Create cupid workflow #176
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Created template.cupid file and added a workflow to run it. Added module load conda to run successfully for. Added a load conda command to the config_machines.xml file for derecho. Updated the scratch path on casper.
machines/template.cupid
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| # Batch system directives | ||
| {{ batchdirectives }} | ||
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| module load conda |
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@jedwards4b even though @ingridc2051 added module load conda/latest to the derecho config_machines.xml file, without this line she gets a CondaError: Run 'conda init' before 'conda activate' error from the conda activate cupid-dev line. Do you happen to know why we seemingly need to load the module twice?
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I suspect that it's because the cesm environment is not being loaded by your script - let me look into how to do that and get back to you.
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@jedwards4b What if we replace the module load conda with source .env_mach_specific.sh? That should get everything from env_machines.xml into the environment of the compute node, right? @ingridc2051 can you try that when you get a chance?
- module load conda
+ source .env_mach_specific.shThere was a problem hiding this comment.
Yes - that should work - good idea.
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It sounds like this worked given the test that @ingridc2051 performed.
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Before this PR can be opened up for review and merged in:
A second PR to make CUPiD more usable would include
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…mmands in the template are run with the correct environment set up. Add module load nco to config_machines.xml file
ccs_config_cesm1.0.6
template.cupid assumes CUPiD is in the CESM source tree (tools/CUPiD) and runs the generate script from there. Also cleaned up some white space
generate_cupid_config_file.py now expects some commandline arguments, so the cupid template as been modified accordingly.
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@jedwards4b What controls whether |
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I think that case.st_archive might be a hardcoded special case in the python - I'll look at the code tomorrow and let you know. |
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In utils.py at line 2533. I think that we should remove that and make it an option in the config_workflow.xml file instead. |
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Cool, I'll make do with the file being hidden for now but we can talk about what it would look like to add a |
machines/template.cupid
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| {{ batchdirectives }} | ||
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| source .env_mach_specific.sh | ||
| conda activate cupid-dev |
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Cupid-dev is now cupid-infrastructure.
We should then add in generating timeseries files, creating an ADF config file, and running ADF.
We will also want to use cupid-diagnostics (the updated name for cupid-run) below (line 11).
After cupid-diagnostics, we can add cupid-webpage to build the webpage.
These will eventually be populated from an env_?.xml file, but for now starting a list of variables we want the user to be able to set. Also added two minor updates: 1. unset PYTHONPATH to ensure we are only using conda-installed python packages 2. The API for the script to generate the ADF config file has been changed - we now point to the directory containing a CUPiD config file rather than the CUPiD example
Create a new workflow to allow users to run CUPiD after the short-term archiver.