thetis error

[charithaRdissanayaka]

Dear all,

I am very new for thetis.
i installed firedrake and clone the thetis folder from github.
how can I run the example cases?
I just run examples/channel3d/channel3d.py, then following error encountered.

(firedrake) yachiyo@DRS101092606:/mnt/c/Users/Z02263/Desktop/THETIS/thetis/examples/channel3d$ python3 channel3d.py
Traceback (most recent call last):
File "/mnt/c/Users/Z02263/Desktop/THETIS/thetis/examples/channel3d/channel3d.py", line 13, in
from thetis import *
ModuleNotFoundError: No module named 'thetis'

Please be kind enough to explain me how to start thetis modelling work.

[cpjordan]

Hello! Looks like you have activated the Firedrake virtual environment but Thetis is not found when you try to run an example - did you install Thetis when you installed Firedrake i.e. python3 firedrake-install --install thetis?

If not, you should be able to install Thetis as explained on the website with firedrake-update --install thetis.

[charithaRdissanayaka]

Hello sir,

yes i installed thetis in to the following directory in wsl by the command python3 firedrake-install --install thetis

Install log saved in /home/charitha/firedrake-install.log

[charithaRdissanayaka]

how can i run the example please?

[cpjordan]

The example is not running because Thetis is not being imported, which suggests a problem with the install or the path to Thetis. Firstly, you can check that Firedrake has fully installed correctly by running (within your Firedrake environment)?

cd $VIRTUAL_ENV/src/firedrake
pytest tests/regression/ -k "poisson_strong or stokes_mini or dg_advection"

[charithaRdissanayaka]

Hello sir,

I will check this and let you know. I extremely sorry for the late reply. Due to a field visit I unable to do the works related to the thetis on the weekend.

[charithaRdissanayaka]

Hello sir,

this is the output of the above command.

Traceback (most recent call last):
File "/usr/lib/python2.7/dist-packages/_pytest/config.py", line 365, in _importconftest
mod = conftestpath.pyimport()
File "/usr/lib/python2.7/dist-packages/py/_path/local.py", line 668, in pyimport
import(modname)
File "/usr/lib/python2.7/dist-packages/pytest/assertion/rewrite.py", line 213, in load_module
py.builtin.exec(co, mod.dict)
File "/usr/lib/python2.7/dist-packages/py/builtin.py", line 221, in exec
exec2(obj, globals, locals)
File "", line 7, in exec2
File "/home/charitha/firedrake/src/firedrake/tests/conftest.py", line 4, in
from firedrake.petsc import get_external_packages
ImportError: No module named firedrake.petsc
ERROR: could not load /home/charitha/firedrake/src/firedrake/tests/conftest.py

[jwallwork23]

I notice you’re using Python 2. This is unlikely to work as Firedrake (and therefore Thetis) have Python 3 as a dependency. Please could you try reinstalling Firedrake and Thetis using a recent version of Python 3?

[stephankramer]

@charithaRdissanayaka : are you sure you ran that command with the firedrake environment activated? Can you try again but now using:

cd $VIRTUAL_ENV/src/firedrake
python -mpytest tests/regression/ -k "poisson_strong or stokes_mini or dg_advection"

(notice the change in the second command)

[charithaRdissanayaka]

I notice you’re using Python 2. This is unlikely to work as Firedrake (and therefore Thetis) have Python 3 as a dependency. Please could you try reinstalling Firedrake and Thetis using a recent version of Python 3?

Hello Sir,

I installed python3.12 and set the environment.

[charithaRdissanayaka]

@charithaRdissanayaka : are you sure you ran that command with the firedrake environment activated? Can you try again but now using:

cd $VIRTUAL_ENV/src/firedrake
python -mpytest tests/regression/ -k "poisson_strong or stokes_mini or dg_advection"

(notice the change in the second command)

Hello Sir,

I uninstalled the firedrake.
I will reinstall it and check according to your suggestions.
Thank you very much for your kind reply.

[charithaRdissanayaka]

Hello sir,

I installed poython3.12 and change the environment.
Also re-installed firedrake.
please find the attached log file of the firedrake installation.
I be able to activate the firedrake environment from the following command.
source /home/charitha
firedrake-install.log
/firedrake/bin/activate

(firedrake) charitha@DRS101092606:/firedrake$ cd src/thetis/examples/
(firedrake) charitha@DRS101092606:/firedrake/src/thetis/examples$ ls
init.py dome sediment_meander_2d
balzano freshwaterCylinder sediment_trench_2d
baroclinic_channel geostrophicGyre stommel2d
baroclinic_eddies idealizedEstuary stommel3d
bottomFriction katophillips tidal_barrage
channel2d lockExchange tidalfarm
channel3d nonhydrostatic_cases tohoku_inversion
channel_inversion north_sea tracerBox
columbia_plume overflow waveEq2d
cylinder_eddies reaction waveEq3d
discrete_turbines rhineROFI

now how can I run the tutorial please?

[cpjordan]

It looks like there are still some problems with the Firedrake install as libsupermesh is not being installed due to some dependencies, to fix this you can follow these steps: firedrakeproject/firedrake#3374

Please try this and then run the tests as Stephan described above to check that Firedrake has installed correctly. Unfortunately it can be a little tricky to install Firedrake, but once it is installed we can run the Thetis examples.

[charithaRdissanayaka]

Hello sir,

Thank you very much for your reply. I will follow the method explain in the given discussion link.