Closed gcapes closed 3 weeks ago
This is because the same version of MatFlow needs to be installed in the "software" environment that is used for each task. In your case, there is a mismatch. If you are using the shared MatFlow conda environment matflow_full_env
, this has not yet been updated (as discussed here). So, you can either update the shared conda environment, or you could help @YuchenZZheng set up their own conda environment with the current matflow version. You would need to update MatFlow's environment file so it points to the new conda environment.
Currently trying to get the action to run (https://github.com/LightForm-group/non-repo-issues/issues/25), in order to build the environment file for Yuchen to use.
I've been unpacking the environment file on CSF3 for a long time now (into my own user space), so just making a note in case I need to return to it another time. I've installed matflow-new using pip, and was going to look into editing a copy of the environment file once this has unpacked. This is likely duplication of work yuchen is doing, but will be useful practice for updating a shared installation in the future
Restarted it and it went quicker. I noticed when modifying a duplicate of the csf3 env file that previously each env e.g. damask_parse_env
defdap_env
have different paths, but I only get the one path for the matflow_full_env conda environment I've unpacked. Does the full env include all the others, which were previously done separately?
I am currently running the demo workflow, and get this warning
$ matflow show
/mnt/iusers01/support/mbexegc2/yuchen-zheng/.venv/lib/python3.11/site-packages/paramiko/pkey.py:100: CryptographyDeprecationWarning: TripleDES has been moved to cryptography.hazmat.decrepit.ciphers.algorithms.TripleDES and will be removed
from this module in 48.0.0.
"cipher": algorithms.TripleDES,
/mnt/iusers01/support/mbexegc2/yuchen-zheng/.venv/lib/python3.11/site-packages/paramiko/transport.py:259: CryptographyDeprecationWarning: TripleDES has been moved to cryptography.hazmat.decrepit.ciphers.algorithms.TripleDES and will be
removed from this module in 48.0.0.
"class": algorithms.TripleDES,
MatFlow, version 0.3.0a129
The demo workflow ran without errors :) Looks like I'll be able to update matflow on CSF3 following discussion
In summary, this wasn't a MatFlow error at all - it was just that the environment wasn't up-to-date.
HI @aplowman I've reproduced an error that @yuchenZZheng is having using MatFlow, version 0.3.0a128 on CSF. I've installed matflow in a python venv, Yuchen has installed it following these instructions https://docs.matflow.io/stable/installation.html#matflow-cli
We're running this workflow:
matflow demo-workflow go tension_DAMASK_Al
, but get the same error fortension_DAMASK_Ti
. The error is in the first task, which then looks to cause the rest to fail. Looking inartifacts/submissions/...
at the SGE error fileTypeError: Command.__init__() got an unexpected keyword argument 'rules'
Not sure where to go from here really - is this a problem with the task schema?