[yt-users] Re: Error when loading "AmrEx/BoxLib" (plotfile) by yt

I tried this just now, using a LyA plotfile generated with Nyx 18.05 and amrex 18.05, using yt 3.4.1 as downloaded from the install_script and I was able to print the field list. Max Katz Solutions Architect | NVIDIA Corporation www.mkatz.net On Thu, May 24, 2018 at 4:58 PM, Nathan Goldbaum wrote:

Hey Casey,

Which version of yt are you using? If you're not using the latest version from the git master branch, I'd try that. Support for AMReX data is still pretty new in yt and there's some code changes that haven't made it into a release yet that might fix this issue.

There are instructions for building yt from source here:

http://yt-project.org/doc/installing.html#installing-yt-from-source

If you continue to have trouble after installing the development version, then I'd recommend filing an issue (https://github.com/yt-project /yt/issues/new). If you can include the data file that triggers the issue along with a test script that would help.

-Nathan

On Thu, May 24, 2018 at 6:51 PM, wrote:

...

Hi,

I run a code(Nyx) and it generates "AmrEx/BoxLib" (plotfile) files The code I run to generate "AmrEx/BoxLib" (plotfile) files is here. I have cloned these two code https://github.com/AMReX-Codes/amrex and https://github.com/AMReX-Astro/Nyx and follow the chapter 1 in Nyx User guide to run the most basic Lya example.

It generates the several plotfile directories and I want to use yt to read the plotfile and visualize it.

I have read these two links https://amrex-codes.github.io/amrex/docs_html/Visualization.html#yt http://yt-project.org/doc/examining/loading_data.html (Section of AMReX / BoxLib Data) and follow the instruction to load the one of the plotfile directory.

The problem is here.... This is my python(yt) code to read the plotfile ("plt00302" is the plotfile directory)

import yt print(yt.__version__) ds = yt.load("plt00302") print(ds.field_list)

The first three lines is ok and no error. This line,"ds = yt.load("plt00302")", even print some information which looks reasonable. But the last line, "print(ds.field_list)" gives me the following error message.

Traceback (most recent call last): File "boxlibTest.py", line 4, in <module> print(ds.field_list) File "/home/myUserName/anaconda3/lib/python3.6/site-packages/yt/data_objects/static_output.py", line 546, in field_list return self.index.field_list File "/home/myUserName/anaconda3/lib/python3.6/site-packages/yt/data_objects/static_output.py", line 504, in index self, dataset_type=self.dataset_type) File "/home/myUserName/anaconda3/lib/python3.6/site-packages/yt/f rontends/boxlib/data_structures.py", line 1215, in __init__ super(NyxHierarchy, self).__init__(ds, dataset_type) File "/home/myUserName/anaconda3/lib/python3.6/site-packages/yt/f rontends/boxlib/data_structures.py", line 337, in __init__ self._cache_endianness(self.grids[-1]) File "/home/myUserName/anaconda3/lib/python3.6/site-packages/yt/f rontends/boxlib/data_structures.py", line 467, in _cache_endianness _header_pattern[self.dimensionality-1].search(header).groups() AttributeError: 'NoneType' object has no attribute 'groups'

Any one has suggestion or solution about this?

Thanks _______________________________________________ yt-users mailing list -- yt-users@python.org To unsubscribe send an email to yt-users-leave@python.org

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