Hi all. Hopefully someone has PBS clusters working with xp65. I’m unable to do so. With analysis-25.03 or 25.04 I get warnings about mismatched versions (varies a bit though): 2025-05-02 16:39:06,372 - distributed.worker - WARNING - Mismatched versions found ±------------±----------------------…

Yes I was able to run with analysis3-25.05, as long as I deactivated conda first.

[image] ag0498: Can I upload my minimal test script here somehow? (Upload button above says no to .py format). Pasted below. It’s fine to use the in-built forum code box as above, but if you want to share longer snippets or programs there are some suggestions in this topic: [ima…

Hi Aurel, a couple of debugging steps: Can you add openmpi to your requirements. I’ve been testing this with the following modules & I don’t get any libmpi.so errors. [Screenshot 2025-05-05 at 8.28.28 am] I’m pretty sure that error is basically telling you that the mpi library can’t be found. S…

Okay, I’ve dug into the xarray source code, and I suspect I understand the source of the issue. In the xarray source code , calling open_mfdataset() with parallel=True will create a bunch of dask tasks, one associated with opening each dataset (using open_dataset). These are then computed & combined…

@ag0498 , what makes you think things aren’t working? I am able to successfully run your script in analysis-25.02, analysis-25.04 and analysis-25.05. Bear in mind that dask jobqueue submits PBS scripts for each of the dask workers you request, and work will not start until these jobs begin. Could you…

Hmmm, there does appear to be an issue with analysis-25.03. I get KilledWorker worker errors when trying to run @ag0498 ’s script in this environment. Ping @rbeucher , @CharlesTurner

Thank you all for your help so far! I’ve added the openmpi module and the job_script_prologue but am getting warnings related to versions still (as per ‘dask-worker.eXXX’ files). 2025-05-05 13:28:53,652 - distributed.worker - WARNING - Mismatched versions found +-------------+--------------------…

I was using 24.07 to start with because all later ones failed with HDF errors in Jupyter notebook testing. Am now working with 25.04. Don’t know why HDF errors aren’t happening - perhaps they’ll re-appear once the dask issue is dealt with. Sorry, that’s a little confusing…

[image] dougiesquire: Hmmm, there does appear to be an issue with analysis-25.03. I get KilledWorker worker errors when trying to run @ag0498 ’s script in this environment. Ping @rbeucher , @CharlesTurner Potentially the same issue as this: Xp65 conda/analysis3 environment + regional_mom6 versi…

[image] ag0498: I can see with qstat that the cluster starts, but then dies and the Python process seems to be left waiting for a return which will never arrive. Okay, given that things worked for me, my guess is that your worker PBS jobs are possibly dying for some simple reason, e.g. a miss…

Hi. Sure. Early on, it seems each worker is telling me about mismatched versions: 2025-05-05 14:20:30,729 - distributed.worker - WARNING - Mismatched versions found ±------------±--------------------------------------------±----------------±----------------+ | Package | Worker-c01609f2-66c…

Using dask jobqueue with xp65 conda env

Technical

CharlesTurner (Charles Turner) 5 May 2025 04:04 11

Potentially the same issue as this: Xp65 conda/analysis3 environment + regional_mom6 versioning - #9 by CharlesTurner.

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Using dask jobqueue with xp65 conda env

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