ires, domain_dims, refine_by) 1059 if level == 0 and tot != 0: 1060 raise RuntimeError 1061 self._update_level_state(ls) Best wishes, He Yifeng

1 0

REQ: Help yt cite your papers
by Matthew Turk 13 Sep '22

13 Sep '22

Hi everyone, tl;dr: tell us how to cite your yt-using papers at https://forms.gle/Vkvab2RXLf8oTp3z6 For the last few years, we've been working on a paper about yt-4.0, and the updates since the last paper was published over a decade ago. I've dragged my feet on it a little bit, but I'm hoping that over the next few months the last bits can be written up, polished, and the paper submitted. (See the end of this email for authorship information on the paper!) The current "build" of the paper is here: https://yt-project.github.io/yt-4.0-paper/ with a repository at github.com/yt-project/yt-4.0-paper/ . The paper isn't *yet* complete... which is where this email comes in! I've been trying to collect a somewhat representative set of references to the papers that describe or utilize yt for different simulation platforms. There are two types of citations that we're trying to track down -- citations that describe the simulation platform (i.e., the "method paper" that talks about the code) and those that use yt to analyze data output by the simulation platform (i.e., maybe you wrote a paper and used yt). To make this easy, I've made up a google form: https://forms.gle/Vkvab2RXLf8oTp3z6 If you are able to take a minute and submit a couple references to your work or work you know about that used yt, it would be very, very helpful! And as for the paper itself, we're preparing an email inviting authorship to anyone who has had changes committed into the yt repository, but the authorship policy for the paper is by design very inclusive and described here: https://github.com/yt-project/yt-4.0-paper#authorship-policy . If you have contributed, you are likely going to receive this email, but if you are certain you would like to be included, please follow the instructions in that link to see how to be added to the manuscript. Thanks very much, Matt

1 0

ANN: yt 4.0.5 is out
by Clément Robert 25 Aug '22

25 Aug '22

Fresh bugfix batch is out of the oven: announcing yt 4.0.5 ! We strongly recommend upgrading if you're using yt to analyse SPH data. See the release notes for details https://github.com/yt-project/yt/releases/tag/yt-4.0.5 Happy analysis ! Clément

3 5

Jump to page:

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

yt-users