error when loading xbout data

[amircogan]

Dear,

We installed latest BOUT with docker: sudo docker pull boutproject/bout-next:9f4c663-sundials-ubuntu

on host machine installed python 3.7 and xbout ran simulation of examples/conduction in docker, copied data files to host and ran xbout in host. When we run this line:

bd = open_boutdataset('./shared/BOUT.dmp.*.nc', inputfilepath='./shared/BOUT.inp')

We get this error:

Traceback (most recent call last): File "", line 1, in File "/home/nt-tao1/miniconda3/envs/xbout/lib/python3.7/site-packages/xbout/load.py", line 226, in open_boutdataset ds = _add_options(ds, inputfilepath) File "/home/nt-tao1/miniconda3/envs/xbout/lib/python3.7/site-packages/xbout/load.py", line 278, in _add_options nz=ds.metadata["nz"], KeyError: 'nz'

The BOUT.inp file is listed below. I do see a nz variable there. Please advise - what is wrong ? Many thanks and great new year , better than last one :) Amir

#

Input file for conduction case

#

nout = 100 # Number of output timesteps timestep = 0.1 # Time between outputs

MXG = 0 # No X communications

################################################## [mesh] # Geometry of the mesh

nx = 1 ny = 100 nz = 1

dy = 0.2

Puts the boundaries half a step outside the last gridpoints

symmetricGlobalY=true

These flags make the y-direction non-periodic

ixseps1 = -1 ixseps2 = -1

################################################## [conduction] # Settings for the conduction model

chi = 1.0

################################################## [T] # Settings for the T variable

scale = 1.0 # Size of the initial perturbation function = gauss(y-pi, 0.2) # The form of the initial perturbation. y from 0 to 2*pi

Set the value on the boundaries to 0 (4th order extrapolation to ghostpoint)

bndry_all = dirichlet_o4(0.0)

[johnomotani]

I think the problem is that the version of BOUT++ on the Docker images is rather old (from 2018), see https://github.com/boutproject/BOUT-dev/issues/2186. I suspect it only wrote mz for the number of points in the z-direction, and not nz, which xbout is trying to use.

I think mz may be removed entirely in future, for consistency, so I don't think we should add backward-compatibility support to get around this. Possible workarounds:

• you probably don't actually need the input file. It's nice to have the options from BOUT.inp available, but they are not required for the functions in xbout. So you could try not passing inputfilename and see if it works. There might be other problems due to the old version of BOUT++ though...
• Update BOUT++ to the latest master. I haven't used the Docker myself, but I think you should be able to go into the BOUT-dev directory and do something like

  $ git checkout master
  $ git pull
  $ ./configure
  $ make clean
  $ make

  then try again to build/run conduction

• Don't use the Docker image and follow the build instructions from https://bout-dev.readthedocs.io/en/latest/user_docs/installing.html#obtaining-bout

[amircogan]

Thank you so much, we will follow you suggestions and update soon. Thanks!!

[bendudson]

The docker images have now been updated: boutproject/bout-master:3b23201-arch is the latest BOUT-dev master branch, compiled with Sundials (2.7.0) and PETSc (3.14.2).

[johnomotani]

I think the original issue is fixed @amircogan. If not please reopen, or start a new issue for other problems/questions.