I'm trying to access Exodus II Data from a [MOOSE](https://mooseframework.inl.gov/) application. I'm following the instructions provided [here](http://yt-project.org/doc/examining/loading_data.html#exodus-ii-data). My particular script is follows:
file_name = "results.e"
ds = yt.load(file_name, step=-1)
time = float(ds.current_time)
ad = ds.all_data()
where ("connect1", "rho") is a valid field. This script fails on the last line with a traceback and the following error message:
RuntimeError: Region right edge < left edge: width = 0.0
The particular MOOSE simulation consists of two, 1D meshes. Would anyone know why I'm getting this error and how to overcome it?
Thanks in advance,
SciPy 2019, the 18th annual Scientific Computing with Python conference,
will be held July 8-14, 2019 in Austin, Texas. The annual SciPy Conference
brings together over 800 participants from industry, academia, and
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developers, and collaborate on code development. The call for abstracts for
SciPy 2019 for talks, posters and tutorials is now open. The deadline for
submissions is February 10, 2019.
Conference Website: https://www.scipy2019.scipy.org/
Submission Website: https://easychair.org/conferences/?conf=scipy2019
Talks and Posters (July 10-12, 2019)
In addition to the general track, this year will have specialized tracks
Data Driven Discoveries (including Machine Learning and Data Science)
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There will also be a SciPy Tools Plenary Session each day with 2 to 5
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Tutorials should be focused on covering a well-defined topic in a hands-on
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I have a question about running Rockstar. It appears that yt runs each
writer, each reader, and the main server each on a separate MPI rank.
002 yt : [ERROR ] 2019-01-08 11:39:05,929 6 reader + 6 writers + 1
server != 7 mpi
However, Rockstar documentation
recommends setting both numbers of readers and writers to the number of
Is there any reason why we cannot run reader and writer tasks on the
I listed the commands I executed - just git clone and python3 setup.py
I cannot use pip, on BW it first tries to uninstall the system-wide
distribution of yt, so their Python expert suggested I try setup.py.
On 1/7/19 12:24 PM, Nathan Goldbaum wrote:
> Hi Nick,
> This "setup.py build" thing is new to me. It's not a setup.py command
> we've ever supported or documented for use with yt. I wonder why the
> blue waters staff told you to use it.
> That said, I'm not able to reproduce the failure you're seeing (python3
> setup.py build runs without error after making a fresh clone of the yt
> What branch and changeset are you building yt from?
> What were the rest of the steps in the installation instructions you
> were trying to follow?
> I bet if you do "pip install ." inside of your checkout of the
> repository, things will "just work". However since I'm not able to
> reproduce the failure you're seeing you may run into the same issue with
> "pip install". If that happens answering the questions above will allow
> me to do additional debugging steps on my local machine.
> On Mon, Jan 7, 2019 at 12:03 PM Nick Gnedin <ngnedin(a)gmail.com
> <mailto:email@example.com>> wrote:
> I am getting an error trying to install the latest version of yt using
> setup.py (I have to use this method per BlueWaters staff instructions):
> >git clone https://firstname.lastname@example.org/yt-project/yt.git
> Checking out files: 100% (1258/1258), done.
> >cd yt
> yt >python3 setup.py build
> [48/48] Cythonizing yt/utilities/lib/write_array.pyx
> reading manifest template 'MANIFEST.in'
> no previously-included directories found matching
> no previously-included directories found matching 'doc/build'
> writing manifest file 'yt.egg-info/SOURCES.txt'
> error: can't copy 'yt/analysis_modules': doesn't exist or not a
> regular file
> yt >
> Thank you,
> yt-users mailing list -- yt-users(a)python.org
> To unsubscribe send an email to yt-users-leave(a)python.org
I am getting an error trying to install the latest version of yt using
setup.py (I have to use this method per BlueWaters staff instructions):
>git clone https://email@example.com/yt-project/yt.git
Checking out files: 100% (1258/1258), done.
yt >python3 setup.py build
[48/48] Cythonizing yt/utilities/lib/write_array.pyx
reading manifest template 'MANIFEST.in'
no previously-included directories found matching
no previously-included directories found matching 'doc/build'
writing manifest file 'yt.egg-info/SOURCES.txt'
error: can't copy 'yt/analysis_modules': doesn't exist or not a regular file
I've been trying to get this derived field to work, but it's more
complicated to define than anything I've done before.
I am working in a plane parallel geometry. I want to make a field that
contains gas surface density below (i.e. from z=0 to z=current cell) the
given cell. I naively thought I could filter the whole data set 'ad'
inside of the function def (field, data) definition using ad['z'] <
data['z'], but data['z'] is not a single value from cell.
What I can think of right now is to find a gas density profile
(accumulated) and then interpolate that function when I want to use it in a
Maybe I'm missing something here.
ad = ds.all_data()
current_z = np.absolute(data['z'])
all_z = np.absolute(ad['z'])
z_cut = (all_z < current_z)
m_tot = np.sum( ad[('gas','cell_mass')]*z_cut)
return (m_tot / (area)**2).in_units('Msun/pc**2')
Thanks for the help!