ACCESS-AM2/AM3 error with ozone step when cycling to a new year

Atmosphere
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Hi :slight_smile:

I’ve run into this issue with both ACCESS-AM3 (although this was some months ago now- using a prototype suite Is there an ACCESS-AM3 prototype available?) and ACCESS-AM2, where the retrieve_ozone and redistribute_ozone steps fail when cycling to a new year, so thought I would make a post about it.

Currently I’m doing AM2 runs with suite u-dr943, and at retrieve_ozone I got this error from not being able to access these python scripts:

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I did find scripts (um_fields_subset.py and um2netcdf_iris.py) in the access directory here /g/data/access/projects/access/apps/pythonlib/umfile_utils/cmip6/, (which I assume are the same?) and so i changed retrieve_ozone.sh to match these file paths. This has fixed the permission error, but now I have an issue with the retrieve_ozone step.

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I found that um_fields_subset.py successfully creates a subset of the monthly outputs of tropopause and density data. However the .nc files moved into the output directory byum2netcdf_iris.py appear empty.

I’ve tried to use a different script I have which converts UM output files to netcdf using '/g/data/access/projects/access/apps/pythonlib/umfile_utils/cmip6/um2netcdf4.py', and using those files for the next cylc task redistribute_ozone, but so far haven’t been successful (errors tracing back to redistribute_ozone.py).

So I guess my main question is whether I am using the right files ('/g/data/access/projects/access/apps/pythonlib/umfile_utils/cmip6/um_fields_subset.py' and '/g/data/access/projects/access/apps/pythonlib/umfile_utils/cmip6/um2netcdf_iris.py' for the retrieve_ozone task); and whether anyone else has come across this/has any ideas.

Thanks,
Alanah

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Thanks for your post @alanah.chapman! I’m determining how we can help you with this - we will get back to you soon!

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@paigem Please assign this Forum post to me.

1 Like
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Hi Alanah, the two corresponding scripts in the original branch of https://github.com/ACCESS-NRI/umfile_utils are identical to those from /home/599/mrd599/src/python/umfile/. To use them, in a suitable directory on Gadi:

$ git clone https://github.com/ACCESS-NRI/umfile_utils.git
$ cd umfile_utils
$ git checkout original

Please note that not all of the scripts in this branch are identical to those in /home/599/mrd599/src/python/umfile/:

$ diff -q src /home/599/mrd599/src/python/umfile/ | grep differ
Files src/access_landmask.py and /home/599/mrd599/src/python/umfile/access_landmask.py differ
Files src/change_calendar365.py and /home/599/mrd599/src/python/umfile/change_calendar365.py differ
Files src/change_calendar_header.py and /home/599/mrd599/src/python/umfile/change_calendar_header.py differ
Files src/change_calendar.py and /home/599/mrd599/src/python/umfile/change_calendar.py differ
Files src/change_dump_date.py and /home/599/mrd599/src/python/umfile/change_dump_date.py differ
Files src/change_endianness.py and /home/599/mrd599/src/python/umfile/change_endianness.py differ
Files src/get_calendar.py and /home/599/mrd599/src/python/umfile/get_calendar.py differ
Files src/mergefiles_region.py and /home/599/mrd599/src/python/umfile/mergefiles_region.py differ
Files src/nccmp_um2netcdf.py and /home/599/mrd599/src/python/umfile/nccmp_um2netcdf.py differ
Files src/show_land_overlap.py and /home/599/mrd599/src/python/umfile/show_land_overlap.py differ
Files src/um2netcdf4.py and /home/599/mrd599/src/python/umfile/um2netcdf4.py differ
Files src/um2netcdf_iris_mon.py and /home/599/mrd599/src/python/umfile/um2netcdf_iris_mon.py differ
Files src/umfile.py and /home/599/mrd599/src/python/umfile/umfile.py differ
Files src/um_grid_flip.py and /home/599/mrd599/src/python/umfile/um_grid_flip.py differ
Files src/um_timeseries.py and /home/599/mrd599/src/python/umfile/um_timeseries.py differ
6

Just giving an update - I was able to get the OZONE task to succeed, but not very elegantly.

  • I manually created .nc monthly output files with tropopause and density variables from the last year (the retrieve_ozone task succeeded but created empty files..)
  • adjusted the metadata for the variables
  • edited the redistribute_ozone.py script in redistribute_ozone task to be able to load the files I made without metadata throwing errors (iris)

Thanks Paul!
I’ll see if retrieve_ozone works with the python files from https://github.com/ACCESS-NRI/umfile_utils
:slight_smile:

1 Like
7

Hi Alanah, have you tried the files from GitHub - ACCESS-NRI/umfile_utils ? How did it go?

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Hi @alanah.chapman . Have you resolved this issue?

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Hi, yes sorry I have! Thank you!